BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy2880
(166 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1N5N|A Chain A, Crystal Structure Of Peptide Deformylase From Pseudomonas
Aeruginosa
pdb|1N5N|B Chain B, Crystal Structure Of Peptide Deformylase From Pseudomonas
Aeruginosa
pdb|1S17|A Chain A, Identification Of Novel Potent Bicyclic Peptide
Deformylase Inhibitors
pdb|1S17|B Chain B, Identification Of Novel Potent Bicyclic Peptide
Deformylase Inhibitors
Length = 180
Score = 179 bits (455), Expect = 5e-46, Method: Compositional matrix adjust.
Identities = 77/166 (46%), Positives = 124/166 (74%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
M +L I+ +PD RL+ IA+P+ D ++++I +M ETMY A GIGLAA+QV++HK++++
Sbjct: 13 MAILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVV 72
Query: 61 LDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMF 120
+D+S++ ++ +VFINP+ ++E Y EGCLS+PG + + R +++R+ AL+ +G F
Sbjct: 73 MDLSEDKSEPRVFINPEFEPLTEEMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPF 132
Query: 121 EIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
E +AEGLLA+C+QHE DHLNGK+F++YLS K++RI KK K ++
Sbjct: 133 EEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQ 178
>pdb|1IX1|A Chain A, Crystal Structure Of P.Aeruginosa Peptide Deformylase
Complexed With Antibiotic Actinonin
pdb|1IX1|B Chain B, Crystal Structure Of P.Aeruginosa Peptide Deformylase
Complexed With Antibiotic Actinonin
Length = 171
Score = 178 bits (451), Expect = 2e-45, Method: Compositional matrix adjust.
Identities = 76/166 (45%), Positives = 124/166 (74%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
M +L I+ +PD RL+ IA+P+ D ++++I +M ETMY A GIGLAA+QV++HK++++
Sbjct: 1 MAILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVV 60
Query: 61 LDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMF 120
+D+S++ ++ +VFINP+ +++ Y EGCLS+PG + + R +++R+ AL+ +G F
Sbjct: 61 MDLSEDKSEPRVFINPEFEPLTEDMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPF 120
Query: 121 EIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
E +AEGLLA+C+QHE DHLNGK+F++YLS K++RI KK K ++
Sbjct: 121 EEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQ 166
>pdb|1LRY|A Chain A, Crystal Structure Of P. Aeruginosa Peptide Deformylase
Complexed With Antibiotic Actinonin
Length = 167
Score = 176 bits (446), Expect = 6e-45, Method: Compositional matrix adjust.
Identities = 75/165 (45%), Positives = 123/165 (74%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
+L I+ +PD RL+ IA+P+ D ++++I +M ETMY A GIGLAA+QV++HK+++++
Sbjct: 1 AILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVM 60
Query: 62 DISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
D+S++ ++ +VFINP+ +++ Y EGCLS+PG + + R +++R+ AL+ +G FE
Sbjct: 61 DLSEDKSEPRVFINPEFEPLTEDMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFE 120
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
+AEGLLA+C+QHE DHLNGK+F++YLS K++RI KK K ++
Sbjct: 121 EVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQ 165
>pdb|3K6L|A Chain A, The Structure Of E.Coli Peptide Deformylase (Pdf) In
Complex With Peptidomimetic Ligand Bb2827
pdb|3K6L|B Chain B, The Structure Of E.Coli Peptide Deformylase (Pdf) In
Complex With Peptidomimetic Ligand Bb2827
pdb|3K6L|C Chain C, The Structure Of E.Coli Peptide Deformylase (Pdf) In
Complex With Peptidomimetic Ligand Bb2827
Length = 169
Score = 165 bits (417), Expect = 1e-41, Method: Compositional matrix adjust.
Identities = 74/162 (45%), Positives = 123/162 (75%), Gaps = 1/162 (0%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
M++L +++ PD RL+K+A+P+ E + +++I+ +M ETMY GIGLAA+QVDIH+++++
Sbjct: 1 MSVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIV 60
Query: 61 LDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMF 120
+D+S+N ++ V INP+++ S E I EGCLS+P + R++++++ AL+ +GK F
Sbjct: 61 IDVSENRDERLVLINPELLEKSGETGI-EEGCLSIPEQRALVPRAEKVKIRALDRDGKPF 119
Query: 121 EIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLK 162
E+ A+GLLAIC+QHE+DHL GK+F++YLS K++RI +K K
Sbjct: 120 ELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEK 161
>pdb|4AL2|A Chain A, Peptide Deformylase (Ni-Form) With Hydrosulfide
pdb|4AL2|B Chain B, Peptide Deformylase (Ni-Form) With Hydrosulfide
pdb|4AL2|C Chain C, Peptide Deformylase (Ni-Form) With Hydrosulfide
Length = 186
Score = 163 bits (413), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 73/161 (45%), Positives = 122/161 (75%), Gaps = 1/161 (0%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
++L +++ PD RL+K+A+P+ E + +++I+ +M ETMY GIGLAA+QVDIH++++++
Sbjct: 1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVI 60
Query: 62 DISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
D+S+N ++ V INP+++ S E I EGCLS+P + R++++++ AL+ +GK FE
Sbjct: 61 DVSENRDERLVLINPELLEKSGETGI-EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE 119
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLK 162
+ A+GLLAIC+QHE+DHL GK+F++YLS K++RI +K K
Sbjct: 120 LEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEK 160
>pdb|2W3T|A Chain A, Chloro Complex Of The Ni-Form Of E.Coli Deformylase
pdb|2W3U|A Chain A, Formate Complex Of The Ni-Form Of E.Coli Deformylase
Length = 188
Score = 163 bits (413), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 73/161 (45%), Positives = 122/161 (75%), Gaps = 1/161 (0%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
++L +++ PD RL+K+A+P+ E + +++I+ +M ETMY GIGLAA+QVDIH++++++
Sbjct: 1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVI 60
Query: 62 DISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
D+S+N ++ V INP+++ S E I EGCLS+P + R++++++ AL+ +GK FE
Sbjct: 61 DVSENRDERLVLINPELLEKSGETGI-EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE 119
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLK 162
+ A+GLLAIC+QHE+DHL GK+F++YLS K++RI +K K
Sbjct: 120 LEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEK 160
>pdb|1ICJ|A Chain A, Pdf Protein Is Crystallized As Ni2+ Containing Form,
Cocrystallized With Inhibitor Polyethylene Glycol (Peg)
pdb|1ICJ|B Chain B, Pdf Protein Is Crystallized As Ni2+ Containing Form,
Cocrystallized With Inhibitor Polyethylene Glycol (Peg)
pdb|1ICJ|C Chain C, Pdf Protein Is Crystallized As Ni2+ Containing Form,
Cocrystallized With Inhibitor Polyethylene Glycol (Peg)
pdb|1BS4|A Chain A, Peptide Deformylase As Zn2+ Containing Form (Native) In
Complex With Inhibitor Polyethylene Glycol
pdb|1BS4|B Chain B, Peptide Deformylase As Zn2+ Containing Form (Native) In
Complex With Inhibitor Polyethylene Glycol
pdb|1BS4|C Chain C, Peptide Deformylase As Zn2+ Containing Form (Native) In
Complex With Inhibitor Polyethylene Glycol
pdb|1BS5|A Chain A, Peptide Deformylase As Zn2+ Containing Form
pdb|1BS5|B Chain B, Peptide Deformylase As Zn2+ Containing Form
pdb|1BS5|C Chain C, Peptide Deformylase As Zn2+ Containing Form
pdb|1BS6|A Chain A, Peptide Deformylase As Ni2+ Containing Form In Complex
With Tripeptide Met-Ala-Ser
pdb|1BS6|B Chain B, Peptide Deformylase As Ni2+ Containing Form In Complex
With Tripeptide Met-Ala-Ser
pdb|1BS6|C Chain C, Peptide Deformylase As Ni2+ Containing Form In Complex
With Tripeptide Met-Ala-Ser
pdb|1BS7|A Chain A, Peptide Deformylase As Ni2+ Containing Form
pdb|1BS7|B Chain B, Peptide Deformylase As Ni2+ Containing Form
pdb|1BS7|C Chain C, Peptide Deformylase As Ni2+ Containing Form
pdb|1BS8|A Chain A, Peptide Deformylase As Zn2+ Containing Form In Complex
With Tripeptide Met-Ala-Ser
pdb|1BS8|B Chain B, Peptide Deformylase As Zn2+ Containing Form In Complex
With Tripeptide Met-Ala-Ser
pdb|1BS8|C Chain C, Peptide Deformylase As Zn2+ Containing Form In Complex
With Tripeptide Met-Ala-Ser
pdb|1BSZ|A Chain A, Peptide Deformylase As Fe2+ Containing Form (Native) In
Complex With Inhibitor Polyethylene Glycol
pdb|1BSZ|B Chain B, Peptide Deformylase As Fe2+ Containing Form (Native) In
Complex With Inhibitor Polyethylene Glycol
pdb|1BSZ|C Chain C, Peptide Deformylase As Fe2+ Containing Form (Native) In
Complex With Inhibitor Polyethylene Glycol
pdb|1BSJ|A Chain A, Cobalt Deformylase Inhibitor Complex From E.Coli
pdb|1BSK|A Chain A, Zinc Deformylase Inhibitor Complex From E.Coli
pdb|1G27|A Chain A, Crystal Structure Of E.Coli Polypeptide Deformylase
Complexed With The Inhibitor Bb-3497
pdb|1G27|B Chain B, Crystal Structure Of E.Coli Polypeptide Deformylase
Complexed With The Inhibitor Bb-3497
pdb|1G27|C Chain C, Crystal Structure Of E.Coli Polypeptide Deformylase
Complexed With The Inhibitor Bb-3497
pdb|1G2A|A Chain A, The Crystal Structure Of E.Coli Peptide Deformylase
Complexed With Actinonin
pdb|1G2A|B Chain B, The Crystal Structure Of E.Coli Peptide Deformylase
Complexed With Actinonin
pdb|1G2A|C Chain C, The Crystal Structure Of E.Coli Peptide Deformylase
Complexed With Actinonin
pdb|1LRU|A Chain A, Crystal Structure Of E.Coli Peptide Deformylase Complexed
With Antibiotic Actinonin
pdb|1LRU|B Chain B, Crystal Structure Of E.Coli Peptide Deformylase Complexed
With Antibiotic Actinonin
pdb|1LRU|C Chain C, Crystal Structure Of E.Coli Peptide Deformylase Complexed
With Antibiotic Actinonin
pdb|1XEM|A Chain A, High Resolution Crystal Structure Of Escherichia Coli
Zinc- Peptide Deformylase Bound To Formate
pdb|1XEN|A Chain A, High Resolution Crystal Structure Of Escherichia Coli
Iron- Peptide Deformylase Bound To Formate
pdb|1XEO|A Chain A, High Resolution Crystals Structure Of Cobalt- Peptide
Deformylase Bound To Formate
pdb|2AI8|A Chain A, E.Coli Polypeptide Deformylase Complexed With Sb-485343
pdb|2AI8|B Chain B, E.Coli Polypeptide Deformylase Complexed With Sb-485343
pdb|2AI8|C Chain C, E.Coli Polypeptide Deformylase Complexed With Sb-485343
Length = 168
Score = 163 bits (412), Expect = 5e-41, Method: Compositional matrix adjust.
Identities = 73/161 (45%), Positives = 122/161 (75%), Gaps = 1/161 (0%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
++L +++ PD RL+K+A+P+ E + +++I+ +M ETMY GIGLAA+QVDIH++++++
Sbjct: 1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVI 60
Query: 62 DISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
D+S+N ++ V INP+++ S E I EGCLS+P + R++++++ AL+ +GK FE
Sbjct: 61 DVSENRDERLVLINPELLEKSGETGI-EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE 119
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLK 162
+ A+GLLAIC+QHE+DHL GK+F++YLS K++RI +K K
Sbjct: 120 LEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEK 160
>pdb|1DFF|A Chain A, Peptide Deformylase
Length = 164
Score = 162 bits (411), Expect = 6e-41, Method: Compositional matrix adjust.
Identities = 73/161 (45%), Positives = 122/161 (75%), Gaps = 1/161 (0%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
++L +++ PD RL+K+A+P+ E + +++I+ +M ETMY GIGLAA+QVDIH++++++
Sbjct: 1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVI 60
Query: 62 DISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
D+S+N ++ V INP+++ S E I EGCLS+P + R++++++ AL+ +GK FE
Sbjct: 61 DVSENRDERLVLINPELLEKSGETGI-EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE 119
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLK 162
+ A+GLLAIC+QHE+DHL GK+F++YLS K++RI +K K
Sbjct: 120 LEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEK 160
>pdb|4AZ4|A Chain A, E.Coli Deformylase With Co(Ii) And Hydrosulfide
Length = 186
Score = 159 bits (402), Expect = 8e-40, Method: Compositional matrix adjust.
Identities = 72/161 (44%), Positives = 121/161 (75%), Gaps = 1/161 (0%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
++L +++ PD RL+K+A+P+ E + +++I+ +M ETMY GIGLAA+QVDIH++++++
Sbjct: 1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVI 60
Query: 62 DISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
D+S+N ++ V INP+++ S E I EGCLS+P + R++++++ AL+ +GK FE
Sbjct: 61 DVSENRDERLVLINPELLEKSGETGI-EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE 119
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLK 162
+ A+GLLAI +QHE+DHL GK+F++YLS K++RI +K K
Sbjct: 120 LEADGLLAIXIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEK 160
>pdb|4AL3|A Chain A, Peptide Deformylase (Co-Form) With Mercaptoethanol
Length = 186
Score = 159 bits (402), Expect = 8e-40, Method: Compositional matrix adjust.
Identities = 72/161 (44%), Positives = 121/161 (75%), Gaps = 1/161 (0%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
++L +++ PD RL+K+A+P+ E + +++I+ +M ETMY GIGLAA+QVDIH++++++
Sbjct: 1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVI 60
Query: 62 DISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
D+S+N ++ V INP+++ S E I EG LS+P + R++++++ AL+ +GK FE
Sbjct: 61 DVSENRDERLVLINPELLEKSGETGI-EEGXLSIPEQRALVPRAEKVKIRALDRDGKPFE 119
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLK 162
+ A+GLLAIC+QHE+DHL GK+F++YLS K++RI +K K
Sbjct: 120 LEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEK 160
>pdb|1DEF|A Chain A, Peptide Deformylase Catalytic Core (Residues 1-147), Nmr,
9 Structures
pdb|2KMN|A Chain A, Solution Structure Of Peptide Deformylase Complexed With
Actinonin
Length = 147
Score = 154 bits (390), Expect = 2e-38, Method: Compositional matrix adjust.
Identities = 68/148 (45%), Positives = 114/148 (77%), Gaps = 1/148 (0%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
++L +++ PD RL+K+A+P+ E + +++I+ +M ETMY GIGLAA+QVDIH++++++
Sbjct: 1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVI 60
Query: 62 DISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
D+S+N ++ V INP+++ S E I EGCLS+P + R++++++ AL+ +GK FE
Sbjct: 61 DVSENRDERLVLINPELLEKSGETGI-EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE 119
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLS 149
+ A+GLLAIC+QHE+DHL GK+F++YLS
Sbjct: 120 LEADGLLAICIQHEMDHLVGKLFMDYLS 147
>pdb|2DEF|A Chain A, Peptide Deformylase Catalytic Core (Residues 1-147), Nmr,
20 Structures
Length = 147
Score = 154 bits (388), Expect = 3e-38, Method: Compositional matrix adjust.
Identities = 68/148 (45%), Positives = 113/148 (76%), Gaps = 1/148 (0%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
+L +++ PD RL+K+A+P+ E + +++I+ +M ETMY GIGLAA+QVDIH++++++
Sbjct: 1 AVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVI 60
Query: 62 DISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
D+S+N ++ V INP+++ S E I EGCLS+P + R++++++ AL+ +GK FE
Sbjct: 61 DVSENRDERLVLINPELLEKSGETGI-EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE 119
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLS 149
+ A+GLLAIC+QHE+DHL GK+F++YLS
Sbjct: 120 LEADGLLAICIQHEMDHLVGKLFMDYLS 147
>pdb|3FWX|A Chain A, The Crystal Structure Of The Peptide Deformylase From
Vibrio Cholerae O1 Biovar El Tor Str. N16961
pdb|3FWX|B Chain B, The Crystal Structure Of The Peptide Deformylase From
Vibrio Cholerae O1 Biovar El Tor Str. N16961
Length = 169
Score = 149 bits (377), Expect = 6e-37, Method: Compositional matrix adjust.
Identities = 71/165 (43%), Positives = 114/165 (69%), Gaps = 2/165 (1%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
++L ++ +PD RL+ +A+P+ + +++I+ + ET Y GIGLAA+QVDIH++++++
Sbjct: 2 SVLQVLTFPDDRLRTVAKPVEQVTPEIQQIVDDXLETXYAEEGIGLAATQVDIHQRIVVI 61
Query: 62 DISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
DIS+ +Q V INP+II E I EGCLS+PG + R+ + V AL+ G+ ++
Sbjct: 62 DISETRDQPXVLINPEIIEKRGEDGI-EEGCLSVPGARALVPRAAEVTVKALDRNGQEYQ 120
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
A+ LLAIC+QHE+DHL GK+F++YLS K+ R IK+ L+ IK+
Sbjct: 121 FDADDLLAICVQHELDHLAGKLFVDYLSPLKRNR-IKEKLEKIKR 164
>pdb|3OCA|A Chain A, Crystal Structure Of Peptide Deformylase From Ehrlichia
Chaffeensis
pdb|3OCA|B Chain B, Crystal Structure Of Peptide Deformylase From Ehrlichia
Chaffeensis
Length = 209
Score = 134 bits (336), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 74/181 (40%), Positives = 111/181 (61%), Gaps = 19/181 (10%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
M++L I+ PD RL +E + + D +++K++ +M ETM+ G+GLAA QV +HK++L+
Sbjct: 22 MSVLSIVTVPDKRLSLCSEEVEKVDQSIRKLVDDMFETMHANQGLGLAAVQVGVHKRILV 81
Query: 61 L----------DISKNNNQLQVF---------INPKIIWYSKEKQIYNEGCLSLPGIFNK 101
+ DI ++++ + INPKI+ S+EK EGCLS+PG F+
Sbjct: 82 MNVPEEFEDSEDIENVEDKIEGYELYGGPYCIINPKIVDISQEKVKLKEGCLSVPGYFDY 141
Query: 102 IKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFL 161
I R +RI V L+ G I A+G LA CLQHEIDHLNG +F++YLS FK++ I+K
Sbjct: 142 IVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGTVFLKYLSKFKRDFAIEKVK 201
Query: 162 K 162
K
Sbjct: 202 K 202
>pdb|3U04|A Chain A, Crystal Structure Of Peptide Deformylase From Ehrlichia
Chaffeensis In Complex With Actinonin
Length = 190
Score = 133 bits (335), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 74/181 (40%), Positives = 111/181 (61%), Gaps = 19/181 (10%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
M++L I+ PD RL +E + + D +++K++ +M ETM+ G+GLAA QV +HK++L+
Sbjct: 3 MSVLSIVTVPDKRLSLCSEEVEKVDQSIRKLVDDMFETMHANQGLGLAAVQVGVHKRILV 62
Query: 61 L----------DISKNNNQLQVF---------INPKIIWYSKEKQIYNEGCLSLPGIFNK 101
+ DI ++++ + INPKI+ S+EK EGCLS+PG F+
Sbjct: 63 MNVPEEFEDSEDIENVEDKIEGYELYGGPYCIINPKIVDISQEKVKLKEGCLSVPGYFDY 122
Query: 102 IKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFL 161
I R +RI V L+ G I A+G LA CLQHEIDHLNG +F++YLS FK++ I+K
Sbjct: 123 IVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGTVFLKYLSKFKRDFAIEKVK 182
Query: 162 K 162
K
Sbjct: 183 K 183
>pdb|3QU1|A Chain A, Peptide Deformylase From Vibrio Cholerae
pdb|3QU1|B Chain B, Peptide Deformylase From Vibrio Cholerae
Length = 171
Score = 124 bits (310), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 65/166 (39%), Positives = 106/166 (63%), Gaps = 3/166 (1%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAM-GIGLAASQVDIHKQLL 59
M +L I+ PD RL+ ++ +T+ +++ +I ++ +T+Y GIGLAA QV + ++
Sbjct: 4 MAVLEILTAPDPRLRVQSKQVTDV-ASVQTLIDDLLDTLYATDNGIGLAAPQVGREEAIV 62
Query: 60 ILDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKM 119
++D+S N +Q V INPK++ S K++ EGCLS+P + ++R + V AL+ EGK
Sbjct: 63 VIDLSDNRDQPLVLINPKVVSGSN-KEMGQEGCLSVPDYYADVERYTSVVVEALDREGKP 121
Query: 120 FEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIK 165
I LAI +QHEIDHL+G +FI+YLS K++ +KK K++K
Sbjct: 122 LRIETSDFLAIVMQHEIDHLSGNLFIDYLSPLKQQMAMKKVKKHVK 167
>pdb|1LME|A Chain A, Crystal Structure Of Peptide Deformylase From Thermotoga
Maritima
pdb|1LME|B Chain B, Crystal Structure Of Peptide Deformylase From Thermotoga
Maritima
Length = 176
Score = 121 bits (304), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 67/153 (43%), Positives = 92/153 (60%), Gaps = 3/153 (1%)
Query: 9 YPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDISKNNN 68
+ D L+K A+P+T+FD NLKK I M ETMYH G+GLAA QV I ++ ++D+ N
Sbjct: 19 FGDPVLRKRAKPVTKFDENLKKTIERMIETMYHYDGVGLAAPQVGISQRFFVMDVG---N 75
Query: 69 QLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFEIIAEGLL 128
INP+I+ E ++ EG LS P IF +I+RSKRI+V N G+ E EG
Sbjct: 76 GPVAVINPEILEIDPETEVAEEGXLSFPEIFVEIERSKRIKVKYQNTRGEYVEEELEGYA 135
Query: 129 AICLQHEIDHLNGKIFIEYLSNFKKERIIKKFL 161
A QHE DHLNG + I+ +S K+ + KK +
Sbjct: 136 ARVFQHEFDHLNGVLIIDRISPAKRLLLRKKLM 168
>pdb|4DR9|A Chain A, Crystal Structure Of A Peptide Deformylase From
Synechococcus Elongatus In Complex With Actinonin
pdb|4DR9|B Chain B, Crystal Structure Of A Peptide Deformylase From
Synechococcus Elongatus In Complex With Actinonin
pdb|4DR9|C Chain C, Crystal Structure Of A Peptide Deformylase From
Synechococcus Elongatus In Complex With Actinonin
pdb|4DR9|D Chain D, Crystal Structure Of A Peptide Deformylase From
Synechococcus Elongatus In Complex With Actinonin
Length = 192
Score = 118 bits (296), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 58/145 (40%), Positives = 93/145 (64%), Gaps = 2/145 (1%)
Query: 8 YYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDISKNN 67
Y D L++ A+ ++ D L++ I M +TMY A GIGLAA QV I+KQL+++D+ +
Sbjct: 23 YLGDRVLRQPAKRVSRIDDELRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDLELED 82
Query: 68 NQLQ--VFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFEIIAE 125
Q V INPKI + + + EGCLS+PG++ ++R + + V + G+ ++A+
Sbjct: 83 EQAPPLVLINPKIERTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVAD 142
Query: 126 GLLAICLQHEIDHLNGKIFIEYLSN 150
GLLA C+QHE+DHLNG +F++ + N
Sbjct: 143 GLLARCIQHEMDHLNGVLFVDRVEN 167
>pdb|1WS0|A Chain A, Structure Analysis Of Peptide Deformylase From Bacillus
Cereus
pdb|1WS1|A Chain A, Structure Analysis Of Peptide Deformylase From Bacillus
Cereus
Length = 156
Score = 107 bits (266), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 61/154 (39%), Positives = 97/154 (62%), Gaps = 2/154 (1%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
M +L II +P+ L+ E + FD L K++ +M ETM A G+GLAA QV + Q+ +
Sbjct: 1 MAVLEIIKHPNEVLETPCERVINFDKKLVKLLKDMHETMLIADGVGLAAPQVGVSLQVAV 60
Query: 61 LDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMF 120
+D+ + +++ INP I+ E Q+ EGCLS PG++ +++R+ I+V A N GK+F
Sbjct: 61 VDVDDDTGKIE-LINPSILEKRGE-QVGPEGCLSFPGLYGEVERADYIKVRAQNRRGKVF 118
Query: 121 EIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKE 154
+ AEG LA +QHEIDHL+G +F ++ + +E
Sbjct: 119 LLEAEGFLARAIQHEIDHLHGVLFTSKVTRYYEE 152
>pdb|1RL4|A Chain A, Plasmodium Falciparum Peptide Deformylase Complex With
Inhibitor
pdb|1RL4|B Chain B, Plasmodium Falciparum Peptide Deformylase Complex With
Inhibitor
Length = 188
Score = 107 bits (266), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 59/159 (37%), Positives = 95/159 (59%), Gaps = 5/159 (3%)
Query: 6 IIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDI-- 63
I+ YPD L++ +E +T FD NLK+++ M + MY + GIGL+A QV+I K++++ +
Sbjct: 11 IVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALY 70
Query: 64 --SKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
K N+ ++FINP I+ S K EGCLS PGI K++R + + +I G
Sbjct: 71 EKRKEENE-RIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHL 129
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKF 160
I +G+ + QHE DHLNG +FI+ ++ K+++ K
Sbjct: 130 KILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKL 168
>pdb|3CPM|A Chain A, Plant Peptide Deformylase Pdf1b Crystal Structure
Length = 193
Score = 105 bits (263), Expect = 9e-24, Method: Compositional matrix adjust.
Identities = 56/151 (37%), Positives = 89/151 (58%), Gaps = 2/151 (1%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
T L I+ YPD L+ + I FD NLK ++ M + MY GIGL+A QV ++ QL++
Sbjct: 15 TPLKIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVF 74
Query: 62 DISKNNNQLQ--VFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKM 119
+ + + + V +NPKI YS + ++EGCLS PGI+ ++ R + +++ A +I G+
Sbjct: 75 NPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGER 134
Query: 120 FEIIAEGLLAICLQHEIDHLNGKIFIEYLSN 150
F I L A QHE DHL G +F + +++
Sbjct: 135 FSISLSRLPARIFQHEYDHLEGVLFFDRMTD 165
>pdb|2EW5|A Chain A, Structure Of Helicobacter Pylori Peptide Deformylase In
Complex With Inhibitor
pdb|2EW6|A Chain A, Structure Of Helicobacter Pylori Peptide Deformylase In
Complex With Inhibitor
pdb|2EW7|A Chain A, Crystal Structure Of Helicobacter Pylori Peptide
Deformylase
Length = 181
Score = 105 bits (261), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 63/171 (36%), Positives = 106/171 (61%), Gaps = 12/171 (7%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
LL II+YP L+ I++ + FD L + + +M ETM + GIGLAA QV + ++LI+
Sbjct: 1 ALLEIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQVGLPLRMLII 60
Query: 62 DISKNN------NQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNI 115
++ + + + L++ INPK I + +Y EGCLS+PG + +++R +++++ N
Sbjct: 61 NLPQEDGVQHKEDCLEI-INPKFIE-TGGSMMYKEGCLSVPGFYEEVERFEKVKIEYQNR 118
Query: 116 EGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
++ + A LLA+ +QHEIDHLNG +F++ LS K+ KKF K +K+
Sbjct: 119 FAEVKVLEASELLAVAIQHEIDHLNGVLFVDKLSILKR----KKFEKELKE 165
>pdb|3M6O|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b)
pdb|3M6O|B Chain B, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b)
pdb|3M6P|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) In Complex With Actinonin
pdb|3M6P|B Chain B, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) In Complex With Actinonin
pdb|3O3J|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) In Complex With Inhibitor 6b
pdb|3PN2|A Chain A, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) (Crystallized In Peg-550-Mme)
pdb|3PN3|A Chain A, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) In Complex With Inhibitor 21
pdb|3PN3|B Chain B, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) In Complex With Inhibitor 21
pdb|3PN4|A Chain A, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) In Complex With Actinonin
(Crystallized In Peg-550-Mme)
Length = 193
Score = 103 bits (258), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 54/147 (36%), Positives = 87/147 (59%), Gaps = 2/147 (1%)
Query: 6 IIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDISK 65
I+ YPD L+ + I FD NLK ++ M + MY GIGL+A QV ++ QL++ + +
Sbjct: 3 IVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVFNPAG 62
Query: 66 NNNQLQ--VFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFEII 123
+ + V +NPKI YS + ++EGCLS PGI+ ++ R + +++ A +I G+ F I
Sbjct: 63 EPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSIS 122
Query: 124 AEGLLAICLQHEIDHLNGKIFIEYLSN 150
L A QHE DHL G +F + +++
Sbjct: 123 LSRLPARIFQHEYDHLEGVLFFDRMTD 149
>pdb|1Y6H|A Chain A, Crystal Structure Of Lipdf
pdb|1Y6H|B Chain B, Crystal Structure Of Lipdf
pdb|1SV2|A Chain A, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans (lipdf) At Ph7.5
pdb|1SV2|B Chain B, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans (lipdf) At Ph7.5
pdb|1VEV|A Chain A, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans (Lipdf) At Ph6.5
pdb|1VEV|B Chain B, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans (Lipdf) At Ph6.5
pdb|1VEY|A Chain A, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans (Lipdf) At Ph7.0
pdb|1VEY|B Chain B, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans (Lipdf) At Ph7.0
pdb|1VEZ|A Chain A, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans(lipdf) At Ph8.0
pdb|1VEZ|B Chain B, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans(lipdf) At Ph8.0
Length = 177
Score = 103 bits (256), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 55/150 (36%), Positives = 93/150 (62%), Gaps = 12/150 (8%)
Query: 14 LKKIAEPITEFDIN---LKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDISKNNNQL 70
L+KI+EP+TE +I KK+I +M +TM HA G+GLAA Q+ I KQ++++ S++N +
Sbjct: 13 LRKISEPVTEDEIQTKEFKKLIRDMFDTMRHAEGVGLAAPQIGILKQIVVVG-SEDNERY 71
Query: 71 --------QVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFEI 122
++ +NP I +K+ + EGCLS+PG+ ++R +IR+ ++ +G F+
Sbjct: 72 PGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDE 131
Query: 123 IAEGLLAICLQHEIDHLNGKIFIEYLSNFK 152
+G AI QHE DHL G ++++ L + K
Sbjct: 132 TIDGYKAIVYQHECDHLQGILYVDRLKDTK 161
>pdb|1SZZ|A Chain A, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|B Chain B, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|C Chain C, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|D Chain D, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|E Chain E, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|F Chain F, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|G Chain G, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|H Chain H, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
Length = 177
Score = 102 bits (254), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 55/150 (36%), Positives = 92/150 (61%), Gaps = 12/150 (8%)
Query: 14 LKKIAEPITEFDIN---LKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDISKNNNQL 70
L+KI+EP+TE +I KK+I +M TM HA G+GLAA Q+ I KQ++++ S++N +
Sbjct: 13 LRKISEPVTEDEIQTKEFKKLIRDMFTTMRHAEGVGLAAPQIGILKQIVVVG-SEDNERY 71
Query: 71 --------QVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFEI 122
++ +NP I +K+ + EGCLS+PG+ ++R +IR+ ++ +G F+
Sbjct: 72 PGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDE 131
Query: 123 IAEGLLAICLQHEIDHLNGKIFIEYLSNFK 152
+G AI QHE DHL G ++++ L + K
Sbjct: 132 TIDGYKAIVYQHECDHLQGILYVDRLKDTK 161
>pdb|1RQC|A Chain A, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|B Chain B, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|C Chain C, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|D Chain D, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|E Chain E, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|F Chain F, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|G Chain G, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|H Chain H, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|I Chain I, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|J Chain J, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
Length = 185
Score = 100 bits (250), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 57/159 (35%), Positives = 92/159 (57%), Gaps = 5/159 (3%)
Query: 6 IIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDI-- 63
I+ YPD L++ +E +T FD NLK+++ + Y + GIGL+A QV+I K++++ +
Sbjct: 5 IVKYPDPILRRRSEEVTNFDDNLKRVVRKXFDIXYESKGIGLSAPQVNISKRIIVWNALY 64
Query: 64 --SKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
K N+ ++FINP I+ S K EGCLS PGI K++R + + +I G
Sbjct: 65 EKRKEENE-RIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHL 123
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKF 160
I +G+ + QHE DHLNG +FI+ + K+++ K
Sbjct: 124 KILKGIHSRIFQHEFDHLNGTLFIDKXTQVDKKKVRPKL 162
>pdb|3M6Q|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) G41q Mutant In Complex With
Actinonin
pdb|3PN5|A Chain A, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) G41q Mutant
Length = 193
Score = 100 bits (249), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 53/147 (36%), Positives = 86/147 (58%), Gaps = 2/147 (1%)
Query: 6 IIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDISK 65
I+ YPD L+ + I FD NLK ++ M + MY IGL+A QV ++ QL++ + +
Sbjct: 3 IVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDQIGLSAPQVGLNVQLMVFNPAG 62
Query: 66 NNNQLQ--VFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFEII 123
+ + V +NPKI YS + ++EGCLS PGI+ ++ R + +++ A +I G+ F I
Sbjct: 63 EPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSIS 122
Query: 124 AEGLLAICLQHEIDHLNGKIFIEYLSN 150
L A QHE DHL G +F + +++
Sbjct: 123 LSRLPARIFQHEYDHLEGVLFFDRMTD 149
>pdb|3M6R|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) G41m Mutant In Complex With
Actinonin
pdb|3M6R|B Chain B, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) G41m Mutant In Complex With
Actinonin
pdb|3M6R|C Chain C, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) G41m Mutant In Complex With
Actinonin
pdb|3M6R|D Chain D, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) G41m Mutant In Complex With
Actinonin
pdb|3PN6|A Chain A, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) G41m Mutant
pdb|3PN6|B Chain B, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) G41m Mutant
Length = 193
Score = 99.8 bits (247), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 53/147 (36%), Positives = 86/147 (58%), Gaps = 2/147 (1%)
Query: 6 IIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDISK 65
I+ YPD L+ + I FD NLK ++ M + MY IGL+A QV ++ QL++ + +
Sbjct: 3 IVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDMIGLSAPQVGLNVQLMVFNPAG 62
Query: 66 NNNQLQ--VFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFEII 123
+ + V +NPKI YS + ++EGCLS PGI+ ++ R + +++ A +I G+ F I
Sbjct: 63 EPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSIS 122
Query: 124 AEGLLAICLQHEIDHLNGKIFIEYLSN 150
L A QHE DHL G +F + +++
Sbjct: 123 LSRLPARIFQHEYDHLEGVLFFDRMTD 149
>pdb|3UWA|A Chain A, Crystal Structure Of A Probable Peptide Deformylase From
Synechococcus Phage S-Ssm7
pdb|3UWB|A Chain A, Crystal Structure Of A Probable Peptide Deformylase From
Strucynechococcus Phage S-Ssm7 In Complex With Actinonin
Length = 154
Score = 95.1 bits (235), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 52/143 (36%), Positives = 88/143 (61%), Gaps = 4/143 (2%)
Query: 11 DIRLKKIAEPITEFDINLKKIIFNM-TETMYHAMGIGLAASQVDIHKQLLILD--ISKNN 67
D L++ +E + EFD +++ E + + GIGLAA QV I+K+++++D ++
Sbjct: 10 DRCLRQKSEEV-EFDKKEXSELYDQXCEAXWASDGIGLAAPQVGINKRVIVVDETTEEHG 68
Query: 68 NQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFEIIAEGL 127
+ +NPKI W S+EK +++EGCLS+P ++ R K I+V N +GK + +GL
Sbjct: 69 KYAHLXVNPKITWKSEEKVLFDEGCLSVPDQNGEVLRPKSIKVTFQNKDGKYKKWKLDGL 128
Query: 128 LAICLQHEIDHLNGKIFIEYLSN 150
A +QHEIDHL G +F++Y ++
Sbjct: 129 AARVVQHEIDHLEGILFVDYFND 151
>pdb|1V3Y|A Chain A, The Crystal Structure Of Peptide Deformylase From Thermus
Thermophilus Hb8
pdb|1V3Y|B Chain B, The Crystal Structure Of Peptide Deformylase From Thermus
Thermophilus Hb8
Length = 192
Score = 93.2 bits (230), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 57/164 (34%), Positives = 91/164 (55%), Gaps = 16/164 (9%)
Query: 5 PIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL--- 61
PI Y D L++ A P+ +F +K++ +M ETM+ A G+GLAA Q+ + ++L +
Sbjct: 4 PIRLYGDPVLRRKARPVEDFS-GIKRLAEDMLETMFEAKGVGLAAPQIGLSQRLFVAVEY 62
Query: 62 -DISKNNNQ---------LQVFINPKIIWYSKEKQIYNEGCLSLPGIFNK-IKRSKRIRV 110
D + + + V NP +I Y + EG LSLPG++++ + R++RIRV
Sbjct: 63 ADEPEGEEERPLRELVRRVYVVANP-VITYREGLVEGTEGXLSLPGLYSEEVPRAERIRV 121
Query: 111 HALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKE 154
+ EG+ + EG +A QHEIDHL+G +F E L K+E
Sbjct: 122 EYQDEEGRGRVLELEGYMARVFQHEIDHLDGILFFERLPKPKRE 165
>pdb|1JYM|A Chain A, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|B Chain B, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|C Chain C, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|D Chain D, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|E Chain E, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|F Chain F, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|G Chain G, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|H Chain H, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|I Chain I, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|J Chain J, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
Length = 183
Score = 89.0 bits (219), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 56/159 (35%), Positives = 91/159 (57%), Gaps = 7/159 (4%)
Query: 6 IIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDI-- 63
I+ YPD L++ +E +T FD NLK+++ + Y + GIGL+A QV+I K++++ +
Sbjct: 5 IVKYPDPILRRRSE-VTNFDDNLKRVVRKXFDIXYESKGIGLSAPQVNISKRIIVWNALY 63
Query: 64 --SKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
K N+ ++FINP I+ S K EGCLS GI K++R + + +I G
Sbjct: 64 EKRKEENE-RIFINPSIVEQSLVKLKLIEGCLSF-GIEGKVERPSIVSISYYDINGYKHL 121
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKF 160
I +G+ + QHE DHLNG +FI+ + K+++ K
Sbjct: 122 KILKGIHSRIFQHEFDHLNGTLFIDKXTQVDKKKVRPKL 160
>pdb|3E3U|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Peptide
Deformylase In Complex With Inhibitor
Length = 197
Score = 85.5 bits (210), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 54/180 (30%), Positives = 86/180 (47%), Gaps = 22/180 (12%)
Query: 1 MTLLPIIYYPDIRLKKIAEPIT-----EFDINLKKIIFNMTETMYHAMGIGLAASQVDIH 55
M ++PI D L P+T +L ++I M +TM A G+GLAA+Q+
Sbjct: 1 MAVVPIRIVGDPVLHTATTPVTVAADGSLPADLAQLIATMYDTMDAANGVGLAANQIGCS 60
Query: 56 KQLLILDISKNN----NQLQVFINP-----KIIWYSKEKQIYNEGCLSLPGIFNKIKRSK 106
+L + D + + + V INP +I + +EGCLS+PG R+K
Sbjct: 61 LRLFVYDCAADRAMTARRRGVVINPVLETSEIPETMPDPDTDDEGCLSVPGESFPTGRAK 120
Query: 107 RIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
RV L+ +G I GL A LQHE HL+G +++ +R+I ++ +N K+
Sbjct: 121 WARVTGLDADGSPVSIEGTGLFARMLQHETGHLDGFLYL--------DRLIGRYARNAKR 172
>pdb|3DLD|A Chain A, Crystal Structure Of Peptide Deformylase, Xoo1075, From
Xanthomonas Oryzae Pv. Oryzae Kacc10331
Length = 171
Score = 83.2 bits (204), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 52/155 (33%), Positives = 75/155 (48%), Gaps = 8/155 (5%)
Query: 6 IIYYPDIRLKKIAEPITEF-DINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDIS 64
II D RL ++A +T L ++ +M ETM A G+GLAA Q+ + QL++
Sbjct: 5 IIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLMVFGFE 64
Query: 65 KNNN-------QLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEG 117
+ L N +I S E + EGCLS+PG+ I R + IR +G
Sbjct: 65 ASERYPEAPAVPLTALANAQIEPLSDEMENGWEGCLSIPGLRAVIPRYRYIRYRGFAPDG 124
Query: 118 KMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFK 152
E AEG A +QHE DHL G+++ + NF
Sbjct: 125 SPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFD 159
>pdb|2OKL|A Chain A, Crystal Structure Of Peptide Deformylase 2 With Actinonin
From Bacillus Cereus
pdb|2OKL|B Chain B, Crystal Structure Of Peptide Deformylase 2 With Actinonin
From Bacillus Cereus
Length = 185
Score = 77.0 bits (188), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 58/170 (34%), Positives = 89/170 (52%), Gaps = 24/170 (14%)
Query: 1 MTLLPIIYYPDIRLKKIAE----PITEFDIN-LKKII--------FNMTETMYHAMGIGL 47
+T+ +I D L+ +AE P +E D LK++I M E GIGL
Sbjct: 3 LTMKDVIREGDPILRNVAEEVSLPASEEDTTTLKEMIEFVINSQDPEMAEKYSLRPGIGL 62
Query: 48 AASQVDIHKQLLILDISKNNNQL--QVFINPKIIWYSKEKQIY--NEGCLSL----PGIF 99
AA Q+ + K+++ + ++ + L NPKII +S E+ EGCLS+ PG
Sbjct: 63 AAPQIGVSKKMIAVHVTDADGTLYSHALFNPKIISHSVERTYLQGGEGCLSVDREVPGY- 121
Query: 100 NKIKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLS 149
+ R RI V A +I G+ ++ +GL AI QHEIDHLNG +F ++++
Sbjct: 122 --VPRYTRITVKATSINGEEVKLRLKGLPAIVFQHEIDHLNGVMFYDHIN 169
>pdb|1ZXZ|A Chain A, X-Ray Structure Of Peptide Deformylase From Arabidopsis
Thaliana (Atpdf1a); Crystals Grown In Peg-5000 Mme As
Precipitant
pdb|1ZXZ|B Chain B, X-Ray Structure Of Peptide Deformylase From Arabidopsis
Thaliana (Atpdf1a); Crystals Grown In Peg-5000 Mme As
Precipitant
pdb|1ZY0|A Chain A, X-Ray Structure Of Peptide Deformylase From Arabidopsis
Thaliana (Atpdf1a); Crystals Grown In Peg-6000
pdb|1ZY0|B Chain B, X-Ray Structure Of Peptide Deformylase From Arabidopsis
Thaliana (Atpdf1a); Crystals Grown In Peg-6000
pdb|1ZY1|A Chain A, X-Ray Structure Of Peptide Deformylase From Arabidopsis
Thaliana (Atpdf1a) In Complex With Met-Ala-Ser
pdb|1ZY1|B Chain B, X-Ray Structure Of Peptide Deformylase From Arabidopsis
Thaliana (Atpdf1a) In Complex With Met-Ala-Ser
Length = 197
Score = 74.7 bits (182), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 49/167 (29%), Positives = 85/167 (50%), Gaps = 19/167 (11%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDIN---LKKIIFNMTETMYHAMGIGLAASQVDIHKQ 57
M L I+ D L + A + +I ++KII +M + M A G+GLAA Q+ + +
Sbjct: 1 MDLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLR 60
Query: 58 LLILDISKN----------------NNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNK 101
+++L+ +K + L V +NP + S +K ++ EGCLS+ G
Sbjct: 61 IIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAA 120
Query: 102 IKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYL 148
++R + V + +GK E+ A G A LQHE DHL+G ++++ +
Sbjct: 121 VERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKM 167
>pdb|1LQY|A Chain A, Crystal Structure Of Bacillus Stearothermophilus Peptide
Deformylase Complexed With Antibiotic Actinonin
Length = 184
Score = 71.2 bits (173), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 52/155 (33%), Positives = 84/155 (54%), Gaps = 26/155 (16%)
Query: 14 LKKIAEPI----TEFDINLKKIIFN---MTETMYHAM------GIGLAASQVDIHKQLLI 60
L+K+AEP+ +E D + + + + M++ A GIGLAA Q+++ K+++
Sbjct: 15 LRKVAEPVPLPPSEEDKRILQSLLDYVKMSQDPELAAKYGLRPGIGLAAPQINVSKRMIA 74
Query: 61 LDISKNNNQLQVF--INPKIIWYSKEKQIY---NEGCLSL----PGIFNKIKRSKRIRVH 111
+ ++ N L + NPKI+ +S + Q Y EGCLS+ PG + R RI V
Sbjct: 75 VHVTDENGTLYSYALFNPKIVSHSVQ-QCYLTTGEGCLSVDRDVPGY---VLRYARITVT 130
Query: 112 ALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIE 146
++G+ + +GL AI QHEIDHLNG +F +
Sbjct: 131 GTTLDGEEVTLRLKGLPAIVFQHEIDHLNGIMFYD 165
>pdb|1LQW|A Chain A, Crystal Structure Of S.Aureus Peptide Deformylase
pdb|1LQW|B Chain B, Crystal Structure Of S.Aureus Peptide Deformylase
pdb|2AI9|A Chain A, S.Aureus Polypeptide Deformylase
pdb|2AI9|B Chain B, S.Aureus Polypeptide Deformylase
Length = 183
Score = 70.9 bits (172), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 41/112 (36%), Positives = 65/112 (58%), Gaps = 6/112 (5%)
Query: 44 GIGLAASQVDIHKQL---LILDISKNNNQLQVFINPKIIWYSKEKQI--YNEGCLSLP-G 97
G+GLAA Q++I K++ LI D + + +NPKI+ +S ++ EGCLS+
Sbjct: 58 GVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDN 117
Query: 98 IFNKIKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLS 149
+ + R RI + A +IEG ++ +G AI QHEIDHLNG +F +++
Sbjct: 118 VAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHID 169
>pdb|1LMH|A Chain A, Crystal Structure Of S. Aureus Peptide Deformylase
Length = 184
Score = 67.0 bits (162), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 40/112 (35%), Positives = 63/112 (56%), Gaps = 6/112 (5%)
Query: 44 GIGLAASQVDIHKQ---LLILDISKNNNQLQVFINPKIIWYSKEKQI--YNEGCLSLP-G 97
G+GLAA Q++I K+ +LI D + +NPKI+ +S ++ EGCLS+
Sbjct: 58 GVGLAAPQINISKRXIAVLIPDDGSGKSYDYXLVNPKIVSHSVQEAYLPTGEGCLSVDDN 117
Query: 98 IFNKIKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLS 149
+ + R +I + A +IEG ++ +G AI QHEIDHLNG F +++
Sbjct: 118 VAGLVHRHNKITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVXFYDHID 169
>pdb|3G5K|A Chain A, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5K|B Chain B, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5K|C Chain C, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5K|D Chain D, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5P|A Chain A, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5P|B Chain B, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5P|C Chain C, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5P|D Chain D, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
Length = 183
Score = 66.2 bits (160), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 38/159 (23%), Positives = 75/159 (47%), Gaps = 19/159 (11%)
Query: 11 DIRLKKIAEPITEFDIN---LKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDISKNN 67
D L+ +A P+ + L+++ + + M +GL+A Q+ + +Q+L L++ +
Sbjct: 12 DPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEAL 71
Query: 68 NQ----------------LQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVH 111
+ L+VF+NP + + EGC S+ G + R + +++
Sbjct: 72 CRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQIS 131
Query: 112 ALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSN 150
L+ G+ A G A +QHE+DHL G +FI+ + +
Sbjct: 132 GLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDS 170
>pdb|1Q1Y|A Chain A, Crystal Structures Of Peptide Deformylase From
Staphylococcus Aureus Complexed With Actinonin
pdb|3U7K|A Chain A, Crystal Structures Of The Staphylococcus Aureus Peptide
Deformylase In Complex With Two Classes Of New
Inhibitors
pdb|3U7L|A Chain A, Crystal Structures Of The Staphylococcus Aureus Peptide
Deformylase In Complex With Two Classes Of New
Inhibitors
pdb|3U7M|A Chain A, Crystal Structures Of The Staphylococcus Aureus Peptide
Deformylase In Complex With Two Classes Of New
Inhibitors
pdb|3U7N|A Chain A, Crystal Structures Of The Staphylococcus Aureus Peptide
Deformylase In Complex With Two Classes Of New
Inhibitors
Length = 191
Score = 66.2 bits (160), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 40/112 (35%), Positives = 64/112 (57%), Gaps = 6/112 (5%)
Query: 44 GIGLAASQVDIHKQL---LILDISKNNNQLQVFINPKIIWYSKEKQI--YNEGCLSLP-G 97
G+GLAA Q++I K++ LI D + + +NPKI+ +S ++ EG LS+
Sbjct: 58 GVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGXLSVDDN 117
Query: 98 IFNKIKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLS 149
+ + R RI + A +IEG ++ +G AI QHEIDHLNG +F +++
Sbjct: 118 VAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHID 169
>pdb|1LM4|A Chain A, Structure Of Peptide Deformylase From Staphylococcus
Aureus At 1.45 A
pdb|1LM4|B Chain B, Structure Of Peptide Deformylase From Staphylococcus
Aureus At 1.45 A
Length = 194
Score = 66.2 bits (160), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 40/112 (35%), Positives = 64/112 (57%), Gaps = 6/112 (5%)
Query: 44 GIGLAASQVDIHKQL---LILDISKNNNQLQVFINPKIIWYSKEKQI--YNEGCLSLP-G 97
G+GLAA Q++I K++ LI D + + +NPKI+ +S ++ EG LS+
Sbjct: 69 GVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGXLSVDDN 128
Query: 98 IFNKIKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLS 149
+ + R RI + A +IEG ++ +G AI QHEIDHLNG +F +++
Sbjct: 129 VAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHID 180
>pdb|3G6N|A Chain A, Crystal Structure Of An Efpdf Complex With Met-Ala-Ser
pdb|3G6N|B Chain B, Crystal Structure Of An Efpdf Complex With Met-Ala-Ser
Length = 191
Score = 65.1 bits (157), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 45/157 (28%), Positives = 83/157 (52%), Gaps = 24/157 (15%)
Query: 15 KKIAEPITEFDINLKKIIFNM---------TETMYHAMGIGLAASQVDIHKQLLILDISK 65
K+++ P++E DI+L K + E ++ G+GLAA Q+DI K+++ + +
Sbjct: 24 KEVSLPLSEEDISLGKEMLEFLKNSQDPIKAEELHLRGGVGLAAPQLDISKRIIAVHVPS 83
Query: 66 NNNQLQ------VFINPKIIWYSKEKQIYNEG--CLSL----PGIFNKIKRSKRIRVHAL 113
+ + V NPKI+ +S + EG CLS+ PG + R +I V
Sbjct: 84 PDPEADGPSLSTVMYNPKILSHSVQDACLGEGEGCLSVDREVPGY---VVRHAKITVSYY 140
Query: 114 NIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSN 150
++ G+ +I + +I +QHEIDH+NG +F +++++
Sbjct: 141 DMNGEKHKIRLKNYESIVVQHEIDHINGVMFYDHIND 177
>pdb|3CMD|A Chain A, Crystal Structure Of Peptide Deformylase From
Vre-E.Faecium
pdb|3CMD|B Chain B, Crystal Structure Of Peptide Deformylase From
Vre-E.Faecium
Length = 196
Score = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 45/157 (28%), Positives = 83/157 (52%), Gaps = 24/157 (15%)
Query: 15 KKIAEPITEFDINLKKIIFNM---------TETMYHAMGIGLAASQVDIHKQLLILDISK 65
K+++ P++E DI+L K + E ++ G+GLAA Q+DI K+++ + +
Sbjct: 29 KEVSLPLSEEDISLGKEMLEFLKNSQDPIKAEELHLRGGVGLAAPQLDISKRIIAVHVPS 88
Query: 66 NNNQLQ------VFINPKIIWYSKEKQIYNEG--CLSL----PGIFNKIKRSKRIRVHAL 113
+ + V NPKI+ +S + EG CLS+ PG + R +I V
Sbjct: 89 PDPEADGPSLSTVMYNPKILSHSVQDACLGEGEGCLSVDREVPGY---VVRHAKITVSYY 145
Query: 114 NIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSN 150
++ G+ +I + +I +QHEIDH+NG +F +++++
Sbjct: 146 DMNGEKHKIRLKNYESIVVQHEIDHINGVMFYDHIND 182
>pdb|2OS1|A Chain A, Structures Of Actinonin Bound Peptide Deformylases From E.
Faecalis And S. Pyogenes
Length = 188
Score = 64.3 bits (155), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 51/174 (29%), Positives = 88/174 (50%), Gaps = 28/174 (16%)
Query: 1 MTLLPIIYYPDIRLKKIAE----PITEFDINLKKIIFNM---------TETMYHAMGIGL 47
+T+ II + L+ +AE PITE D L + + E + G+GL
Sbjct: 2 ITMKDIIREGNPTLRAVAEEVPVPITEEDRQLGEDMLTFLKNSQDPVKAEELQLRGGVGL 61
Query: 48 AASQVDIHKQLLILDISKNNNQLQ------VFINPKIIWYSKEKQIYNEG--CLSL---- 95
AA Q+DI K+++ + + N+ + + V NPKI+ +S + EG CLS+
Sbjct: 62 AAPQLDISKRIIAVHVPSNDPENETPSLSTVMYNPKILSHSVQDVCLGEGEGCLSVDRDV 121
Query: 96 PGIFNKIKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLS 149
PG + R +I V ++ G+ ++ + AI +QHEIDH+NG +F ++++
Sbjct: 122 PGY---VVRHNKITVSYFDMAGEKHKVRLKNYEAIVVQHEIDHINGIMFYDHIN 172
>pdb|2OS3|A Chain A, Structures Of Actinonin Bound Peptide Deformylases From E.
Faecalis And S. Pyogenes
Length = 205
Score = 62.8 bits (151), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 46/155 (29%), Positives = 78/155 (50%), Gaps = 23/155 (14%)
Query: 15 KKIAEPITEFDINLKKIIFN---------MTETMYHAMGIGLAASQVDIHKQLLILDI-- 63
K+++ P+ + DI L + + M E + G+GLAA Q+D+ K+++ + +
Sbjct: 31 KEVSLPLCDEDILLGEKMMQFLKHSQDPVMAEKLGLRAGVGLAAPQIDVSKRIIAVLVPN 90
Query: 64 --SKNNNQ-------LQVFINPKIIWYSKEKQIYN--EGCLSLPGIFNK-IKRSKRIRVH 111
K N +V NPKI+ +S + + EGCLS+ + + R R+ V
Sbjct: 91 LPDKEGNPPKEAYSWQEVLYNPKIVSHSVQDAALSDGEGCLSVDRVVEGYVVRHARVTVD 150
Query: 112 ALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIE 146
+ EG+ I +G AI +QHEIDH+NG +F +
Sbjct: 151 YYDKEGQQHRIKLKGYNAIVVQHEIDHINGVLFYD 185
>pdb|2OS0|A Chain A, Structures Of Actinonin Bound Peptide Deformylases From E.
Faecalis And S. Pyogenes
Length = 188
Score = 61.2 bits (147), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 50/174 (28%), Positives = 87/174 (50%), Gaps = 28/174 (16%)
Query: 1 MTLLPIIYYPDIRLKKIAE----PITEFDINLKKIIFNM---------TETMYHAMGIGL 47
+T+ II + L+ +AE PITE D L + + E + +GL
Sbjct: 2 ITMKDIIREGNPTLRAVAEEVPVPITEEDRQLGEDMLTFLKNSQDPVKAEELQLRGDVGL 61
Query: 48 AASQVDIHKQLLILDISKNNNQLQ------VFINPKIIWYSKEKQIYNEG--CLSL---- 95
AA Q+DI K+++ + + N+ + + V NPKI+ +S + EG CLS+
Sbjct: 62 AAPQLDISKRIIAVHVPSNDPENETPSLSTVMYNPKILSHSVQDVCLGEGEGCLSVDRDV 121
Query: 96 PGIFNKIKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLS 149
PG + R +I V ++ G+ ++ + AI +QHEIDH+NG +F ++++
Sbjct: 122 PGY---VVRHNKITVSYFDMAGEKHKVRLKNYEAIVVQHEIDHINGIMFYDHIN 172
>pdb|2AIE|P Chain P, S.Pneumoniae Polypeptide Deformylase Complexed With Sb-
505684
Length = 203
Score = 60.5 bits (145), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 50/161 (31%), Positives = 79/161 (49%), Gaps = 34/161 (21%)
Query: 14 LKKIAEPITEFDINLKKIIFN--------------MTETMYHAMGIGLAASQVDIHKQL- 58
L+ +AE +T F ++ ++II M E M G+GLAA Q+DI K++
Sbjct: 27 LRTVAEEVT-FPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRII 85
Query: 59 --LILDISKNNNQLQ-------VFINPKIIWYSKEKQIYNEG--CLSL----PGIFNKIK 103
L+ +I + Q + NPKI+ +S + EG CLS+ PG +
Sbjct: 86 AVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEGCLSVDRNVPGY---VV 142
Query: 104 RSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIF 144
R R+ V + +G+ I +G +I +QHEIDH+NG +F
Sbjct: 143 RHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMF 183
>pdb|3STR|P Chain P, Strep Peptide Deformylase With A Time Dependent
Thiazolidine Hydroxamic Acid
pdb|3SW8|P Chain P, Strep Peptide Deformylase With A Time Dependent
Dichlorobenzamide- Reverse Hydroxamic Acid
pdb|4EOX|P Chain P, X-Ray Structure Of Polypeptide Deformylase Bound To A
Acylprolinamide Inhibitor
Length = 203
Score = 60.5 bits (145), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 50/166 (30%), Positives = 82/166 (49%), Gaps = 34/166 (20%)
Query: 14 LKKIAEPITEFDINLKKIIFN--------------MTETMYHAMGIGLAASQVDIHKQL- 58
L+ +AE +T F ++ ++II M E M G+GLAA Q+DI K++
Sbjct: 27 LRTVAEEVT-FPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRII 85
Query: 59 --LILDISKNNNQLQ-------VFINPKIIWYSKEKQIYNEG--CLSL----PGIFNKIK 103
L+ +I + Q + NPKI+ +S + EG CLS+ PG +
Sbjct: 86 AVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEGCLSVDRNVPGY---VV 142
Query: 104 RSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLS 149
R R+ V + +G+ I +G +I +QHEIDH+NG +F + ++
Sbjct: 143 RHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRIN 188
>pdb|2AI7|A Chain A, S.Pneumoniae Polypeptide Deformylase Complexed With Sb-
485345
pdb|2AIA|A Chain A, S.Pneumoniae Pdf Complexed With Sb-543668
Length = 203
Score = 60.5 bits (145), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 50/161 (31%), Positives = 79/161 (49%), Gaps = 34/161 (21%)
Query: 14 LKKIAEPITEFDINLKKIIFN--------------MTETMYHAMGIGLAASQVDIHKQL- 58
L+ +AE +T F ++ ++II M E M G+GLAA Q+DI K++
Sbjct: 27 LRTVAEEVT-FPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRII 85
Query: 59 --LILDISKNNNQLQ-------VFINPKIIWYSKEKQIYNEG--CLSL----PGIFNKIK 103
L+ +I + Q + NPKI+ +S + EG CLS+ PG +
Sbjct: 86 AVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEGCLSVDRNVPGY---VV 142
Query: 104 RSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIF 144
R R+ V + +G+ I +G +I +QHEIDH+NG +F
Sbjct: 143 RHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMF 183
>pdb|3SVJ|P Chain P, Strep Peptide Deformylase With A Time Dependent
Thiazolidine Amide
Length = 203
Score = 56.2 bits (134), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 48/166 (28%), Positives = 79/166 (47%), Gaps = 34/166 (20%)
Query: 14 LKKIAEPITEFDINLKKIIFN--------------MTETMYHAMGIGLAASQVDIHKQL- 58
L+ +AE +T F ++ ++II M E M G+GLAA Q+DI K++
Sbjct: 27 LRTVAEEVT-FPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRII 85
Query: 59 --LILDISKNNNQLQ-------VFINPKIIWYSKEKQIYNEGCLSL------PGIFNKIK 103
L+ +I + Q + NPKI+ +S + EG L PG +
Sbjct: 86 AVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEGXLSVDRNVPGY---VV 142
Query: 104 RSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLS 149
R R+ V + +G+ I +G +I +QHEIDH+NG +F + ++
Sbjct: 143 RHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRIN 188
>pdb|1LM6|A Chain A, Crystal Structure Of Peptide Deformylase From
Streptococcus Pneumoniae
Length = 215
Score = 56.2 bits (134), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 48/166 (28%), Positives = 79/166 (47%), Gaps = 34/166 (20%)
Query: 14 LKKIAEPITEFDINLKKIIFN--------------MTETMYHAMGIGLAASQVDIHKQL- 58
L+ +AE +T F ++ ++II M E M G+GLAA Q+DI K++
Sbjct: 39 LRTVAEEVT-FPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRII 97
Query: 59 --LILDISKNNNQLQ-------VFINPKIIWYSKEKQIYNEGCLSL------PGIFNKIK 103
L+ +I + Q + NPKI+ +S + EG L PG +
Sbjct: 98 AVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEGXLSVDRNVPGY---VV 154
Query: 104 RSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLS 149
R R+ V + +G+ I +G +I +QHEIDH+NG +F + ++
Sbjct: 155 RHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRIN 200
>pdb|3L87|A Chain A, The Crystal Structure Of Smu.143c From Streptococcus
Mutans Ua159
Length = 238
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 44/164 (26%), Positives = 75/164 (45%), Gaps = 29/164 (17%)
Query: 14 LKKIAEPITEFDINLKKIIFN--------------MTETMYHAMGIGLAASQVDIHKQLL 59
L+ +A+ +T F +N II E M G+GLAA Q+DI K+++
Sbjct: 61 LRAVAQDVT-FPLNEDDIILGEKMLQFLKNSQDPVTAEKMELRGGVGLAAPQLDISKRII 119
Query: 60 ILDI----SKNNNQL-------QVFINPKIIWYSKEKQIY--NEGCLSLPGIFNK-IKRS 105
+ I K+ N +V NP+II +S + EG LS+ + + R
Sbjct: 120 AVLIPNPEDKDGNPPKEAYALKEVMYNPRIIAHSVQDAALADGEGXLSVDRVVEGYVIRH 179
Query: 106 KRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLS 149
R+ + + ++ +G +I +QHEIDH NG +F + ++
Sbjct: 180 SRVTIEYYDKNSDKKKLKLKGYQSIVVQHEIDHTNGIMFFDRIN 223
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.325 0.143 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,709,003
Number of Sequences: 62578
Number of extensions: 172932
Number of successful extensions: 679
Number of sequences better than 100.0: 56
Number of HSP's better than 100.0 without gapping: 52
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 575
Number of HSP's gapped (non-prelim): 56
length of query: 166
length of database: 14,973,337
effective HSP length: 92
effective length of query: 74
effective length of database: 9,216,161
effective search space: 681995914
effective search space used: 681995914
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 47 (22.7 bits)