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= 032139
(146 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|O Chain O, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 144
Score = 237 bits (604), Expect = 2e-63, Method: Compositional matrix adjust.
Identities = 117/146 (80%), Positives = 130/146 (89%), Gaps = 2/146 (1%)
Query: 1 MTTRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHHHRILFDKYHPGFFGKVGMRY 60
MTTRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHHHRILFDKYHPG+FGKVGMRY
Sbjct: 1 MTTRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHHHRILFDKYHPGYFGKVGMRY 60
Query: 61 FHKLRNKFHCPIVNIDKLWSMVPQDVKAKASKDNVPMIDVTQFGYFKVLGKGVLPENQPV 120
FH+L N+FHCP VN+++LWSMVP + A A P+IDVTQFGY KVLGKG+LP +P+
Sbjct: 61 FHRLSNRFHCPAVNVERLWSMVPAE--AGAGAGKAPVIDVTQFGYTKVLGKGMLPPERPI 118
Query: 121 VVKAKLVSKTAEKKIKEAGGAVVLTA 146
VVKAKL+SK AEKKIK AGGAV+LTA
Sbjct: 119 VVKAKLISKVAEKKIKAAGGAVLLTA 144
>pdb|2ZKR|LL Chain l, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 148
Score = 193 bits (491), Expect = 3e-50, Method: Compositional matrix adjust.
Identities = 95/149 (63%), Positives = 116/149 (77%), Gaps = 4/149 (2%)
Query: 1 MTTRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHHHRILFDKYHPGFFGKVGMRY 60
M +R +K RK RGHVS GHGRIGKHRKHPGGRGNAGGMHHHRI FDKYHPG+FGKVGM++
Sbjct: 1 MPSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMKH 60
Query: 61 FHKLRNKFHCPIVNIDKLWSMVPQDVKAKASKDNV---PMIDVTQFGYFKVLGKGVLPEN 117
+H RN+ CP VN+DK W++V + + A+K+ P+IDV + GY+KVLGKG LP+
Sbjct: 61 YHLKRNQSFCPTVNLDKPWTLVSEQTRVNAAKNKTGVAPIIDVVRSGYYKVLGKGKLPK- 119
Query: 118 QPVVVKAKLVSKTAEKKIKEAGGAVVLTA 146
QPV+VKAK S+ AE+KIK GGA VL A
Sbjct: 120 QPVIVKAKFFSRRAEEKIKSVGGACVLVA 148
>pdb|3IZS|O Chain O, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5E|AA Chain a, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|AA Chain a, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|AA Chain a, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 149
Score = 188 bits (477), Expect = 1e-48, Method: Compositional matrix adjust.
Identities = 94/150 (62%), Positives = 114/150 (76%), Gaps = 5/150 (3%)
Query: 1 MTTRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHHHRILFDKYHPGFFGKVGMRY 60
M +RF K RK RGHVSAG GRIGKHRKHPGGRG AGG HHHRI DKYHPG+FGKVGMRY
Sbjct: 1 MPSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGQHHHRINMDKYHPGYFGKVGMRY 60
Query: 61 FHKLRNKFHCPIVNIDKLWSMVPQDVKAK----ASKDNVPMIDVTQFGYFKVLGKGVLPE 116
FHK + F P++N+DKLW+++P+D + + ASK+ P+ID GY K+LGKG +P
Sbjct: 61 FHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPVIDTLAAGYGKILGKGRIP- 119
Query: 117 NQPVVVKAKLVSKTAEKKIKEAGGAVVLTA 146
N PV+VKA+ VSK AE+KI+ AGG V L A
Sbjct: 120 NVPVIVKARFVSKLAEEKIRAAGGVVELIA 149
>pdb|3O58|Y Chain Y, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|Y Chain Y, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit
Length = 149
Score = 187 bits (475), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 94/150 (62%), Positives = 114/150 (76%), Gaps = 5/150 (3%)
Query: 1 MTTRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHHHRILFDKYHPGFFGKVGMRY 60
M +RF K RK RGHVSAG GRIGKHRKHPGGRG AGG HHHRI DKYHPG+FGKVGMRY
Sbjct: 1 MPSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGEHHHRINMDKYHPGYFGKVGMRY 60
Query: 61 FHKLRNKFHCPIVNIDKLWSMVPQDVKAK----ASKDNVPMIDVTQFGYFKVLGKGVLPE 116
FHK + F P++N+DKLW+++P+D + + ASK+ P+ID GY K+LGKG +P
Sbjct: 61 FHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPVIDTLAAGYGKILGKGRIP- 119
Query: 117 NQPVVVKAKLVSKTAEKKIKEAGGAVVLTA 146
N PV+VKA+ VSK AE+KI+ AGG V L A
Sbjct: 120 NVPVIVKARFVSKLAEEKIRAAGGVVELIA 149
>pdb|1S1I|V Chain V, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 148
Score = 185 bits (470), Expect = 7e-48, Method: Compositional matrix adjust.
Identities = 93/148 (62%), Positives = 113/148 (76%), Gaps = 5/148 (3%)
Query: 3 TRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHHHRILFDKYHPGFFGKVGMRYFH 62
+RF K RK RGHVSAG GRIGKHRKHPGGRG AGG HHHRI DKYHPG+FGKVGMRYFH
Sbjct: 2 SRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGEHHHRINMDKYHPGYFGKVGMRYFH 61
Query: 63 KLRNKFHCPIVNIDKLWSMVPQDVKAK----ASKDNVPMIDVTQFGYFKVLGKGVLPENQ 118
K + F P++N+DKLW+++P+D + + ASK+ P+ID GY K+LGKG +P N
Sbjct: 62 KQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPVIDTLAAGYGKILGKGRIP-NV 120
Query: 119 PVVVKAKLVSKTAEKKIKEAGGAVVLTA 146
PV+VKA+ VSK AE+KI+ AGG V L A
Sbjct: 121 PVIVKARFVSKLAEEKIRAAGGVVELIA 148
>pdb|3JYW|V Chain V, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 142
Score = 172 bits (436), Expect = 6e-44, Method: Compositional matrix adjust.
Identities = 89/142 (62%), Positives = 108/142 (76%), Gaps = 6/142 (4%)
Query: 7 KNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHHHRILFDKYHPGFFGKVGMRYFHKLRN 66
K RK RGHVSAG GRIGKHRKHPGG G AGG HHHRI DKYHPG+FGKVGMRYFHK +
Sbjct: 2 KTRKHRGHVSAGKGRIGKHRKHPGG-GMAGGEHHHRINMDKYHPGYFGKVGMRYFHKQQA 60
Query: 67 KFHCPIVNIDKLWSMVPQDVKAK----ASKDNVPMIDVTQFGYFKVLGKGVLPENQPVVV 122
F P++N+DKLW+++P+D + + ASK+ P+ID GY K+LGKG +P N PV+V
Sbjct: 61 HFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPVIDTLAAGYGKILGKGRIP-NVPVIV 119
Query: 123 KAKLVSKTAEKKIKEAGGAVVL 144
KA+ VSK AE+KI+ AGG V L
Sbjct: 120 KARFVSKLAEEKIRAAGGVVEL 141
>pdb|4A17|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 149
Score = 167 bits (423), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 91/150 (60%), Positives = 109/150 (72%), Gaps = 5/150 (3%)
Query: 1 MTTRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGG--MHHHRILFDKYHPGFFGKVGM 58
M + KK RK RGHVS GHGR+GKHRK G MHHHRIL +K+HPG++GK+GM
Sbjct: 1 MVSHLKKTRKLRGHVSHGHGRVGKHRKGGCRGGRGKAGGMHHHRILMEKWHPGYYGKLGM 60
Query: 59 RYFHKLRNKFHCPIVNIDKLWSMVPQDVKAKASKD--NVPMIDVTQFGYFKVLGKGVLPE 116
R FH +N HCP+VNIDKLWS+V + K ++D VP+IDVT+ G+FKVLGKG LP
Sbjct: 61 RTFHLKKNPLHCPVVNIDKLWSLVSDATRQKYAEDKKKVPVIDVTKAGFFKVLGKGRLP- 119
Query: 117 NQPVVVKAKLVSKTAEKKIKEAGGAVVLTA 146
NQPVVVKAK SKTAE++I GGA VLTA
Sbjct: 120 NQPVVVKAKYFSKTAERRIVAVGGACVLTA 149
>pdb|3ZF7|BB Chain b, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 145
Score = 158 bits (399), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 82/147 (55%), Positives = 104/147 (70%), Gaps = 3/147 (2%)
Query: 1 MTTRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHHHRILFDKYHPGFFGKVGMRY 60
M TRFKK R +RG G+GR+GKHRKHP GRGNAGG HHHRI F KYHPG+FGK GM +
Sbjct: 1 MPTRFKKTRHQRGSTFCGYGRVGKHRKHPSGRGNAGGEHHHRINFRKYHPGYFGKCGMNH 60
Query: 61 FHKLRNKFHCPIVNIDKLWSMVPQDVKAKASK-DNVPMIDVTQFGYFKVLGKGVLPENQP 119
+HK +N P +N+D L ++ +D KA K + +P+ID+ GY K+LG G L P
Sbjct: 61 YHKKKNTTWKPTINLDNLTKLMAKDEAMKAKKGEALPVIDLLANGYSKLLGNGHL--QAP 118
Query: 120 VVVKAKLVSKTAEKKIKEAGGAVVLTA 146
+VKA+ VSK A+KKI++AGGAVVL A
Sbjct: 119 CIVKARWVSKLADKKIRKAGGAVVLQA 145
>pdb|3J21|L Chain L, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 147
Score = 42.7 bits (99), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/48 (54%), Positives = 33/48 (68%), Gaps = 3/48 (6%)
Query: 97 MIDVTQFGYFKVLGKGVLPENQPVVVKAKLVSKTAEKKIKEAGGAVVL 144
++DVTQF KVLG G L +P+V+KA+ S AE+KIK AGG VL
Sbjct: 102 IVDVTQFAD-KVLGTGKL--TRPLVIKARAFSPKAEEKIKAAGGEAVL 146
>pdb|2J01|P Chain P, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4).
This File Contains The 50s Subunit From Molecule I.
pdb|2J03|P Chain P, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 4 Of 4).
This File Contains The 50s Subunit From Molecule Ii.
pdb|2HGJ|O Chain O, Crystal Structure Of The 70s Thermus Thermophilus Ribosome
Showing How The 16s 3'-End Mimicks Mrna E And P Codons.
This Entry 2hgj Contains 50s Ribosomal Subunit. The 30s
Ribosomal Subunit Can Be Found In Pdb Entry 2hgi.
pdb|2HGQ|O Chain O, Crystal Structure Of The 70s Thermus Thermophilus Ribosome
With Translocated And Rotated Shine-Dalgarno Duplex.
This Entry 2hgq Contains 50s Ribosomal Subunit. The 30s
Ribosomal Subunit Can Be Found In Pdb Entry 2hgp.
pdb|2HGU|O Chain O, 70s T.Th. Ribosome Functional Complex With Mrna And E- And
P-Site Trnas At 4.5a. This Entry 2hgu Contains 50s
Ribosomal Subunit. The 30s Ribosomal Subunit Can Be
Found In Pdb Entry 2hgr.
pdb|1VSA|J Chain J, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals
Functional Interactions And Rearrangements. This File,
1vsa, Contains The 50s Ribosome Subunit. 30s Ribosome
Subunit Is In The File 2ow8
pdb|2V47|P Chain P, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 2 Of 4). This File Contains The 50s
Subunit For Molecule 1.
pdb|2V49|P Chain P, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 4 Of 4). This File Contains The 50s
Subunit Of Molecule 2.
pdb|1VSP|J Chain J, Interactions And Dynamics Of The Shine-Dalgarno Helix In
The 70s Ribosome. This File, 1vsp, Contains The 50s
Ribosome Subunit. 30s Ribosome Subunit Is In The File
2qnh
pdb|3D5B|P Chain P, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 50s Subunit Of One 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes As Described In Remark 400.
pdb|3D5D|P Chain P, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 50s Subunit Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|3F1F|P Chain P, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes As Described In
Remark 400.
pdb|3F1H|P Chain P, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
50s Subunit Of The Second 70s Ribosome. The Entire
Crystal Structure Contains Two 70s Ribosomes As
Described In Remark 400.
pdb|2WDI|P Chain P, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A-Site Trna,
Deacylated P-Site Trna, And E-Site Trna. This File
Contains The 50s Subunit For Molecule I.
pdb|2WDJ|P Chain P, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A-Site Trna,
Deacylated P-Site Trna, And E-Site Trna. This File
Contains The 50s Subunit For Molecule Ii.
pdb|2WDL|P Chain P, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A- And P-Site
Trnas, And E-Site Trna. This File Contains The 50s
Subunit For Molecule I.
pdb|2WDN|P Chain P, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A- And P-Site
Trnas, And E-Site Trna. This File Contains The 50s
Subunit For Molecule Ii.
pdb|2WH2|P Chain P, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|2WH4|P Chain P, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|3HUX|P Chain P, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 50s Subunit For Molecule I.
pdb|3HUZ|P Chain P, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 50s Subunit For Molecule Ii.
pdb|2WRJ|P Chain P, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State (Part 2 Of 4).
pdb|2WRL|P Chain P, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State. (Part 4 Of
4).
pdb|2WRO|P Chain P, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 2 Of 4).
pdb|2WRR|P Chain P, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 4 Of 4).
pdb|3KIR|P Chain P, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 2 Of 4)
pdb|3KIT|P Chain P, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 4 Of 4)
pdb|3KIW|P Chain P, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 2 Of 4)
pdb|3KIY|P Chain P, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 4 Of 4)
pdb|3KNI|P Chain P, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 50s Subunit For Molecule I
pdb|3KNK|P Chain P, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 50s Subunit For Molecule Ii.
pdb|3KNM|P Chain P, The Structures Of Capreomycin Bound To The 70s Ribosome.
Thi Contains The 50s Subunit For Molecule I.
pdb|3KNO|P Chain P, The Structures Of Capreomycin Bound To The 70s Ribosome.
Thi Contains The 50s Subunit For Molecule Ii
pdb|3I8F|O Chain O, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8f Contains 50s Ribosomal Subunit. The 30s
Ribosoma Can Be Found In Pdb Entry 3i8g. Molecule B In
The Same Asym Unit Is Deposited As 3i8g (30s) And 3i8f
(50s).
pdb|3I8I|O Chain O, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8i Contains 50s Ribosomal Subnit. The 30s
Ribosomal Can Be Found In Pdb Entry 3i8h. Molecule A In
The Same Asym Unit Is Deposited As 3i8f (50s) And 3i8g
(30s).
pdb|3I9C|O Chain O, Initiation Complex Of 70s Ribosome With Two Trnas And
Mrna. 3i9c Contains 50s Ribosomal Subunit Of Molecule B.
The 30s Subunit Can Be Found In Pdb Entry 3i9b. Molecule
A In The S Asymmetric Unit Is Deposited As 3i9d (30s)
And 3i9e (50s)
pdb|3I9E|O Chain O, Initiation Complex Of 70s Ribosome With Two Trnas And
Mrna. 3i9e Contains 50s Ribosomal Subunit Of Molecule A.
The 30s Subunit Can Be Found In Pdb Entry 3i9d. Molecule
B In The S Asymmetric Unit Is Deposited As 3i9b (30s)
And 3i9c (50s)
pdb|2X9S|P Chain P, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9U|P Chain P, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|3MRZ|L Chain L, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3mrz Contains 50s Ribosomal Subunit. The 30s
Ribosomal Subunit Can Be Found In Pdb Entry 3ms0.
Molecule A In The Same Asymmetric Unit Is Deposited As
3mr8 (50s) And 3ms1 (30s).
pdb|3MS1|L Chain L, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3ms1 Contains 50s Ribosomal Subunit. The 30s
Ribosomal Subunit Can Be Found In Pdb Entry 3mr8.
Molecule B In The Same Asymmetric Unit Is Deposited As
3mrz (50s) And 3ms0 (30s).
pdb|2XG0|P Chain P, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 2 Of 4)
pdb|2XG2|P Chain P, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 4 Of 4)
pdb|3OH5|P Chain P, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Chloramphenicol. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OH7|P Chain P, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Chloramphenicol. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OHJ|P Chain P, Structure Of The Thermus Thermophilus Ribosome Complexed
With Erythromycin. This File Contains The 50s Subunit Of
One 70s Ribosome. The Entire Crystal Structure Contains
Two 70s Ribosomes.
pdb|3OHK|P Chain P, Structure Of The Thermus Thermophilus Ribosome Complexed
With Erythromycin. This File Contains The 50s Subunit Of
One 70s Ribosome. The Entire Crystal Structure Contains
Two 70s Ribosomes.
pdb|3OHZ|P Chain P, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Azithromycin. This File Contains The 50s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI1|P Chain P, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Azithromycin. This File Contains The 50s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI3|P Chain P, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Telithromycin. This File Contains The 50s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI5|P Chain P, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Telithromycin. This File Contains The 50s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|2XQE|P Chain P, The Structure Of Ef-Tu And Aminoacyl-Trna Bound To The 70s
Ribosome With A Gtp Analog
pdb|2XTG|P Chain P, Trna Tranlocation On The 70s Ribosome: The Pre-
Translocational Translocation Intermediate Ti(Pre)
pdb|2XUX|P Chain P, Trna Translocation On The 70s Ribosome: The Post-
Translocational Translocation Intermediate Ti(Post)
pdb|2Y0V|P Chain P, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0X|P Chain P, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0Z|P Chain P, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y11|P Chain P, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome.
pdb|2Y13|P Chain P, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y15|P Chain P, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Cognate Codon On The 70s Ribosome.
pdb|2Y17|P Chain P, Ef-Tu Complex 3
pdb|2Y19|P Chain P, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome.
pdb|3ZVP|P Chain P, Crystal Structure Of The Hybrid State Of Ribosome In
Complex With The Guanosine Triphosphatase Release Factor
3
pdb|3UXQ|P Chain P, The Structure Of Thermorubin In Complex With The 70s
Ribosome From Thermus Thermophilus. This File Contains
The 50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3UXR|P Chain P, The Structure Of Thermorubin In Complex With The 70s
Ribosome From Thermus Thermophilus. This File Contains
The 50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3TVE|O Chain O, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Leu Complex
pdb|3TVH|O Chain O, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Leu Complex
pdb|3UYE|O Chain O, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Leu Complex
pdb|3UYG|O Chain O, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Leu Complex
pdb|3UZ1|O Chain O, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Leu Complex With Paromomycin
pdb|3UZ2|O Chain O, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Leu Complex With Paromomycin.
pdb|3UZ8|O Chain O, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Tyr Complex.
pdb|3UZ9|O Chain O, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Tyr Complex.
pdb|3UZF|O Chain O, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Tyr Complex
pdb|3UZH|O Chain O, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Tyr Complex.
pdb|3UZK|O Chain O, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Tyr Complex With Paromomycin
pdb|3UZN|O Chain O, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Near-cognate
Trna-tyr Complex With Paromomycin
pdb|4ABS|P Chain P, Complex Of Smpb, A Tmrna Fragment And Ef-Tu-Gdp-Kirromycin
With The 70s Ribosome
pdb|4DHA|P Chain P, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|4DHC|P Chain P, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|3V23|P Chain P, Crystal Structure Of Rmf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 50s Subunit Of
The 1st Ribosome In The Asu
pdb|3V25|P Chain P, Crystal Structure Of Rmf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 50s Subunit Of
The 2nd Ribosome In The Asu
pdb|3V27|P Chain P, Crystal Structure Of Hpf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 50s Subunit Of
The 1st Ribosome In The Asu
pdb|3V29|P Chain P, Crystal Structure Of Hpf Bound To The 70s Ribosome. This
Entry Contains The 50s Subunit Of The 2nd Molecule In
The Asu.
pdb|3V2D|P Chain P, Crystal Structure Of Yfia Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 50s Subunit Of
The 1st Ribosome In The Asu
pdb|3V2F|P Chain P, Crystal Structure Of Yfia Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 50s Subunit Of
The 2nd Ribosome In The Asu
pdb|4G5L|O Chain O, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 50s Subunit Of Molecule A.
pdb|4G5N|O Chain O, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 50s Subunit Of Molecule B.
pdb|4G5U|O Chain O, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 50s Subunit Of Molecule A.
pdb|4G5W|O Chain O, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 50s Subunit Of Molecule B
Length = 150
Score = 29.3 bits (64), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 27/42 (64%), Gaps = 4/42 (9%)
Query: 104 GY-FKVLGKGVLPENQPVVVKAKLVSKTAEKKIKEAGGAVVL 144
GY K+LG+G E +P+ V A SK+A +K+K AGG VL
Sbjct: 109 GYRLKILGEG---EAKPLKVVAHAFSKSALEKLKAAGGEPVL 147
>pdb|3FIN|P Chain P, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas
And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A
6.4 A Cryo-Em Map. This File Contains The 50s Subunit.
pdb|3PYO|L Chain L, Crystal Structure Of A Complex Containing Domain 3 From
The Psiv Igr Ires Rna Bound To The 70s Ribosome. This
File Contains The 50s Subunit Of The First 70s Ribosome.
pdb|3PYR|L Chain L, Crystal Structure Of A Complex Containing Domain 3 From
The Psiv Igr Ires Rna Bound To The 70s Ribosome. This
File Contains The 50s Subunit Of The Second 70s
Ribosome.
pdb|3PYT|L Chain L, Crystal Structure Of A Complex Containing Domain 3 Of Crpv
Igr Ires Rna Bound To The 70s Ribosome. This File
Contains The 50s Subunit Of The First 70s Ribosome.
pdb|3PYV|L Chain L, Crystal Structure Of A Complex Containing Domain 3 Of Crpv
Igr Ires Rna Bound To The 70s Ribosome. This File
Contains The 50s Subunit Of The Second 70s Ribosome
Length = 146
Score = 29.3 bits (64), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 27/42 (64%), Gaps = 4/42 (9%)
Query: 104 GY-FKVLGKGVLPENQPVVVKAKLVSKTAEKKIKEAGGAVVL 144
GY K+LG+G E +P+ V A SK+A +K+K AGG VL
Sbjct: 105 GYRLKILGEG---EAKPLKVVAHAFSKSALEKLKAAGGEPVL 143
>pdb|2P28|B Chain B, Structure Of The Phe2 And Phe3 Fragments Of The Integrin
Beta2 Subunit
Length = 217
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 13 GHVSAGHGR----IGKHRKHPGGRGNAGGMHHH 41
G V G GR GK R HPG G+A HHH
Sbjct: 185 GQVCGGPGRGLCFCGKCRCHPGFEGSACQHHHH 217
>pdb|1S72|L Chain L, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|L Chain L, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|L Chain L, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|L Chain L, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|L Chain L, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|L Chain L, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|L Chain L, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|L Chain L, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|L Chain L, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|L Chain L, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|L Chain L, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|L Chain L, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|L Chain L, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|L Chain L, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|L Chain L, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|L Chain L, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|L Chain L, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|L Chain L, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|L Chain L, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|L Chain L, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|L Chain L, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|L Chain L, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|L Chain L, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|L Chain L, The Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution With Rrna Sequence For The 23s Rrna And
Genome-Derived Sequences For R-Proteins
pdb|3CC4|L Chain L, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|L Chain L, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|L Chain L, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|L Chain L, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|L Chain L, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|L Chain L, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|L Chain L, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|L Chain L, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|L Chain L, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|L Chain L, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|L Chain L, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|L Chain L, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|K Chain K, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|L Chain L, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|L Chain L, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|L Chain L, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3G4S|L Chain L, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|L Chain L, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|L Chain L, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3I55|L Chain L, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|L Chain L, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|L Chain L, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 165
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 44/152 (28%), Positives = 71/152 (46%), Gaps = 15/152 (9%)
Query: 1 MTTRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHHHRILFDKYHPGFFGKVGMRY 60
MT++ K+ R R H H + + H GGRG+AG H F + P GK G +
Sbjct: 1 MTSKKKRQRGSRTHGGGSH-KNRRGAGHRGGRGDAGRDKHE---FHNHEP--LGKSGFKR 54
Query: 61 FHKLRNKFHC-PIVNIDKLWSMVPQDVKAKASKD--NVPMIDVTQFG----YFKVLGKGV 113
K++ + + ID+ +++ D A+ V + DV + Y KVLG G
Sbjct: 55 PQKVQEEAATIDVREIDENVTLLAADDVAEVEDGGFRVDVRDVVEEADDADYVKVLGAGQ 114
Query: 114 LPENQPVVVKAKLVSKTAEKKIKEAGGAVVLT 145
+ + + A S+ A +K++ AGG+V LT
Sbjct: 115 V--RHELTLIADDFSEGAREKVEGAGGSVELT 144
>pdb|3J21|P Chain P, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 120
Score = 26.6 bits (57), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 108 VLGKGVLPENQPVVVKAKLVSKTAEKKIKEAGGAVV 143
VLG G L + V+V A S+TA +KI EAGG +
Sbjct: 68 VLGAGKL--EKKVIVAAWKFSETARRKIIEAGGEAI 101
>pdb|3UGM|A Chain A, Structure Of Tal Effector Pthxo1 Bound To Its Dna Target
Length = 1047
Score = 26.2 bits (56), Expect = 7.4, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 19/47 (40%), Gaps = 3/47 (6%)
Query: 37 GMHHHRILFDKYHPGFFGKVGMRYFH---KLRNKFHCPIVNIDKLWS 80
G H I+ HP G V + Y H L H IV + K WS
Sbjct: 85 GFTHAHIVALSQHPAALGTVAVTYQHIITALPEATHEDIVGVGKQWS 131
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
0.322 0.139 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,109,025
Number of Sequences: 62578
Number of extensions: 224440
Number of successful extensions: 481
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 441
Number of HSP's gapped (non-prelim): 20
length of query: 146
length of database: 14,973,337
effective HSP length: 90
effective length of query: 56
effective length of database: 9,341,317
effective search space: 523113752
effective search space used: 523113752
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)