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= 027767
(219 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3C7T|A Chain A, Crystal Structure Of The Ecdysone Phosphate Phosphatase,
Eppase, From Bombix Mori In Complex With Tungstate
pdb|3C7T|B Chain B, Crystal Structure Of The Ecdysone Phosphate Phosphatase,
Eppase, From Bombix Mori In Complex With Tungstate
pdb|3C7T|C Chain C, Crystal Structure Of The Ecdysone Phosphate Phosphatase,
Eppase, From Bombix Mori In Complex With Tungstate
pdb|3C7T|D Chain D, Crystal Structure Of The Ecdysone Phosphate Phosphatase,
Eppase, From Bombix Mori In Complex With Tungstate
Length = 263
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 40/91 (43%), Gaps = 6/91 (6%)
Query: 17 DAHLSPLGWQQVGNLRKRVEASGLTQKIDLVITSPLLRTLQTAVGVFGGDGESQTDGIDA 76
D L+ LGW Q + + + +G++ I V SP LR ++TA G G + I
Sbjct: 57 DTPLTRLGWFQAQLVGEGMRMAGVS--IKHVYASPALRCVETAQGFLDGLRADPSVKIKV 114
Query: 77 HPSLTATATVNCPPII----AVELCRERLGV 103
P L + P I +ELC+ L V
Sbjct: 115 EPGLFEFKNWHMPKGIDFMTPIELCKAGLNV 145
>pdb|3RCY|A Chain A, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING ENZYME- Like Protein From Roseovarius Sp.
Tm1035
pdb|3RCY|B Chain B, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING ENZYME- Like Protein From Roseovarius Sp.
Tm1035
pdb|3RCY|C Chain C, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING ENZYME- Like Protein From Roseovarius Sp.
Tm1035
pdb|3RCY|D Chain D, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING ENZYME- Like Protein From Roseovarius Sp.
Tm1035
pdb|3RCY|E Chain E, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING ENZYME- Like Protein From Roseovarius Sp.
Tm1035
pdb|3RCY|F Chain F, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING ENZYME- Like Protein From Roseovarius Sp.
Tm1035
pdb|3RCY|G Chain G, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING ENZYME- Like Protein From Roseovarius Sp.
Tm1035
pdb|3RCY|H Chain H, Crystal Structure Of Mandelate RacemaseMUCONATE
LACTONIZING ENZYME- Like Protein From Roseovarius Sp.
Tm1035
Length = 433
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 13/62 (20%)
Query: 6 GPEALLS--QEFFDAHLSPLGWQQVGNLRKRVEASGLTQKIDLVITSPLLRTLQTAVGVF 63
GPEA+ + ++ F H+ + + + +RV +SG TQ+ DL TA+G F
Sbjct: 47 GPEAMRAVIEDVFARHMEGENPENIELMFRRVYSSGFTQRPDL-----------TAIGAF 95
Query: 64 GG 65
G
Sbjct: 96 SG 97
>pdb|2L82|A Chain A, Solution Nmr Structure Of De Novo Designed Protein, P-Loop
Ntpase Fold, Northeast Structural Genomics Consortium
Target Or32
Length = 162
Score = 27.7 bits (60), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 107 DKRRSISEYHSLFPAIDFKLIESEDDKLWKADAREPFEEVTARGME 152
D R +I E +P +D +I + DDK W D EE RG+E
Sbjct: 63 DFRENIREIWERYPQLDVVVIVTTDDKEWIKDF---IEEAKERGVE 105
>pdb|3F2I|A Chain A, Crystal Structure Of The Alr0221 Protein From Nostoc,
Northeast Structural Genomics Consortium Target Nsr422.
pdb|3F2I|B Chain B, Crystal Structure Of The Alr0221 Protein From Nostoc,
Northeast Structural Genomics Consortium Target Nsr422.
pdb|3F2I|C Chain C, Crystal Structure Of The Alr0221 Protein From Nostoc,
Northeast Structural Genomics Consortium Target Nsr422.
pdb|3F2I|D Chain D, Crystal Structure Of The Alr0221 Protein From Nostoc,
Northeast Structural Genomics Consortium Target Nsr422.
pdb|3F2I|E Chain E, Crystal Structure Of The Alr0221 Protein From Nostoc,
Northeast Structural Genomics Consortium Target Nsr422.
pdb|3F2I|F Chain F, Crystal Structure Of The Alr0221 Protein From Nostoc,
Northeast Structural Genomics Consortium Target Nsr422
Length = 172
Score = 27.3 bits (59), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 40 LTQKIDLVITSPLLRTLQTA 59
L ++ DL++TSPL+R QTA
Sbjct: 43 LGRQFDLIVTSPLIRARQTA 62
>pdb|2KE5|A Chain A, Solution Structure And Dynamics Of The Small Gtpase Ralb
In Its Active Conformation: Significance For Effector
Protein Binding
Length = 174
Score = 27.3 bits (59), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 1/83 (1%)
Query: 3 GNNGPEALLSQEFFDAHLSPLGWQQVGNLRKRVEASGLTQKIDLVITSPLLRTLQTAVGV 62
G G AL Q +D + + + RK+V G +ID++ T+ L
Sbjct: 12 GGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTAGLEDYAAIRDNY 71
Query: 63 F-GGDGESQTDGIDAHPSLTATA 84
F G+G I H S TATA
Sbjct: 72 FRSGEGFLLVFSITEHESFTATA 94
>pdb|2KWI|A Chain A, Ralb-Rlip76 (Ralbp1) Complex
Length = 178
Score = 26.9 bits (58), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 1/83 (1%)
Query: 3 GNNGPEALLSQEFFDAHLSPLGWQQVGNLRKRVEASGLTQKIDLVITSPLLRTLQTAVGV 62
G G AL Q +D + + + RK+V G +ID++ T+ L
Sbjct: 16 GGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTAGLEDYAAIRDNY 75
Query: 63 F-GGDGESQTDGIDAHPSLTATA 84
F G+G I H S TATA
Sbjct: 76 FRSGEGFLLVFSITEHESFTATA 98
>pdb|4F5N|A Chain A, Open Ternary Complex Of R283k Dna Polymerase Beta With A
Metal Free Dctp Analog
pdb|4F5O|A Chain A, Open Ternary Complex Of R283k Dna Polymerase Beta With A
One Metal Bound Dctp Analog
pdb|4F5P|A Chain A, Open Ternary Mismatch Complex Of R283k Dna Polymerase Beta
With A Datp Analog
pdb|4F5Q|A Chain A, Closed Ternary Complex Of R283k Dna Polymerase Beta
pdb|4F5R|A Chain A, Open And Closed Ternary Complex Of R283k Dna Polymerase
Beta With A Dctp Analog In The Same Asymmetric Unit
pdb|4F5R|B Chain B, Open And Closed Ternary Complex Of R283k Dna Polymerase
Beta With A Dctp Analog In The Same Asymmetric Unit
pdb|4GXI|A Chain A, R283k Dna Polymerase Beta Binary Complex With A Templating
8og
pdb|4GXJ|A Chain A, R283k Dna Polymerase Beta Ternary Complex With A
Templating 8og And Incoming Dctp Analog
pdb|4GXK|A Chain A, R283k Dna Polymerase Beta Ternary Complex With A
Templating 8og And Incoming Datp Analog
Length = 335
Score = 26.9 bits (58), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 19 HLSPLGWQQVGNLRKRVEASGLTQKIDLVITSPLL---RTLQTAVGVF--GGDGESQTDG 73
H +G + G+ KR+ + Q D+V+ + T G F G + D
Sbjct: 134 HHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDV 193
Query: 74 IDAHPSLTATAT 85
+ HPS T+ +T
Sbjct: 194 LLTHPSFTSEST 205
>pdb|9ICG|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|9ICH|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dgtp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|9ICI|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|9ICJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna
pdb|9ICK|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Artificial Mother Liquor
pdb|9ICL|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Pyrophosphate And Mncl2
pdb|9ICM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Double Stranded Dna (No 5'-Phosphate)
pdb|9ICN|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2',3'-
Dideoxycytidine-5'-Triphosphate, Soaked In The Presence
Of Ddctp And Mgcl2
pdb|9ICO|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Dttp And Mgcl2
pdb|9ICP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of
Pyrophosphate (1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|9ICQ|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Datp (1
Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICR|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxycytidine-5'-Triphosphate, Soaked In The Presence Of
Dctp And Mncl2
pdb|9ICS|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2',3'-
Dideoxycytidine-5'-Triphosphate, Soaked In The Presence
Of Ddctp And Mncl2
pdb|9ICT|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxyguanosine-5'-Triphosphate, Soaked In The Presence
Of Dgtp And Mncl2
pdb|9ICU|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Dttp (1
Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICV|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex + 2'-
Deoxyadenosine-5'-triphosphate, Soaked In The Presence
Of Datp And Zncl2
pdb|9ICW|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Native Structure
pdb|9ICX|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Six Base Pairs Of Dna (non Gapped Dna Only)
pdb|9ICY|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7) Complexed With Seven
Base Pairs Of Dna (Non Gapped Dna Only)
pdb|8ICB|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of
Artificial Mother Liquor
pdb|8ICC|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna (no 5'-phosphate)
pdb|8ICE|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cdcl2 (1 Millimolar)
pdb|8ICF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(10 Millimolar) And Mgcl2 (50 Millimolar)
pdb|8ICG|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|8ICH|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|8ICI|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dgtp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|8ICJ|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + THYMIDINE-
5'-Triphosphate, Soaked In The Presence Of Dttp And
Mgcl2
pdb|8ICK|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar), Mgcl2 (5 Millimolar), And Mncl2 (5
Millimolar)
pdb|8ICL|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Nicl2 (5 Millimolar)
pdb|8ICM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar), Mncl2 (5 Millimolar), And Ammonium
Sulfate (75 Millimolar)
pdb|8ICN|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Atp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICO|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of
Azt-Tp (1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICQ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Of
Datp (0.1 Millimolar) And Mncl2 (0.5 Millimolar)
pdb|8ICR|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICS|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICT|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICU|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Ddatp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICV|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dgtp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICW|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICX|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICY|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + THYMIDINE-
5'-Triphosphate, Soaked In The Presence Of Dttp And
Mncl2
pdb|8ICZ|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Of
Datp (1 Millimolar), Mncl2 (5 Millimolar), And Lithium
Sulfate (75 Millimolar)
pdb|9ICA|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked In The
Presence Of Datp(Alpha)s And Mncl2
pdb|9ICB|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxyadenosine-5'-Triphosphate, Soaked In The Presence
Of Datp And Cocl2
pdb|9ICC|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex + 2'-
Deoxyadenosine-5'-triphosphate, Soaked In The Presence
Of Datp And Crcl3
pdb|9ICE|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cucl2 (0.1 Millimolar)
pdb|9ICF|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxyadenosine-5'-Triphosphate, Soaked In The Presence
Of Datp And Zncl2
pdb|1ZQQ|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(15 Millimolar) And Nacl (15 Millimolar)
pdb|1ZQR|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Nicl2
pdb|1ZQS|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Tlcl
(0.5 Millimolar)
pdb|1ZQT|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(0.01 Millimolar) And Zncl2 (0.02 Millimolar)
pdb|7ICE|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Cacl2
pdb|7ICF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cdcl2
(0.1 Millimolar) (Four-Day Soak)
pdb|7ICG|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex, Soaked In
The Presence Of Cdcl2
pdb|7ICH|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Cocl2
pdb|7ICI|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Crcl3
(0.1 Millimolar)
pdb|7ICJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cucl2
(0.1 Millimolar)
pdb|7ICK|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Mgcl2
pdb|7ICL|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(0.1 Millimolar)
pdb|7ICM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(1.0 Millimolar)
pdb|7ICN|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex, Soaked In
The Presence Of Nicl2
pdb|7ICO|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Zncl2
pdb|7ICP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Zncl2
(0.01 Millimolar)
pdb|7ICQ|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Zncl2
pdb|7ICR|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex, Soaked In
The Presence Of Zncl2
pdb|7ICS|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Zncl2
pdb|7ICT|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Zncl2 And Mgcl2
pdb|7ICU|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cdcl2
(0.1 Millimolar)
pdb|7ICV|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(0.1 Millimolar) And In The Absence Of Nacl
pdb|8ICA|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cacl2 (5 Millimolar)
pdb|1ZQA|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(150 Millimolar) At Ph 7.5
pdb|1ZQB|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Bacl2
(150 Millimolar)
pdb|1ZQC|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(15 Millimolar)
pdb|1ZQD|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(150 Millimolar)
pdb|1ZQE|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Crcl3
(saturated Solution)
pdb|1ZQF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cscl
(150 Millimolar)
pdb|1ZQG|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of A
Sodium-Free Artificial Mother Liquor At Ph 6.5
pdb|1ZQH|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of A
Sodium-Free Artificial Mother Liquor At Ph 7.5
pdb|1ZQI|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(150 Millimolar)
pdb|1ZQJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(15 Millimolar) And Mgcl2 (15 Millimolar)
pdb|1ZQK|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(75 Millimolar) And Mgcl2 (75 Millimolar)
pdb|1ZQL|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(15 Millimolar) And Mgcl2 (15 Millimolar)
pdb|1ZQM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(15 Millimolar)
pdb|1ZQN|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Bacl2
(15 Millimolar) And Nacl (15 Millimolar)
pdb|1ZQO|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(15 Millimolar) And Nacl (15 Millimolar)
pdb|1ZQP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(75 Millimolar) And Nacl (75 Millimolar)
pdb|1BPX|A Chain A, Dna Polymerase BetaDNA COMPLEX
pdb|1BPY|A Chain A, Human Dna Polymerase Beta Complexed With Gapped Dna And
Ddctp
pdb|1BPZ|A Chain A, Human Dna Polymerase Beta Complexed With Nicked Dna
pdb|1MQ2|A Chain A, Human Dna Polymerase Beta Complexed With Gapped Dna
Containing An 8-Oxo-7,8-Dihydro-Guanine And Damp
pdb|1MQ3|A Chain A, Human Dna Polymerase Beta Complexed With Gapped Dna
Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired
With Dctp
pdb|1TV9|A Chain A, Human Dna Polymerase Beta Complexed With Nicked Dna
Containing A Mismatched Template Adenine And Incoming
Cytidine
pdb|1TVA|A Chain A, Human Dna Polymerase Beta Complexed With Nicked Dna
Containing A Mismatched Template Thymidine And Incoming
Cytidine
pdb|1ZJM|A Chain A, Human Dna Polymerase Beta Complexed With Dna Containing An
A-A Mismatched Primer Terminus
pdb|1ZJN|A Chain A, Human Dna Polymerase Beta Complexed With Dna Containing An
A-A Mismatched Primer Terminus With Dgtp
pdb|2FMP|A Chain A, Dna Polymerase Beta With A Terminated Gapped Dna Substrate
And Ddctp With Sodium In The Catalytic Site
pdb|2FMQ|A Chain A, Sodium In Active Site Of Dna Polymerase Beta
pdb|2FMS|A Chain A, Dna Polymerase Beta With A Gapped Dna Substrate And
Dumpnpp With Magnesium In The Catalytic Site
pdb|2I9G|A Chain A, Dna Polymerase Beta With A Benzo[c]phenanthrene Diol
Epoxide Adducted Guanine Base
pdb|2ISO|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta, Gamma-
Difluoromethylene Triphosphate
pdb|2ISP|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta, Gamma-
Methylene Triphosphate
pdb|2P66|A Chain A, Human Dna Polymerase Beta Complexed With Tetrahydrofuran
(abasic Site) Containing Dna
pdb|2PXI|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta, Gamma-
Monofluoromethylene Triphosphate
pdb|3C2K|A Chain A, Dna Polymerase Beta With A Gapped Dna Substrate And
Dumpnpp With Manganese In The Active Site
pdb|3C2L|A Chain A, Ternary Complex Of Dna Polymerase Beta With A C:dapcpp
Mismatch In The Active Site
pdb|3C2M|A Chain A, Ternary Complex Of Dna Polymerase Beta With A G:dapcpp
Mismatch In The Active Site
pdb|3ISB|A Chain A, Binary Complex Of Human Dna Polymerase Beta With A Gapped
Dna
pdb|3ISC|A Chain A, Binary Complex Of Human Dna Polymerase Beta With An Abasic
Site (Thf) In The Gapped Dna
pdb|3ISD|A Chain A, Ternary Complex Of Human Dna Polymerase Beta With An
Abasic Site (Thf): Dapcpp Mismatch
pdb|3JPN|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Dichloro Methyl Triphosphate
pdb|3JPO|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monochloromethy Triphosphate
pdb|3JPP|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monomethyl Meth Triphosphate
pdb|3JPQ|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monobromo Methy Triphosphate
pdb|3JPR|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Dimethyl Methyl Triphosphate
pdb|3JPS|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Fluoro Methyl M Triphosphate
pdb|3JPT|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Fluoro Chloro M Triphosphate
pdb|3MBY|A Chain A, Ternary Complex Of Dna Polymerase Beta With Template Base
A And 8oxodgtp In The Active Site With A Dideoxy
Terminated Primer
pdb|3LK9|A Chain A, Dna Polymerase Beta With A Gapped Dna Substrate And
Dtmp(Cf2)p(Cf2)p
pdb|3RH4|A Chain A, Dna Polymerase Beta With A Dideoxy-Terminated Primer With
An Incoming Ribonucleotide (Rctp)
pdb|3RJE|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing 8odg At Template Position
pdb|3RJF|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing (Syn)8odg At Template Position Paired With
Non-Hydrolyzable Datp Analog (Dapcpp)
pdb|3RJG|A Chain A, Binary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing 8odg:da Base-Pair At Primer Terminus
pdb|3RJH|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing (Syn)8odg:da At Primer Terminus And
Dg:dcmp(Cf2)ppin The Active Site
pdb|3RJI|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing 8odg At Template Position Paired With
Non-Hydrolyzable Dctp Analog (Dcmp(Cf2)pp)
pdb|3RJJ|A Chain A, Ternary Complex Crystal Structure Of Dna Polymerase Beta
With Template 8odg Provides Insight Into Mutagenic
Lesion Bypass
pdb|3RJK|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing 8odg:dc Base Pair At Primer Terminus And
Dg:dcmp(Cf2)pp In The Active Site
pdb|3TFR|A Chain A, Ternary Complex Structure Of Dna Polymerase Beta With A
Gapped Dna Substrate And A, B Damp(Cf2)pp In The Active
Site
pdb|3TFS|A Chain A, Ternary Complex Structure Of Dna Polymerase Beta With A
Gapped Dna Substrate And A, B Damp(Cfh)pp In The Active
Site: Stereoselective Binding Of (S) Isomer
pdb|4DO9|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monofluoromethylene Triphosphate: Stereoselective
Binding Of R-Isomer
pdb|4DOA|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monofluoromethylene Triphosphate: Non-Interactive
Binding Of S-Isomer
pdb|4DOB|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monochlororomethylene Triphosphate:
Stereoselective Binding Of R-Isomer
pdb|4DOC|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monochlororomethylene Triphosphate:binding Of
S-Isomer
Length = 335
Score = 26.9 bits (58), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 19 HLSPLGWQQVGNLRKRVEASGLTQKIDLVITSPLL---RTLQTAVGVF--GGDGESQTDG 73
H +G + G+ KR+ + Q D+V+ + T G F G + D
Sbjct: 134 HHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDV 193
Query: 74 IDAHPSLTATAT 85
+ HPS T+ +T
Sbjct: 194 LLTHPSFTSEST 205
>pdb|3GDX|A Chain A, Dna Polymerase Beta With A Gapped Dnd Substrate And
Dtmp(Cf2)pp
Length = 326
Score = 26.9 bits (58), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 19 HLSPLGWQQVGNLRKRVEASGLTQKIDLVITSPLL---RTLQTAVGVF--GGDGESQTDG 73
H +G + G+ KR+ + Q D+V+ + T G F G + D
Sbjct: 125 HHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDV 184
Query: 74 IDAHPSLTATAT 85
+ HPS T+ +T
Sbjct: 185 LLTHPSFTSEST 196
>pdb|3RH5|A Chain A, Dna Polymerase Beta Mutant (Y271) With A
Dideoxy-Terminated Primer With An Incoming
Deoxynucleotide (Dctp)
pdb|3RH6|A Chain A, Dna Polymerase Beta Mutant (Y271) With A
Dideoxy-Terminated Primer With An Incoming
Ribonucleotide (Rctp)
Length = 335
Score = 26.9 bits (58), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 19 HLSPLGWQQVGNLRKRVEASGLTQKIDLVITSPLL---RTLQTAVGVF--GGDGESQTDG 73
H +G + G+ KR+ + Q D+V+ + T G F G + D
Sbjct: 134 HHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDV 193
Query: 74 IDAHPSLTATAT 85
+ HPS T+ +T
Sbjct: 194 LLTHPSFTSEST 205
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
0.317 0.133 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,829,155
Number of Sequences: 62578
Number of extensions: 214888
Number of successful extensions: 512
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 510
Number of HSP's gapped (non-prelim): 12
length of query: 219
length of database: 14,973,337
effective HSP length: 95
effective length of query: 124
effective length of database: 9,028,427
effective search space: 1119524948
effective search space used: 1119524948
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)