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1Q9X
Asym. Unit
Info
Asym.Unit (1.4 MB)
Biol.Unit 1 (353 KB)
Biol.Unit 2 (350 KB)
Biol.Unit 3 (347 KB)
Biol.Unit 4 (350 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ENTEROBACTERIA PHAGE RB69 GP43 DNA POLYMERASE COMPLEXED WITH TETRAHYDROFURAN CONTAINING DNA
Authors
:
E. Freisinger, A. P. Grollman, H. Miller, C. Kisker
Date
:
26 Aug 03 (Deposition) - 27 Apr 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.69
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,E,I (1x)
Biol. Unit 2: B,F,J (1x)
Biol. Unit 3: C,G,K (1x)
Biol. Unit 4: D,H,L (1x)
Keywords
:
Protein-Dna Complex, Transferase, Replication-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Freisinger, A. P. Grollman, H. Miller, C. Kisker
Lesion (In)Tolerance Reveals Insights Into Dna Replication Fidelity.
Embo J. V. 23 1494 2004
[
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Hetero Components
(4, 22)
Info
All Hetero Components
1a: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRa)
1b: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRb)
1c: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRc)
1d: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRd)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
3a: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE (DGPa)
3b: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE (DGPb)
3c: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE (DGPc)
3d: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE (DGPd)
3e: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE (DGPe)
3f: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE (DGPf)
4a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
4b: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCb)
4c: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCc)
4d: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3DR
4
Ligand/Ion
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2
CA
8
Ligand/Ion
CALCIUM ION
3
DGP
6
Ligand/Ion
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
4
DOC
4
Mod. Residue
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
[
close Hetero Component info
]
Sites
(22, 22)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:623 , SER A:624
BINDING SITE FOR RESIDUE CA A 1001
02
AC2
SOFTWARE
ASP A:684 , HOH A:1112
BINDING SITE FOR RESIDUE CA A 1002
03
AC3
SOFTWARE
ASP B:684
BINDING SITE FOR RESIDUE CA B 1003
04
AC4
SOFTWARE
ASP B:623 , SER B:624
BINDING SITE FOR RESIDUE CA B 1004
05
AC5
SOFTWARE
ASP C:411 , ASP C:623 , HOH C:1093 , DGP G:908
BINDING SITE FOR RESIDUE CA C 1005
06
AC6
SOFTWARE
ASP C:684 , GLU C:716
BINDING SITE FOR RESIDUE CA C 1006
07
AC7
SOFTWARE
ASP D:411 , THR D:413 , ASP D:684 , HOH D:1091
BINDING SITE FOR RESIDUE CA D 1007
08
AC8
SOFTWARE
ASP D:411 , ASP D:623 , SER D:624
BINDING SITE FOR RESIDUE CA D 1008
09
AC9
SOFTWARE
LEU B:415 , TYR B:416 , TYR B:567 , ASP B:623 , HOH F:387 , DG F:913 , DOC J:953
BINDING SITE FOR RESIDUE DGP F 908
10
BC1
SOFTWARE
DGP G:908 , DOC K:953
BINDING SITE FOR RESIDUE DGP G 907
11
BC2
SOFTWARE
LEU C:415 , TYR C:416 , TYR C:567 , ASP C:623 , CA C:1005 , DGP G:907 , DG G:913 , DOC K:953
BINDING SITE FOR RESIDUE DGP G 908
12
BC3
SOFTWARE
LEU D:415 , TYR D:416 , TYR D:567 , ASP D:623 , DG H:913 , DOC L:953
BINDING SITE FOR RESIDUE DGP H 908
13
BC4
SOFTWARE
ARG B:59 , ASP B:95 , DG G:927 , DG G:928 , DG K:940
BINDING SITE FOR RESIDUE DGP K 955
14
BC5
SOFTWARE
SER A:36 , ARG A:59 , ASP A:95 , DG H:927 , DG H:928 , DG L:940
BINDING SITE FOR RESIDUE DGP L 955
15
BC6
SOFTWARE
SER A:360 , PRO A:361 , ILE A:362 , DC E:911 , DG E:913
BINDING SITE FOR RESIDUE 3DR E 912
16
BC7
SOFTWARE
SER B:360 , PRO B:361 , ILE B:362 , DC F:911 , DG F:913
BINDING SITE FOR RESIDUE 3DR F 912
17
BC8
SOFTWARE
SER C:360 , PRO C:361 , ILE C:362 , GLY C:568 , ASN C:572 , DC G:911 , DG G:913
BINDING SITE FOR RESIDUE 3DR G 912
18
BC9
SOFTWARE
SER D:360 , PRO D:361 , ILE D:362 , ASN D:572 , DC H:911 , DG H:913
BINDING SITE FOR RESIDUE 3DR H 912
19
CC1
SOFTWARE
ASP A:621 , THR A:622 , ASP A:623 , TYR A:708 , DG E:913 , DG E:914 , DC I:952
BINDING SITE FOR RESIDUE DOC I 953
20
CC2
SOFTWARE
ASP B:623 , TYR B:708 , MET B:728 , DGP F:908 , DG F:913 , DG F:914 , DC J:952
BINDING SITE FOR RESIDUE DOC J 953
21
CC3
SOFTWARE
ASP C:621 , ASP C:623 , TYR C:708 , MET C:728 , DGP G:907 , DGP G:908 , DG G:913 , DG G:914 , DC K:952
BINDING SITE FOR RESIDUE DOC K 953
22
CC4
SOFTWARE
ASP D:623 , TYR D:708 , MET D:728 , HOH D:1107 , DGP H:908 , DG H:913 , DG H:914 , HOH L:23 , DC L:952
BINDING SITE FOR RESIDUE DOC L 953
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_B (A:619-627,B:619-627,C:619-627,D:61...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_B
PS00116
DNA polymerase family B signature.
DPOL_BPR69
619-627
4
A:619-627
B:619-627
C:619-627
D:619-627
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1q9xa1 (A:1-375)
1b: SCOP_d1q9xb1 (B:1-375)
1c: SCOP_d1q9xc1 (C:1-375)
1d: SCOP_d1q9xd1 (D:1-375)
2a: SCOP_d1q9xa2 (A:376-903)
2b: SCOP_d1q9xb2 (B:376-903)
2c: SCOP_d1q9xc2 (C:376-903)
2d: SCOP_d1q9xd2 (D:376-903)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
DnaQ-like 3'-5' exonuclease
(253)
Protein domain
:
Exonuclease domain of family B DNA polymerases
(102)
Bacteriophage RB69 [TaxId: 12353]
(92)
1a
d1q9xa1
A:1-375
1b
d1q9xb1
B:1-375
1c
d1q9xc1
C:1-375
1d
d1q9xd1
D:1-375
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
DNA polymerase I
(233)
Protein domain
:
Family B DNA polymerase
(100)
Bacteriophage RB69 [TaxId: 12353]
(92)
2a
d1q9xa2
A:376-903
2b
d1q9xb2
B:376-903
2c
d1q9xc2
C:376-903
2d
d1q9xd2
D:376-903
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1q9xC02 (C:109-339)
1b: CATH_1q9xA02 (A:107-339)
1c: CATH_1q9xB02 (B:107-339)
1d: CATH_1q9xD02 (D:107-339)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
[unclassified]
(102)
1a
1q9xC02
C:109-339
1b
1q9xA02
A:107-339
1c
1q9xB02
B:107-339
1d
1q9xD02
D:107-339
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_DNA_pol_B_1q9xD01 (D:362-856)
1b: PFAM_DNA_pol_B_1q9xD02 (D:362-856)
1c: PFAM_DNA_pol_B_1q9xD03 (D:362-856)
1d: PFAM_DNA_pol_B_1q9xD04 (D:362-856)
2a: PFAM_DNA_pol_B_exo1_1q9xD05 (D:28-293)
2b: PFAM_DNA_pol_B_exo1_1q9xD06 (D:28-293)
2c: PFAM_DNA_pol_B_exo1_1q9xD07 (D:28-293)
2d: PFAM_DNA_pol_B_exo1_1q9xD08 (D:28-293)
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Clans
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)
(
)
Families
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(
)
Organisms
(
)
(
)
Clan
:
DNA_pol_B-like
(44)
Family
:
DNA_pol_B
(38)
Enterobacteria phage RB69 (Bacteriophage RB69)
(20)
1a
DNA_pol_B-1q9xD01
D:362-856
1b
DNA_pol_B-1q9xD02
D:362-856
1c
DNA_pol_B-1q9xD03
D:362-856
1d
DNA_pol_B-1q9xD04
D:362-856
Clan
:
RNase_H
(288)
Family
:
DNA_pol_B_exo1
(38)
Enterobacteria phage RB69 (Bacteriophage RB69)
(20)
2a
DNA_pol_B_exo1-1q9xD05
D:28-293
2b
DNA_pol_B_exo1-1q9xD06
D:28-293
2c
DNA_pol_B_exo1-1q9xD07
D:28-293
2d
DNA_pol_B_exo1-1q9xD08
D:28-293
[
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]
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (1.4 MB)
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Biol.Unit 1 (353 KB)
Header - Biol.Unit 1
Biol.Unit 2 (350 KB)
Header - Biol.Unit 2
Biol.Unit 3 (347 KB)
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