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3K5M
Asym. Unit
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Asym.Unit (154 KB)
Biol.Unit 1 (148 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF E.COLI POL II-ABASIC DNA-DDGTP LT(-2, 2) TERNARY COMPLEX
Authors
:
W. Yang, F. Wang
Date
:
07 Oct 09 (Deposition) - 02 Feb 10 (Release) - 02 Feb 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.04
Chains
:
Asym. Unit : A,P,T
Biol. Unit 1: A,P,T (1x)
Keywords
:
Dna Damage, Dna Repair, Dna-Binding, Dna-Directed Dna Polymerase, Nucleotidyltransferase, Sos Response, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Wang, W. Yang
Structural Insight Into Translesion Synthesis By Dna Pol Ii.
Cell(Cambridge, Mass. ) V. 139 1279 2009
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSP... (DG3a)
View:
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Label:
No.
Name
Count
Type
Full Name
1
3DR
1
Mod. Nucleotide
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2
CA
2
Ligand/Ion
CALCIUM ION
3
DG3
1
Ligand/Ion
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:419 , TYR A:420 , LYS A:421 , SER A:422 , LEU A:423 , ARG A:477 , LYS A:493 , ASN A:497 , TYR A:500 , ASP A:547 , HOH A:826 , HOH A:865 , HOH A:930 , HOH A:957 , CA A:1001 , CA A:1002 , HOH A:1115 , DG P:913 , DC T:802 , DC T:803
BINDING SITE FOR RESIDUE DG3 A 914
2
AC2
SOFTWARE
ASP A:419 , TYR A:420 , ASP A:547 , DG3 A:914
BINDING SITE FOR RESIDUE CA A 1001
3
AC3
SOFTWARE
ASP A:419 , ASP A:547 , DG3 A:914 , DG P:913
BINDING SITE FOR RESIDUE CA A 1002
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_DPO2_ECOLI_001 (G401D, chain A, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_DPO2_ECOLI_001
*
G
401
D
DPO2_ECOLI
---
---
A
G
401
D
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_B (A:543-551)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_B
PS00116
DNA polymerase family B signature.
DPO2_ECOLI
543-551
1
A:543-551
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3k5ma1 (A:-1-389)
2a: SCOP_d3k5ma2 (A:390-770)
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Protein Domains
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Organisms
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(
)
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
:
automated matches
(19)
Escherichia coli [TaxId: 562]
(13)
1a
d3k5ma1
A:-1-389
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
:
automated matches
(26)
Escherichia coli [TaxId: 562]
(3)
2a
d3k5ma2
A:390-770
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_DNA_pol_B_3k5mA01 (A:444-770)
1b: PFAM_DNA_pol_B_3k5mA02 (A:444-770)
2a: PFAM_DNA_pol_B_exo1_3k5mA03 (A:49-296)
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)
Organisms
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)
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)
Clan
:
DNA_pol_B-like
(44)
Family
:
DNA_pol_B
(38)
Escherichia coli (strain K12)
(9)
1a
DNA_pol_B-3k5mA01
A:444-770
1b
DNA_pol_B-3k5mA02
A:444-770
Clan
:
RNase_H
(288)
Family
:
DNA_pol_B_exo1
(38)
Escherichia coli (strain K12)
(9)
2a
DNA_pol_B_exo1-3k5mA03
A:49-296
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Asym.Unit (154 KB)
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