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3G6X
Asym. Unit
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Asym.Unit (79 KB)
Biol.Unit 1 (70 KB)
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(1)
Title
:
TERNARY COMPLEX OF DNA POLYMERASE IOTA:DNA:DGTP WITH AN ABASIC SITE AT THE TEMPLATING POSITION
Authors
:
D. T. Nair, A. K. Aggarwal
Date
:
09 Feb 09 (Deposition) - 12 May 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.08
Chains
:
Asym. Unit : A,P,T
Biol. Unit 1: A,P,T (1x)
Keywords
:
Dna Polymerase, Y-Family, Lesion Bypass, Abasic Site, Ternary Complex, Dna Damage, Dna Repair, Dna Replication, Dna Synthesis, Dna-Binding, Dna-Directed Dna Polymerase, Magnesium, Metal-Binding, Mutator Protein, Nucleotidyltransferase, Nucleus, Schiff Base, Transferase, Replication-Dna Complex
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Reference
:
D. T. Nair, R. E. Johnson, L. Prakash, S. Prakash, A. K. Aggarwal
Dna Synthesis Across An Abasic Lesion By Human Dna Polymerase Iota.
Structure V. 17 530 2009
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Hetero Components
(4, 5)
Info
All Hetero Components
1a: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRa)
2a: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTa)
3a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3DR
1
Mod. Nucleotide
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2
DGT
1
Ligand/Ion
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
3
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4
MG
2
Ligand/Ion
MAGNESIUM ION
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:34 , LEU A:35 , ASP A:36 , CYS A:37 , PHE A:38 , TYR A:39 , GLN A:59 , THR A:65 , TYR A:68 , ARG A:71 , LYS A:77 , ASP A:126 , LYS A:214 , HOH A:429 , HOH A:478 , MG A:871 , MG A:872 , DOC P:873 , 3DR T:840 , DG T:841
BINDING SITE FOR RESIDUE DGT A 875
2
AC2
SOFTWARE
ASP A:34 , LEU A:35 , ASP A:126 , DGT A:875
BINDING SITE FOR RESIDUE MG A 871
3
AC3
SOFTWARE
ASP A:34 , GLU A:127 , HOH A:478 , DGT A:875 , DOC P:873
BINDING SITE FOR RESIDUE MG A 872
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SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_021239 (R71G, chain A, )
2: VAR_021240 (I236M, chain A, )
3: VAR_021241 (E251K, chain A, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_021239
R
96
G
POLI_HUMAN
Polymorphism
3218778
A
R
71
G
2
UniProt
VAR_021240
I
261
M
POLI_HUMAN
Polymorphism
3218784
A
I
236
M
3
UniProt
VAR_021241
E
276
K
POLI_HUMAN
Polymorphism
3218783
A
E
251
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: UMUC (A:30-243)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UMUC
PS50173
UmuC domain profile.
POLI_HUMAN
55-268
1
A:30-243
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Exons
(0, 0)
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All Exons
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Note:
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_d3g6xa2 (A:300-414)
2a: SCOP_d3g6xa1 (A:25-299)
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Classes
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Folds
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Families
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(103)
Superfamily
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(103)
Family
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(62)
Protein domain
:
DNA polymerase iota
(19)
Human (Homo sapiens) [TaxId: 9606]
(19)
1a
d3g6xa2
A:300-414
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
Lesion bypass DNA polymerase (Y-family), catalytic domain
(104)
Protein domain
:
DNA polymerase iota
(19)
Human (Homo sapiens) [TaxId: 9606]
(19)
2a
d3g6xa1
A:25-299
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_3g6xA01 (A:25-36,A:99-221)
2a: CATH_3g6xA04 (A:299-414)
3a: CATH_3g6xA03 (A:222-298)
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)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.270, no name defined]
(278)
Human (Homo sapiens)
(12)
1a
3g6xA01
A:25-36,A:99-221
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
[code=3.30.1490.100, no name defined]
(80)
Human (Homo sapiens)
(12)
2a
3g6xA04
A:299-414
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
Human (Homo sapiens)
(34)
3a
3g6xA03
A:222-298
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Pfam Domains
(0, 0)
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all PFAM domains
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Asymmetric Unit 1
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