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1T3N
Asym. Unit
Info
Asym.Unit (279 KB)
Biol.Unit 1 (137 KB)
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Models
(2 )
Title
:
STRUCTURE OF THE CATALYTIC CORE OF DNA POLYMERASE IOTA IN COMPLEX WITH DNA AND DTTP
Authors
:
D. T. Nair, R. E. Johnson, S. Prakash, L. Prakash, A. K. Aggarwal
Date
:
27 Apr 04 (Deposition) - 20 Jul 04 (Release) - 09 Sep 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,P,T (2 x)
Biol. Unit 1: A,B,P,T (1x)
Keywords
:
Protein, Dna, Dttp, Replication-Dna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
D. T. Nair, R. E. Johnson, S. Prakash, L. Prakash, A. K. Aggarwal
Replication By Human Dna Polymerase-Iota Occurs By Hoogstee Base-Pairing.
Nature V. 430 377 2004
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
2a: MAGNESIUM ION (MGa)
3a: THYMIDINE-5'-TRIPHOSPHATE (TTPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
2
MG
1
Ligand/Ion
MAGNESIUM ION
3
TTP
1
Ligand/Ion
THYMIDINE-5'-TRIPHOSPHATE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP B:454 , LEU B:455 , ASP B:546
BINDING SITE FOR RESIDUE MG B 869
2
AC2
SOFTWARE
ASP B:454 , LEU B:455 , ASP B:456 , CYS B:457 , PHE B:458 , TYR B:459 , VAL B:484 , THR B:485 , TYR B:488 , ARG B:491 , LEU B:498 , ASP B:546 , LYS B:634 , DOC P:13 , DA T:5 , DG T:6
BINDING SITE FOR RESIDUE TTP B 868
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SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
1: VAR_021239 (R491G, chain A/B, )
2: VAR_021240 (I656M, chain A/B, )
3: VAR_021241 (E671K, chain A/B, )
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
B
R
71
491
G
2
UniProt
VAR_021240
I
261
M
POLI_HUMAN
Polymorphism
3218784
A
B
I
236
656
M
3
UniProt
VAR_021241
E
276
K
POLI_HUMAN
Polymorphism
3218783
A
B
E
251
671
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: UMUC (A:30-243,B:450-663)
;
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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
2
A:30-243
B:450-663
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1t3na1 (A:300-414)
1b: SCOP_d1t3nb1 (B:720-834)
2a: SCOP_d1t3na2 (A:27-299)
2b: SCOP_d1t3nb2 (B:447-719)
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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
d1t3na1
A:300-414
1b
d1t3nb1
B:720-834
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
d1t3na2
A:27-299
2b
d1t3nb2
B:447-719
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1t3nA01 (A:27-36,A:99-221)
1b: CATH_1t3nB01 (B:447-456,B:519-641)
2a: CATH_1t3nA04 (A:299-414)
2b: CATH_1t3nB04 (B:719-834)
3a: CATH_1t3nA03 (A:222-298)
3b: CATH_1t3nB03 (B:642-718)
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Homologous Superfamilies
(
)
(
)
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)
[unclassified]
(58)
1a
1t3nA01
A:27-36,A:99-221
1b
1t3nB01
B:447-456,B:519-641
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
[code=3.30.1490.100, no name defined]
(80)
[unclassified]
(29)
2a
1t3nA04
A:299-414
2b
1t3nB04
B:719-834
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
[unclassified]
(230)
3a
1t3nA03
A:222-298
3b
1t3nB03
B:642-718
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_IMS_1t3nB01 (B:453-631)
1b: PFAM_IMS_1t3nB02 (B:453-631)
2a: PFAM_IMS_C_1t3nB03 (B:687-822)
2b: PFAM_IMS_C_1t3nB04 (B:687-822)
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Clan
:
no clan defined [family: IMS]
(76)
Family
:
IMS
(76)
Homo sapiens (Human)
(14)
1a
IMS-1t3nB01
B:453-631
1b
IMS-1t3nB02
B:453-631
Clan
:
no clan defined [family: IMS_C]
(74)
Family
:
IMS_C
(74)
Homo sapiens (Human)
(14)
2a
IMS_C-1t3nB03
B:687-822
2b
IMS_C-1t3nB04
B:687-822
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Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (279 KB)
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