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3C5G
Biol. Unit 2
Info
Asym.Unit (148 KB)
Biol.Unit 1 (72 KB)
Biol.Unit 2 (74 KB)
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(1)
Title
:
STRUCTURE OF A TERNARY COMPLEX OF THE R517K POL LAMBDA MUTANT
Authors
:
M. Garcia-Diaz, K. Bebenek, M. C. Foley, L. C. Pedersen, T. Schlick, T. A. Kunkel
Date
:
31 Jan 08 (Deposition) - 29 Jul 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,D,E,P,Q,T,U
Biol. Unit 1: A,D,P,T (1x)
Biol. Unit 2: B,E,Q,U (1x)
Keywords
:
Helix-Hairpin-Helix, Dna Damage, Dna Repair, Dna Replication, Dna Synthesis, Dna-Binding, Dna-Directed Dna Polymerase, Lyase, Manganese, Metal-Binding, Nucleotidyltransferase, Nucleus, Phosphoprotein, Polymorphism, Transferase, Transferase/Dna, Lyase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Bebenek, M. Garcia-Diaz, M. C. Foley, L. C. Pedersen, T. Schlick, T. A. Kunkel
Substrate-Induced Dna Strand Misalignment During Catalytic Cycling By Dna Polymerase Lambda.
Embo Rep. V. 9 459 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE (2DTa)
1b: 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE (2DTb)
2a: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOS... (D3Ta)
2b: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOS... (D3Tb)
3a: 1,2-ETHANEDIOL (EDOa)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
5d: SODIUM ION (NAd)
5e: SODIUM ION (NAe)
5f: SODIUM ION (NAf)
5g: SODIUM ION (NAg)
5h: SODIUM ION (NAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2DT
1
Mod. Nucleotide
3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2
D3T
1
Ligand/Ion
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
3
EDO
-1
Ligand/Ion
1,2-ETHANEDIOL
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
NA
-1
Ligand/Ion
SODIUM ION
[
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Sites
(7, 7)
Info
All Sites
1: AC4 (SOFTWARE)
2: AC7 (SOFTWARE)
3: AC8 (SOFTWARE)
4: AC9 (SOFTWARE)
5: BC1 (SOFTWARE)
6: BC2 (SOFTWARE)
7: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
CYS A:300 , ILE A:302 , PRO A:303 , ILE A:305 , HOH B:953 , DC D:3
BINDING SITE FOR RESIDUE NA A 805
2
AC7
SOFTWARE
ARG B:386 , GLY B:416 , SER B:417 , ARG B:420 , GLY B:426 , ASP B:427 , ASP B:429 , TYR B:505 , PHE B:506 , GLY B:508 , ALA B:510 , ASN B:513 , MG B:601 , NA B:802 , HOH B:840 , HOH B:984 , HOH B:1008 , HOH B:1067 , HOH B:1098 , 2DT Q:6 , HOH Q:16 , DA U:5
BINDING SITE FOR RESIDUE D3T B 577
3
AC8
SOFTWARE
ASP B:427 , ASP B:429 , D3T B:577 , NA B:802 , HOH B:1067
BINDING SITE FOR RESIDUE MG B 601
4
AC9
SOFTWARE
SER B:339 , ILE B:341 , ALA B:344 , DA Q:5 , HOH Q:7 , HOH Q:12
BINDING SITE FOR RESIDUE NA B 801
5
BC1
SOFTWARE
ASP B:427 , ASP B:429 , ASP B:490 , D3T B:577 , MG B:601 , HOH Q:16
BINDING SITE FOR RESIDUE NA B 802
6
BC2
SOFTWARE
LYS A:307 , CYS B:300 , ILE B:302 , ILE B:305 , DC E:3
BINDING SITE FOR RESIDUE NA B 806
7
BC4
SOFTWARE
GLU B:396 , GLN B:400 , CYS B:412 , HOH B:947 , HOH B:949 , HOH B:1076
BINDING SITE FOR RESIDUE NA B 808
[
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_020269 (R438W, chain B, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020269
R
438
W
DPOLL_HUMAN
Polymorphism
3730477
B
R
438
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_X (B:416-435)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_X
PS00522
DNA polymerase family X signature.
DPOLL_HUMAN
416-435
1
-
B:416-435
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d3c5ga1 (A:249-328)
1b: SCOP_d3c5gb1 (B:245-328)
2a: SCOP_d3c5ga2 (A:329-385)
2b: SCOP_d3c5gb2 (B:329-385)
3a: SCOP_d3c5ga3 (A:386-575)
3b: SCOP_d3c5gb3 (B:386-575)
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Classes
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)
(
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Folds
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)
(
)
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
SAM domain-like
(639)
Superfamily
:
DNA polymerase beta, N-terminal domain-like
(205)
Family
:
DNA polymerase beta, N-terminal domain-like
(183)
Protein domain
:
DNA polymerase lambda
(24)
Human (Homo sapiens) [TaxId: 9606]
(24)
1a
d3c5ga1
A:249-328
1b
d3c5gb1
B:245-328
Superfamily
:
PsbU/PolX domain-like
(218)
Family
:
DNA polymerase beta-like, second domain
(190)
Protein domain
:
DNA polymerase lambda
(23)
Human (Homo sapiens) [TaxId: 9606]
(23)
2a
d3c5ga2
A:329-385
2b
d3c5gb2
B:329-385
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Nucleotidyltransferase
(287)
Superfamily
:
Nucleotidyltransferase
(287)
Family
:
DNA polymerase beta-like
(218)
Protein domain
:
DNA polymerase lambda
(23)
Human (Homo sapiens) [TaxId: 9606]
(23)
3a
d3c5ga3
A:386-575
3b
d3c5gb3
B:386-575
[
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]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_3c5gA03 (A:386-508)
1b: CATH_3c5gB03 (B:386-508)
2a: CATH_3c5gA04 (A:509-575)
2b: CATH_3c5gB04 (B:509-575)
3a: CATH_3c5gA01 (A:249-331)
3b: CATH_3c5gB01 (B:245-331)
4a: CATH_3c5gA02 (A:332-385)
4b: CATH_3c5gB02 (B:332-385)
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(
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Beta Polymerase; domain 2
(187)
Homologous Superfamily
:
Beta Polymerase, domain 2
(183)
Human (Homo sapiens)
(22)
1a
3c5gA03
A:386-508
1b
3c5gB03
B:386-508
Topology
:
Beta Polymerase; domain 3
(161)
Homologous Superfamily
:
Beta Polymerase, domain 3
(161)
Human (Homo sapiens)
(21)
2a
3c5gA04
A:509-575
2b
3c5gB04
B:509-575
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.110, no name defined]
(150)
Human (Homo sapiens)
(21)
3a
3c5gA01
A:249-331
3b
3c5gB01
B:245-331
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
Human (Homo sapiens)
(34)
4a
3c5gA02
A:332-385
4b
3c5gB02
B:332-385
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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Asym.Unit (148 KB)
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