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3C5G
Asym. Unit
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
)
[
close entry info
]
Hetero Components
(5, 15)
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
2
Mod. Nucleotide
3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2
D3T
2
Ligand/Ion
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
3
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
4
MG
2
Ligand/Ion
MAGNESIUM ION
5
NA
8
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:427 , ASP A:429 , D3T A:576 , NA A:803 , HOH A:976
BINDING SITE FOR RESIDUE MG A 602
02
AC2
SOFTWARE
ASP A:427 , ASP A:429 , ASP A:490 , D3T A:576 , MG A:602 , HOH P:671
BINDING SITE FOR RESIDUE NA A 803
03
AC3
SOFTWARE
SER A:339 , ILE A:341 , ALA A:344 , DA P:5 , HOH P:170 , HOH P:311
BINDING SITE FOR RESIDUE NA A 804
04
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
05
AC5
SOFTWARE
DG D:1 , DC D:2 , DG T:2 , DG T:3 , HOH T:619
BINDING SITE FOR RESIDUE EDO T 2801
06
AC6
SOFTWARE
GLN A:372 , HOH A:866 , HOH A:934 , DG P:3 , DT P:4 , HOH P:342
BINDING SITE FOR RESIDUE NA P 807
07
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
08
AC8
SOFTWARE
ASP B:427 , ASP B:429 , D3T B:577 , NA B:802 , HOH B:1067
BINDING SITE FOR RESIDUE MG B 601
09
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
10
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
11
BC2
SOFTWARE
LYS A:307 , CYS B:300 , ILE B:302 , ILE B:305 , DC E:3
BINDING SITE FOR RESIDUE NA B 806
12
BC3
SOFTWARE
ARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , GLY A:426 , ASP A:427 , ASP A:429 , TYR A:505 , PHE A:506 , GLY A:508 , ALA A:510 , ASN A:513 , MG A:602 , NA A:803 , HOH A:976 , HOH A:1125 , HOH A:1126 , HOH A:1128 , HOH A:1129 , 2DT P:6 , HOH P:671 , DA T:5
BINDING SITE FOR RESIDUE D3T A 576
13
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
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020269 (R438W, chain A/B, )
View:
Select:
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
A/B
R
438
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_X (A:416-435,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
2
A:416-435
B:416-435
[
close PROSITE info
]
Exons
(5, 10)
Info
All Exons
Exon 1.5e (A:249-297 | B:245-297)
Exon 1.6b (A:298-355 | B:298-355)
Exon 1.7b (A:356-398 | B:356-398)
Exon 1.8c (A:399-455 | B:399-455)
Exon 1.9g (A:455-575 (gaps) | B:455-575 (gaps...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.4b/1.5e
2: Boundary 1.5e/1.6b
3: Boundary 1.6b/1.7b
4: Boundary 1.7b/1.8c
5: Boundary 1.8c/1.9g
6: Boundary 1.9g/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1k
ENST00000370169
1k
ENSE00001451987
chr10:
103347178-103347003
176
DPOLL_HUMAN
1-39
39
0
-
-
1.3
ENST00000370169
3
ENSE00001731892
chr10:
103345913-103345619
295
DPOLL_HUMAN
39-137
99
0
-
-
1.4b
ENST00000370169
4b
ENSE00001100422
chr10:
103345235-103345073
163
DPOLL_HUMAN
137-191
55
0
-
-
1.5e
ENST00000370169
5e
ENSE00001617344
chr10:
103344676-103344359
318
DPOLL_HUMAN
192-297
106
2
A:249-297
B:245-297
49
53
1.6b
ENST00000370169
6b
ENSE00002151653
chr10:
103343438-103343265
174
DPOLL_HUMAN
298-355
58
2
A:298-355
B:298-355
58
58
1.7b
ENST00000370169
7b
ENSE00001593760
chr10:
103342648-103342520
129
DPOLL_HUMAN
356-398
43
2
A:356-398
B:356-398
43
43
1.8c
ENST00000370169
8c
ENSE00001691940
chr10:
103340173-103340005
169
DPOLL_HUMAN
399-455
57
2
A:399-455
B:399-455
57
57
1.9g
ENST00000370169
9g
ENSE00001451993
chr10:
103339574-103338639
936
DPOLL_HUMAN
455-575
121
2
A:455-575 (gaps)
B:455-575 (gaps)
121
121
[
close EXON info
]
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)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
[
close SCOP info
]
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)
View:
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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
View:
Select:
Label:
Sorry, no Info available
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Atom Selection
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Chain D
Chain E
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Chain Q
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Chain U
Asymmetric Unit 1
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Asym.Unit (148 KB)
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