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Asym. Unit
Info
Asym.Unit (265 KB)
Biol.Unit 1 (70 KB)
Biol.Unit 2 (67 KB)
Biol.Unit 3 (68 KB)
Biol.Unit 4 (71 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE LAMBDA IN COMPLEX WITH A ONE NUCLEOTIDE DNA GAP
Authors
:
M. Garcia-Diaz, K. Bebenek, J. M. Krahn, T. A. Kunkel, L. C. Pedersen
Date
:
19 Oct 04 (Deposition) - 18 Jan 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Biol. Unit 4: M,N,O,P (1x)
Keywords
:
Dna Polymerase Lambda, Protein-Dna Complex, Helix-Hairpin-Helix, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Garcia-Diaz, K. Bebenek, J. M. Krahn, T. A. Kunkel, L. C. Pedersen
A Closed Conformation For The Pol Lambda Catalytic Cycle.
Nat. Struct. Mol. Biol. V. 12 97 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 10)
Info
All Hetero Components
1a: CACODYLATE ION (CACa)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CAC
1
Ligand/Ion
CACODYLATE ION
2
MG
3
Ligand/Ion
MAGNESIUM ION
3
NA
6
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:339 , ILE A:341 , ALA A:344 , DG C:5 , HOH C:8 , HOH C:156
BINDING SITE FOR RESIDUE NA A 961
02
AC2
SOFTWARE
SER E:339 , ILE E:341 , ALA E:344 , HOH E:1016 , DG G:5 , HOH G:508
BINDING SITE FOR RESIDUE NA E 962
03
AC3
SOFTWARE
SER I:339 , ILE I:341 , ALA I:344 , DG K:5 , HOH K:303 , HOH K:875
BINDING SITE FOR RESIDUE NA I 963
04
AC4
SOFTWARE
SER M:339 , ILE M:341 , ALA M:344 , HOH M:978 , DG O:5 , HOH O:39
BINDING SITE FOR RESIDUE NA M 964
05
AC5
SOFTWARE
HOH J:641 , HOH J:642 , HOH J:643 , HOH J:644 , HOH L:640 , HOH L:645
BINDING SITE FOR RESIDUE NA J 965
06
AC6
SOFTWARE
HOH N:943 , HOH N:944 , HOH N:945 , HOH P:940
BINDING SITE FOR RESIDUE NA N 966
07
AC7
SOFTWARE
HOH B:700 , HOH B:702 , HOH B:703 , HOH B:704 , HOH B:705 , HOH D:701
BINDING SITE FOR RESIDUE MG B 991
08
AC8
SOFTWARE
HOH F:854 , HOH F:857 , HOH F:858 , HOH F:859 , HOH H:855 , HOH H:856
BINDING SITE FOR RESIDUE MG F 992
09
AC9
SOFTWARE
HOH H:868 , HOH H:871 , HOH H:872 , HOH H:873 , HOH H:874 , HOH L:870
BINDING SITE FOR RESIDUE MG H 993
10
BC1
SOFTWARE
DC D:3 , DG D:4 , DG P:4
BINDING SITE FOR RESIDUE CAC D 950
[
close Site info
]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020269 (R438W, chain A/E/I/M, )
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/E/I/M
R
438
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_X (A:416-435,E:416-435,I:416-435,M:41...)
;
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
4
A:416-435
E:416-435
I:416-435
M:416-435
[
close PROSITE info
]
Exons
(5, 20)
Info
All Exons
Exon 1.5e (A:249-297 | E:251-297 | I:250-297 ...)
Exon 1.6b (A:298-355 | E:298-355 | I:298-355 ...)
Exon 1.7b (A:356-398 | E:356-398 | I:356-398 ...)
Exon 1.8c (A:399-455 | E:399-455 | I:399-455 ...)
Exon 1.9g (A:455-575 | E:455-575 | I:455-575 ...)
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
4
A:249-297
E:251-297
I:250-297
M:249-297
49
47
48
49
1.6b
ENST00000370169
6b
ENSE00002151653
chr10:
103343438-103343265
174
DPOLL_HUMAN
298-355
58
4
A:298-355
E:298-355
I:298-355
M:298-355
58
58
58
58
1.7b
ENST00000370169
7b
ENSE00001593760
chr10:
103342648-103342520
129
DPOLL_HUMAN
356-398
43
4
A:356-398
E:356-398
I:356-398
M:356-398
43
43
43
43
1.8c
ENST00000370169
8c
ENSE00001691940
chr10:
103340173-103340005
169
DPOLL_HUMAN
399-455
57
4
A:399-455
E:399-455
I:399-455
M:399-455
57
57
57
57
1.9g
ENST00000370169
9g
ENSE00001451993
chr10:
103339574-103338639
936
DPOLL_HUMAN
455-575
121
4
A:455-575
E:455-575
I:455-575
M:455-575
121
121
121
121
[
close EXON info
]
SCOP Domains
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1xsla1 (A:249-327)
1b: SCOP_d1xsle1 (E:251-327)
1c: SCOP_d1xsli1 (I:250-327)
1d: SCOP_d1xslm1 (M:249-327)
2a: SCOP_d1xsla2 (A:329-385)
2b: SCOP_d1xsle2 (E:329-385)
2c: SCOP_d1xsli2 (I:329-385)
2d: SCOP_d1xslm2 (M:329-385)
3a: SCOP_d1xsla3 (A:386-575)
3b: SCOP_d1xsle3 (E:386-575)
3c: SCOP_d1xsli3 (I:386-575)
3d: SCOP_d1xslm3 (M:386-575)
View:
Select:
Label:
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
d1xsla1
A:249-327
1b
d1xsle1
E:251-327
1c
d1xsli1
I:250-327
1d
d1xslm1
M:249-327
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
d1xsla2
A:329-385
2b
d1xsle2
E:329-385
2c
d1xsli2
I:329-385
2d
d1xslm2
M: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
d1xsla3
A:386-575
3b
d1xsle3
E:386-575
3c
d1xsli3
I:386-575
3d
d1xslm3
M:386-575
[
close SCOP info
]
CATH Domains
(4, 16)
Info
all CATH domains
1a: CATH_1xslA03 (A:386-508)
1b: CATH_1xslE03 (E:386-508)
1c: CATH_1xslI03 (I:386-508)
1d: CATH_1xslM03 (M:386-508)
2a: CATH_1xslA04 (A:509-575)
2b: CATH_1xslE04 (E:509-575)
2c: CATH_1xslI04 (I:509-575)
2d: CATH_1xslM04 (M:509-575)
3a: CATH_1xslA01 (A:249-331)
3b: CATH_1xslM01 (M:249-331)
3c: CATH_1xslI01 (I:250-331)
3d: CATH_1xslE01 (E:251-331)
4a: CATH_1xslA02 (A:332-385)
4b: CATH_1xslE02 (E:332-385)
4c: CATH_1xslI02 (I:332-385)
4d: CATH_1xslM02 (M:332-385)
View:
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Classes
(
)
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)
Architectures
(
)
(
)
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)
[unclassified]
(117)
1a
1xslA03
A:386-508
1b
1xslE03
E:386-508
1c
1xslI03
I:386-508
1d
1xslM03
M:386-508
Topology
:
Beta Polymerase; domain 3
(161)
Homologous Superfamily
:
Beta Polymerase, domain 3
(161)
[unclassified]
(116)
2a
1xslA04
A:509-575
2b
1xslE04
E:509-575
2c
1xslI04
I:509-575
2d
1xslM04
M: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)
[unclassified]
(116)
3a
1xslA01
A:249-331
3b
1xslM01
M:249-331
3c
1xslI01
I:250-331
3d
1xslE01
E:251-331
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
[unclassified]
(230)
4a
1xslA02
A:332-385
4b
1xslE02
E:332-385
4c
1xslI02
I:332-385
4d
1xslM02
M:332-385
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Chain B
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Asym.Unit (265 KB)
Header - Asym.Unit
Biol.Unit 1 (70 KB)
Header - Biol.Unit 1
Biol.Unit 2 (67 KB)
Header - Biol.Unit 2
Biol.Unit 3 (68 KB)
Header - Biol.Unit 3
Biol.Unit 4 (71 KB)
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