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3HX0
Asym. Unit
Info
Asym.Unit (251 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (65 KB)
Biol.Unit 3 (64 KB)
Biol.Unit 4 (64 KB)
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(1)
Title
:
TERNARY COMPLEX OF L277A, H511A, R514 MUTANT POL LAMBDA BOUND TO A 2 NUCLEOTIDE GAPPED DNA SUBSTRATE WITH A SCRUNCHED DA
Authors
:
M. Garcia-Diaz, K. Bebenek, A. A. Larrea, J. M. Havener, L. Perera, J. M. Krahn, L. C. Pedersen, D. A. Ramsden, T. A. Kunkel
Date
:
19 Jun 09 (Deposition) - 25 Aug 09 (Release) - 25 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,F,G,H,I,K,L,M,N,P,Q,R,S
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: F,G,H,I (1x)
Biol. Unit 3: K,L,M,N (1x)
Biol. Unit 4: P,Q,R,S (1x)
Keywords
:
Scrunch, X-Family, Polymerase Lambda, 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 Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Garcia-Diaz, K. Bebenek, A. A. Larrea, J. M. Havener, L. Perera, J. M. Krahn, L. C. Pedersen, D. A. Ramsden, T. A. Kunkel
Scrunching During Dna Repair Synthesis
To Be Published
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(3, 13)
Info
All Hetero Components
1a: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOS... (D3Ta)
1b: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOS... (D3Tb)
1c: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOS... (D3Tc)
1d: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOS... (D3Td)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
D3T
4
Ligand/Ion
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
NA
5
Ligand/Ion
SODIUM ION
[
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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
HOH A:7 , 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:801 , DA B:6 , DT C:6
BINDING SITE FOR RESIDUE D3T A 701
02
AC2
SOFTWARE
HOH A:7 , ASP A:427 , ASP A:429 , D3T A:701
BINDING SITE FOR RESIDUE MG A 801
03
AC3
SOFTWARE
HOH F:15 , HOH F:16 , ARG F:386 , GLY F:416 , SER F:417 , ARG F:420 , GLY F:426 , ASP F:427 , ASP F:429 , TYR F:505 , PHE F:506 , GLY F:508 , ALA F:510 , ASN F:513 , MG F:802 , DA G:6 , DT H:6
BINDING SITE FOR RESIDUE D3T F 702
04
AC4
SOFTWARE
HOH F:15 , ASP F:427 , ASP F:429 , D3T F:702
BINDING SITE FOR RESIDUE MG F 802
05
AC5
SOFTWARE
HOH F:12 , SER F:339 , ILE F:341 , ALA F:344 , DA H:5
BINDING SITE FOR RESIDUE NA F 806
06
AC6
SOFTWARE
HOH K:34 , ARG K:386 , GLY K:416 , SER K:417 , ARG K:420 , GLY K:426 , ASP K:427 , ASP K:429 , TYR K:505 , ASN K:513 , MG K:803 , NA K:808 , DT M:6
BINDING SITE FOR RESIDUE D3T K 703
07
AC7
SOFTWARE
HOH K:34 , ASP K:427 , ASP K:429 , D3T K:703 , NA K:808
BINDING SITE FOR RESIDUE MG K 803
08
AC8
SOFTWARE
HOH K:21 , SER K:339 , ILE K:341 , ALA K:344 , DT M:6
BINDING SITE FOR RESIDUE NA K 807
09
AC9
SOFTWARE
ASP K:427 , ASP K:429 , ASP K:490 , D3T K:703 , MG K:803
BINDING SITE FOR RESIDUE NA K 808
10
BC1
SOFTWARE
HOH P:35 , ARG P:386 , GLY P:416 , SER P:417 , ARG P:420 , GLY P:426 , ASP P:427 , ASP P:429 , TYR P:505 , PHE P:506 , ALA P:510 , ASN P:513 , MG P:804 , NA P:810 , DT R:6
BINDING SITE FOR RESIDUE D3T P 704
11
BC2
SOFTWARE
HOH P:35 , ASP P:427 , ASP P:429 , D3T P:704
BINDING SITE FOR RESIDUE MG P 804
12
BC3
SOFTWARE
HOH P:29 , SER P:339 , ILE P:341 , ALA P:344 , DT R:6
BINDING SITE FOR RESIDUE NA P 809
13
BC4
SOFTWARE
ASP P:427 , ASP P:429 , ASP P:490 , D3T P:704
BINDING SITE FOR RESIDUE NA P 810
[
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]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020269 (R438W, chain A/F/K/P, )
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/F/K/P
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,F:416-435,K:416-435,P: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
F:416-435
K:416-435
P:416-435
[
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Exons
(5, 20)
Info
All Exons
Exon 1.5e (A:246-297 | F:247-297 | K:249-297 ...)
Exon 1.6b (A:298-355 | F:298-355 | K:298-355 ...)
Exon 1.7b (A:356-398 | F:356-398 | K:356-398 ...)
Exon 1.8c (A:399-455 | F:399-455 | K:399-455 ...)
Exon 1.9g (A:455-575 | F:455-575 | K: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:246-297
F:247-297
K:249-297
P:249-297
52
51
49
49
1.6b
ENST00000370169
6b
ENSE00002151653
chr10:
103343438-103343265
174
DPOLL_HUMAN
298-355
58
4
A:298-355
F:298-355
K:298-355
P:298-355
58
58
58
58
1.7b
ENST00000370169
7b
ENSE00001593760
chr10:
103342648-103342520
129
DPOLL_HUMAN
356-398
43
4
A:356-398
F:356-398
K:356-398
P:356-398
43
43
43
43
1.8c
ENST00000370169
8c
ENSE00001691940
chr10:
103340173-103340005
169
DPOLL_HUMAN
399-455
57
4
A:399-455
F:399-455
K:399-455
P:399-455
57
57
57
57
1.9g
ENST00000370169
9g
ENSE00001451993
chr10:
103339574-103338639
936
DPOLL_HUMAN
455-575
121
4
A:455-575
F:455-575
K:455-575
P:455-575
121
121
121
121
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(4, 16)
Info
all CATH domains
1a: CATH_3hx0A03 (A:386-508)
1b: CATH_3hx0F03 (F:386-508)
1c: CATH_3hx0K03 (K:386-508)
1d: CATH_3hx0P03 (P:386-508)
2a: CATH_3hx0A04 (A:509-575)
2b: CATH_3hx0F04 (F:509-575)
2c: CATH_3hx0K04 (K:509-575)
2d: CATH_3hx0P04 (P:509-575)
3a: CATH_3hx0K01 (K:249-331)
3b: CATH_3hx0P01 (P:249-331)
3c: CATH_3hx0F01 (F:247-331)
3d: CATH_3hx0A01 (A:246-331)
4a: CATH_3hx0A02 (A:332-385)
4b: CATH_3hx0F02 (F:332-385)
4c: CATH_3hx0K02 (K:332-385)
4d: CATH_3hx0P02 (P:332-385)
View:
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Label:
Classes
(
)
(
)
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)
Human (Homo sapiens)
(22)
1a
3hx0A03
A:386-508
1b
3hx0F03
F:386-508
1c
3hx0K03
K:386-508
1d
3hx0P03
P:386-508
Topology
:
Beta Polymerase; domain 3
(161)
Homologous Superfamily
:
Beta Polymerase, domain 3
(161)
Human (Homo sapiens)
(21)
2a
3hx0A04
A:509-575
2b
3hx0F04
F:509-575
2c
3hx0K04
K:509-575
2d
3hx0P04
P: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
3hx0K01
K:249-331
3b
3hx0P01
P:249-331
3c
3hx0F01
F:247-331
3d
3hx0A01
A:246-331
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
Human (Homo sapiens)
(34)
4a
3hx0A02
A:332-385
4b
3hx0F02
F:332-385
4c
3hx0K02
K:332-385
4d
3hx0P02
P:332-385
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Asym.Unit (251 KB)
Header - Asym.Unit
Biol.Unit 1 (65 KB)
Header - Biol.Unit 1
Biol.Unit 2 (65 KB)
Header - Biol.Unit 2
Biol.Unit 3 (64 KB)
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Biol.Unit 4 (64 KB)
Header - Biol.Unit 4
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