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3HX0
Biol. Unit 2
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:
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Gene Ontology, PubMed, Web (Google)
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)
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
)
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Hetero Components
(1, 1)
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:
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No.
Name
Count
Type
Full Name
1
D3T
1
Ligand/Ion
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
NA
-1
Ligand/Ion
SODIUM ION
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Sites
(3, 3)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
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
2
AC4
SOFTWARE
HOH F:15 , ASP F:427 , ASP F:429 , D3T F:702
BINDING SITE FOR RESIDUE MG F 802
3
AC5
SOFTWARE
HOH F:12 , SER F:339 , ILE F:341 , ALA F:344 , DA H:5
BINDING SITE FOR RESIDUE NA F 806
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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 F, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020269
R
438
W
DPOLL_HUMAN
Polymorphism
3730477
F
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 (F:416-435)
;
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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
-
F:416-435
-
-
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(0, 0)
Info
All SCOP Domains
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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)
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(
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(
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(
)
Homologous Superfamilies
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)
(
)
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
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Asymmetric Unit 1
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Show PDB file:
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)
Header - Biol.Unit 3
Biol.Unit 4 (64 KB)
Header - Biol.Unit 4
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