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1XHX
Asym. Unit
Info
Asym.Unit (417 KB)
Biol.Unit 1 (106 KB)
Biol.Unit 2 (107 KB)
Biol.Unit 3 (107 KB)
Biol.Unit 4 (109 KB)
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(1)
Title
:
PHI29 DNA POLYMERASE, ORTHORHOMBIC CRYSTAL FORM
Authors
:
S. Kamtekar, A. J. Berman, J. Wang, J. M. Lazaro, M. De Vega, L. Blanco, M. Salas, T. A. Steitz
Date
:
21 Sep 04 (Deposition) - 07 Dec 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Dna Polymerase, Protein-Primed, Strand Displacement, Processivity, Replication, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Kamtekar, A. J. Berman, J. Wang, J. M. Lazaro, M. De Vega, L. Blanco, M. Salas, T. A. Steitz
Insights Into Strand Displacement And Processivity From The Crystal Structure Of The Protein-Primed Dna Polymerase Of Bacteriophage Phi29
Mol. Cell V. 16 609 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
2
Ligand/Ion
MAGNESIUM ION
2
SO4
2
Ligand/Ion
SULFATE ION
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG D:187 , MET D:188 , SER D:192 , HOH D:3162 , HOH D:3202
BINDING SITE FOR RESIDUE SO4 D 3000
2
AC2
SOFTWARE
SER D:252 , LYS D:371 , ASN D:387 , HOH D:3101 , HOH D:3102 , HOH D:3229
BINDING SITE FOR RESIDUE SO4 D 3001
3
AC3
SOFTWARE
ASP C:523 , HOH C:5370 , HOH C:5371 , HOH C:5372 , HOH C:5373 , HOH C:5374
BINDING SITE FOR RESIDUE MG C 5000
4
AC4
SOFTWARE
ASP B:523 , HOH C:5375 , HOH C:5376 , HOH C:5377 , HOH C:5378 , HOH C:5379
BINDING SITE FOR RESIDUE MG C 5001
[
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SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_DPOL_BPPH2_001 (A176R, chain A/B/C/D, )
2: VAR_DPOL_BPPH2_002 (A355V, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_DPOL_BPPH2_001
*
A
176
R
DPOL_BPPH2
---
---
A/B/C/D
A
176
R
2
UniProt
VAR_DPOL_BPPH2_002
*
A
355
V
DPOL_BPPH2
---
---
A/B/C/D
A
355
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_B (A:454-462,B:454-462,C:454-462,D:45...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_B
PS00116
DNA polymerase family B signature.
DPOL_BPPH2
454-462
4
A:454-462
B:454-462
C:454-462
D:454-462
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1xhxa1 (A:5-187)
1b: SCOP_d1xhxb1 (B:5-187)
1c: SCOP_d1xhxc1 (C:5-187)
1d: SCOP_d1xhxd1 (D:5-187)
2a: SCOP_d1xhxa2 (A:188-575)
2b: SCOP_d1xhxb2 (B:188-575)
2c: SCOP_d1xhxc2 (C:188-575)
2d: SCOP_d1xhxd2 (D:188-575)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
DnaQ-like 3'-5' exonuclease
(253)
Protein domain
:
Exonuclease domain of phi29 DNA polymerase
(8)
Bacteriophage phi-29 [TaxId: 10756]
(8)
1a
d1xhxa1
A:5-187
1b
d1xhxb1
B:5-187
1c
d1xhxc1
C:5-187
1d
d1xhxd1
D:5-187
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
DNA polymerase I
(233)
Protein domain
:
phi29 DNA polymerase
(8)
Bacteriophage phi-29 [TaxId: 10756]
(8)
2a
d1xhxa2
A:188-575
2b
d1xhxb2
B:188-575
2c
d1xhxc2
C:188-575
2d
d1xhxd2
D:188-575
[
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]
CATH Domains
(6, 24)
Info
all CATH domains
1a: CATH_1xhxA01 (A:5-188)
1b: CATH_1xhxB01 (B:5-188)
1c: CATH_1xhxC01 (C:5-188)
1d: CATH_1xhxD01 (D:5-188)
2a: CATH_1xhxA03 (A:262-359)
2b: CATH_1xhxB03 (B:262-359)
2c: CATH_1xhxC03 (C:262-359)
2d: CATH_1xhxD03 (D:262-359)
3a: CATH_1xhxA02 (A:189-261,A:426-531)
3b: CATH_1xhxB02 (B:189-261,B:426-531)
3c: CATH_1xhxC02 (C:189-261,C:426-531)
3d: CATH_1xhxD02 (D:189-261,D:426-531)
4a: CATH_1xhxA05 (A:396-425)
4b: CATH_1xhxB05 (B:396-425)
4c: CATH_1xhxC05 (C:396-425)
4d: CATH_1xhxD05 (D:396-425)
5a: CATH_1xhxA06 (A:532-575)
5b: CATH_1xhxB06 (B:532-575)
5c: CATH_1xhxC06 (C:532-575)
5d: CATH_1xhxD06 (D:532-575)
6a: CATH_1xhxA04 (A:360-395)
6b: CATH_1xhxB04 (B:360-395)
6c: CATH_1xhxC04 (C:360-395)
6d: CATH_1xhxD04 (D:360-395)
View:
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)
(
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(
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
Bacillus phage phi29. Organism_taxid: 10756.
(2)
1a
1xhxA01
A:5-188
1b
1xhxB01
B:5-188
1c
1xhxC01
C:5-188
1d
1xhxD01
D:5-188
Topology
:
TPR 1 domain of DNA polymerase
(8)
Homologous Superfamily
:
TPR 1 domain of DNA polymerase
(8)
Bacillus phage phi29. Organism_taxid: 10756.
(2)
2a
1xhxA03
A:262-359
2b
1xhxB03
B:262-359
2c
1xhxC03
C:262-359
2d
1xhxD03
D:262-359
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Palm domain of DNA polymerase
(8)
Homologous Superfamily
:
Palm domain of DNA polymerase
(8)
Bacillus phage phi29. Organism_taxid: 10756.
(2)
3a
1xhxA02
A:189-261,A:426-531
3b
1xhxB02
B:189-261,B:426-531
3c
1xhxC02
C:189-261,C:426-531
3d
1xhxD02
D:189-261,D:426-531
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Rhinovirus 14, subunit 4
(101)
Homologous Superfamily
:
DNA polymerase; domain 5
(8)
Bacillus phage phi29. Organism_taxid: 10756.
(2)
4a
1xhxA05
A:396-425
4b
1xhxB05
B:396-425
4c
1xhxC05
C:396-425
4d
1xhxD05
D:396-425
Homologous Superfamily
:
DNA polymerase; domain 6
(10)
Bacillus phage phi29. Organism_taxid: 10756.
(2)
5a
1xhxA06
A:532-575
5b
1xhxB06
B:532-575
5c
1xhxC06
C:532-575
5d
1xhxD06
D:532-575
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(10)
Bacillus phage phi29. Organism_taxid: 10756.
(2)
6a
1xhxA04
A:360-395
6b
1xhxB04
B:360-395
6c
1xhxC04
C:360-395
6d
1xhxD04
D:360-395
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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