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1XHZ
Biol. Unit 3
Info
Asym.Unit (402 KB)
Biol.Unit 1 (104 KB)
Biol.Unit 2 (103 KB)
Biol.Unit 3 (104 KB)
Biol.Unit 4 (103 KB)
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(1)
Title
:
PHI29 DNA POLYMERASE, ORTHORHOMBIC CRYSTAL FORM, SSDNA COMPLEX
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
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E (1x)
Biol. Unit 2: B,F (1x)
Biol. Unit 3: C,G (1x)
Biol. Unit 4: D,H (1x)
Keywords
:
Dna Polymerase, Protein-Primed, Strand Displacement, Processivity, Replication, Transferase/Dna Complex
(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
(0, 0)
Info
All Hetero Components
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Sorry, no Info available
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Sites
(0, 0)
Info
All Sites
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Sorry, no Info available
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_DPOL_BPPH2_001 (A176R, chain C, )
2: VAR_DPOL_BPPH2_002 (A355V, chain C, )
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
---
---
C
A
176
R
2
UniProt
VAR_DPOL_BPPH2_002
*
A
355
V
DPOL_BPPH2
---
---
C
A
355
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_B (C:454-462)
;
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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
1
-
-
C:454-462
-
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1xhza1 (A:5-187)
1b: SCOP_d1xhzb1 (B:5-187)
1c: SCOP_d1xhzc1 (C:5-187)
1d: SCOP_d1xhzd1 (D:5-187)
2a: SCOP_d1xhza2 (A:188-575)
2b: SCOP_d1xhzb2 (B:188-575)
2c: SCOP_d1xhzc2 (C:188-575)
2d: SCOP_d1xhzd2 (D:188-575)
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)
(
)
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
d1xhza1
A:5-187
1b
d1xhzb1
B:5-187
1c
d1xhzc1
C:5-187
1d
d1xhzd1
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
d1xhza2
A:188-575
2b
d1xhzb2
B:188-575
2c
d1xhzc2
C:188-575
2d
d1xhzd2
D:188-575
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CATH Domains
(6, 24)
Info
all CATH domains
1a: CATH_1xhzA01 (A:5-188)
1b: CATH_1xhzB01 (B:5-188)
1c: CATH_1xhzC01 (C:5-188)
1d: CATH_1xhzD01 (D:5-188)
2a: CATH_1xhzA03 (A:262-359)
2b: CATH_1xhzB03 (B:262-359)
2c: CATH_1xhzC03 (C:262-359)
2d: CATH_1xhzD03 (D:262-359)
3a: CATH_1xhzA02 (A:189-261,A:426-531)
3b: CATH_1xhzB02 (B:189-261,B:426-531)
3c: CATH_1xhzC02 (C:189-261,C:426-531)
3d: CATH_1xhzD02 (D:189-261,D:426-531)
4a: CATH_1xhzA05 (A:396-425)
4b: CATH_1xhzB05 (B:396-425)
4c: CATH_1xhzC05 (C:396-425)
4d: CATH_1xhzD05 (D:396-425)
5a: CATH_1xhzA06 (A:532-575)
5b: CATH_1xhzB06 (B:532-575)
5c: CATH_1xhzC06 (C:532-575)
5d: CATH_1xhzD06 (D:532-575)
6a: CATH_1xhzA04 (A:360-395)
6b: CATH_1xhzB04 (B:360-395)
6c: CATH_1xhzC04 (C:360-395)
6d: CATH_1xhzD04 (D:360-395)
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(
)
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)
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)
[unclassified]
(102)
1a
1xhzA01
A:5-188
1b
1xhzB01
B:5-188
1c
1xhzC01
C:5-188
1d
1xhzD01
D:5-188
Topology
:
TPR 1 domain of DNA polymerase
(8)
Homologous Superfamily
:
TPR 1 domain of DNA polymerase
(8)
[unclassified]
(6)
2a
1xhzA03
A:262-359
2b
1xhzB03
B:262-359
2c
1xhzC03
C:262-359
2d
1xhzD03
D:262-359
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Palm domain of DNA polymerase
(8)
Homologous Superfamily
:
Palm domain of DNA polymerase
(8)
[unclassified]
(6)
3a
1xhzA02
A:189-261,A:426-531
3b
1xhzB02
B:189-261,B:426-531
3c
1xhzC02
C:189-261,C:426-531
3d
1xhzD02
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)
[unclassified]
(6)
4a
1xhzA05
A:396-425
4b
1xhzB05
B:396-425
4c
1xhzC05
C:396-425
4d
1xhzD05
D:396-425
Homologous Superfamily
:
DNA polymerase; domain 6
(10)
[unclassified]
(6)
5a
1xhzA06
A:532-575
5b
1xhzB06
B:532-575
5c
1xhzC06
C:532-575
5d
1xhzD06
D:532-575
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(10)
[unclassified]
(7)
6a
1xhzA04
A:360-395
6b
1xhzB04
B:360-395
6c
1xhzC04
C:360-395
6d
1xhzD04
D:360-395
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_DNA_pol_B_2_1xhzD01 (D:49-488)
1b: PFAM_DNA_pol_B_2_1xhzD02 (D:49-488)
1c: PFAM_DNA_pol_B_2_1xhzD03 (D:49-488)
1d: PFAM_DNA_pol_B_2_1xhzD04 (D:49-488)
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Clans
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Organisms
(
)
(
)
Clan
:
DNA_pol_B-like
(44)
Family
:
DNA_pol_B_2
(6)
Bacillus phage phi29 (Bacteriophage phi-29)
(6)
1a
DNA_pol_B_2-1xhzD01
D:49-488
1b
DNA_pol_B_2-1xhzD02
D:49-488
1c
DNA_pol_B_2-1xhzD03
D:49-488
1d
DNA_pol_B_2-1xhzD04
D:49-488
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