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2PZS
Biol. Unit 3
Info
Asym.Unit (397 KB)
Biol.Unit 1 (107 KB)
Biol.Unit 2 (98 KB)
Biol.Unit 3 (98 KB)
Biol.Unit 4 (106 KB)
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(1)
Title
:
PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE DNA (POST-TRANSLOCATION BINARY COMPLEX)
Authors
:
A. J. Berman, S. Kamtekar, J. L. Goodman, J. M. Lazaro, M. De Vega, L. Blanco, M. Salas, T. A. Steitz
Date
:
18 May 07 (Deposition) - 17 Jul 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,R,S,T,U,X,Y
Biol. Unit 1: A,X,Y (1x)
Biol. Unit 2: B,T (1x)
Biol. Unit 3: C,U (1x)
Biol. Unit 4: D,R,S (1x)
Keywords
:
Protein-Dna Complex, Replication, Transferase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. J. Berman, S. Kamtekar, J. L. Goodman, J. M. Lazaro, M. De Vega, L. Blanco, M. Salas, T. A. Steitz
Structures Of Phi29 Dna Polymerase Complexed With Substrate: The Mechanism Of Translocation In B-Family Polymerases
Embo J. V. 26 3494 2007
(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
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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:
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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
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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_d2pzsa1 (A:5-187)
1b: SCOP_d2pzsb1 (B:5-187)
1c: SCOP_d2pzsc1 (C:5-187)
1d: SCOP_d2pzsd1 (D:5-187)
2a: SCOP_d2pzsa2 (A:188-575)
2b: SCOP_d2pzsb2 (B:188-575)
2c: SCOP_d2pzsc2 (C:188-575)
2d: SCOP_d2pzsd2 (D:188-574)
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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
d2pzsa1
A:5-187
1b
d2pzsb1
B:5-187
1c
d2pzsc1
C:5-187
1d
d2pzsd1
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
d2pzsa2
A:188-575
2b
d2pzsb2
B:188-575
2c
d2pzsc2
C:188-575
2d
d2pzsd2
D:188-574
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CATH Domains
(6, 24)
Info
all CATH domains
1a: CATH_2pzsA01 (A:5-188)
1b: CATH_2pzsD01 (D:5-188)
1c: CATH_2pzsB01 (B:5-188)
1d: CATH_2pzsC01 (C:5-188)
2a: CATH_2pzsA03 (A:262-359)
2b: CATH_2pzsD03 (D:262-359)
2c: CATH_2pzsC03 (C:262-359)
2d: CATH_2pzsB03 (B:262-359)
3a: CATH_2pzsA02 (A:189-261,A:426-531)
3b: CATH_2pzsD02 (D:189-261,D:426-531)
3c: CATH_2pzsB02 (B:189-261,B:426-531)
3d: CATH_2pzsC02 (C:189-261,C:426-531)
4a: CATH_2pzsA05 (A:396-425)
4b: CATH_2pzsD05 (D:396-425)
4c: CATH_2pzsB05 (B:396-425)
4d: CATH_2pzsC05 (C:396-425)
5a: CATH_2pzsD06 (D:532-574)
5b: CATH_2pzsC06 (C:532-575)
5c: CATH_2pzsA06 (A:532-575)
5d: CATH_2pzsB06 (B:532-575)
6a: CATH_2pzsA04 (A:360-395)
6b: CATH_2pzsD04 (D:360-395)
6c: CATH_2pzsB04 (B:360-395)
6d: CATH_2pzsC04 (C: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
2pzsA01
A:5-188
1b
2pzsD01
D:5-188
1c
2pzsB01
B:5-188
1d
2pzsC01
C:5-188
Topology
:
TPR 1 domain of DNA polymerase
(8)
Homologous Superfamily
:
TPR 1 domain of DNA polymerase
(8)
[unclassified]
(6)
2a
2pzsA03
A:262-359
2b
2pzsD03
D:262-359
2c
2pzsC03
C:262-359
2d
2pzsB03
B: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
2pzsA02
A:189-261,A:426-531
3b
2pzsD02
D:189-261,D:426-531
3c
2pzsB02
B:189-261,B:426-531
3d
2pzsC02
C:189-261,C: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
2pzsA05
A:396-425
4b
2pzsD05
D:396-425
4c
2pzsB05
B:396-425
4d
2pzsC05
C:396-425
Homologous Superfamily
:
DNA polymerase; domain 6
(10)
[unclassified]
(6)
5a
2pzsD06
D:532-574
5b
2pzsC06
C:532-575
5c
2pzsA06
A:532-575
5d
2pzsB06
B:532-575
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(10)
[unclassified]
(7)
6a
2pzsA04
A:360-395
6b
2pzsD04
D:360-395
6c
2pzsB04
B:360-395
6d
2pzsC04
C:360-395
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_DNA_pol_B_2_2pzsD01 (D:49-488)
1b: PFAM_DNA_pol_B_2_2pzsD02 (D:49-488)
1c: PFAM_DNA_pol_B_2_2pzsD03 (D:49-488)
1d: PFAM_DNA_pol_B_2_2pzsD04 (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_2-2pzsD01
D:49-488
1b
DNA_pol_B_2-2pzsD02
D:49-488
1c
DNA_pol_B_2-2pzsD03
D:49-488
1d
DNA_pol_B_2-2pzsD04
D:49-488
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