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2PY5
Biol. Unit 2
Info
Asym.Unit (235 KB)
Biol.Unit 1 (121 KB)
Biol.Unit 2 (113 KB)
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(1)
Title
:
PHI29 DNA POLYMERASE COMPLEXED WITH SINGLE-STRANDED DNA
Authors
:
A. J. Berman, S. Kamtekar, J. L. Goodman, J. M. Lazaro, M. De Vega, L. Blanco, M. Salas, T. A. Steitz
Date
:
15 May 07 (Deposition) - 17 Jul 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B,D,E,J,L,Y
Biol. Unit 1: A,D,J,Y (1x)
Biol. Unit 2: B,E,L (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
(1, 9)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1aa: 1,2-ETHANEDIOL (EDOaa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
1o: 1,2-ETHANEDIOL (EDOo)
1p: 1,2-ETHANEDIOL (EDOp)
1q: 1,2-ETHANEDIOL (EDOq)
1r: 1,2-ETHANEDIOL (EDOr)
1s: 1,2-ETHANEDIOL (EDOs)
1t: 1,2-ETHANEDIOL (EDOt)
1u: 1,2-ETHANEDIOL (EDOu)
1v: 1,2-ETHANEDIOL (EDOv)
1w: 1,2-ETHANEDIOL (EDOw)
1x: 1,2-ETHANEDIOL (EDOx)
1y: 1,2-ETHANEDIOL (EDOy)
1z: 1,2-ETHANEDIOL (EDOz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
9
Ligand/Ion
1,2-ETHANEDIOL
[
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Sites
(10, 10)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: BC6 (SOFTWARE)
07: BC7 (SOFTWARE)
08: BC8 (SOFTWARE)
09: CC4 (SOFTWARE)
10: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
LYS B:238 , GLN B:497 , HOH B:9134
BINDING SITE FOR RESIDUE EDO B 8002
02
AC3
SOFTWARE
ARG B:261 , HOH B:9103 , HOH B:9369 , HOH B:9476
BINDING SITE FOR RESIDUE EDO B 8003
03
AC5
SOFTWARE
ILE B:474 , LEU B:480 , TYR B:482 , HOH B:9084 , HOH B:9273
BINDING SITE FOR RESIDUE EDO B 8005
04
AC6
SOFTWARE
LEU B:216 , ASP B:219 , LYS B:220 , ARG B:223 , PRO B:397
BINDING SITE FOR RESIDUE EDO B 8006
05
AC7
SOFTWARE
GLU B:241 , ILE B:242 , GLY B:243 , ARG B:491 , HOH B:9146
BINDING SITE FOR RESIDUE EDO B 8007
06
BC6
SOFTWARE
TYR B:259 , ASP B:365 , THR B:368 , HOH B:9397 , HOH B:9621
BINDING SITE FOR RESIDUE EDO B 9002
07
BC7
SOFTWARE
HIS B:485 , THR B:488 , GLY B:516
BINDING SITE FOR RESIDUE EDO B 9003
08
BC8
SOFTWARE
GLU B:33 , HIS B:35 , LEU B:178 , LYS B:182 , GLU B:296
BINDING SITE FOR RESIDUE EDO B 9004
09
CC4
SOFTWARE
VAL B:528 , LYS B:529 , CYS B:530 , LYS B:538 , HOH B:9446
BINDING SITE FOR RESIDUE EDO B 9009
10
CC6
SOFTWARE
ILE A:269 , ASP A:278 , HOH A:9370 , HOH A:9518 , GLY B:111
BINDING SITE FOR RESIDUE EDO A 9011
[
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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 B, )
2: VAR_DPOL_BPPH2_002 (A355V, chain B, )
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
---
---
B
A
176
R
2
UniProt
VAR_DPOL_BPPH2_002
*
A
355
V
DPOL_BPPH2
---
---
B
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 (B:454-462)
;
View:
Select:
Label:
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
-
B: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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2py5a1 (A:5-187)
1b: SCOP_d2py5b1 (B:5-187)
2a: SCOP_d2py5a2 (A:188-575)
2b: SCOP_d2py5b2 (B:188-575)
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)
(
)
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)
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)
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)
(
)
Protein Domains
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)
(
)
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
d2py5a1
A:5-187
1b
d2py5b1
B: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
d2py5a2
A:188-575
2b
d2py5b2
B:188-575
[
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CATH Domains
(6, 12)
Info
all CATH domains
1a: CATH_2py5A01 (A:5-188)
1b: CATH_2py5B01 (B:5-188)
2a: CATH_2py5A03 (A:262-359)
2b: CATH_2py5B03 (B:262-359)
3a: CATH_2py5A02 (A:189-261,A:426-531)
3b: CATH_2py5B02 (B:189-261,B:426-531)
4a: CATH_2py5A05 (A:396-425)
4b: CATH_2py5B05 (B:396-425)
5a: CATH_2py5A06 (A:532-575)
5b: CATH_2py5B06 (B:532-575)
6a: CATH_2py5A04 (A:360-395)
6b: CATH_2py5B04 (B:360-395)
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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)
[unclassified]
(102)
1a
2py5A01
A:5-188
1b
2py5B01
B:5-188
Topology
:
TPR 1 domain of DNA polymerase
(8)
Homologous Superfamily
:
TPR 1 domain of DNA polymerase
(8)
[unclassified]
(6)
2a
2py5A03
A:262-359
2b
2py5B03
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
2py5A02
A:189-261,A:426-531
3b
2py5B02
B:189-261,B: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
2py5A05
A:396-425
4b
2py5B05
B:396-425
Homologous Superfamily
:
DNA polymerase; domain 6
(10)
[unclassified]
(6)
5a
2py5A06
A:532-575
5b
2py5B06
B:532-575
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(10)
[unclassified]
(7)
6a
2py5A04
A:360-395
6b
2py5B04
B:360-395
[
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]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_DNA_pol_B_2_2py5B01 (B:49-488)
1b: PFAM_DNA_pol_B_2_2py5B02 (B:49-488)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
DNA_pol_B-like
(44)
Family
:
DNA_pol_B_2
(6)
Bacillus phage phi29 (Bacteriophage phi-29)
(6)
1a
DNA_pol_B_2-2py5B01
B:49-488
1b
DNA_pol_B_2-2py5B02
B:49-488
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