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2PY5
Biol. Unit 1
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, 18)
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
18
Ligand/Ion
1,2-ETHANEDIOL
[
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]
Sites
(18, 18)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC9 (SOFTWARE)
11: CC1 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC3 (SOFTWARE)
14: CC5 (SOFTWARE)
15: CC6 (SOFTWARE)
16: CC7 (SOFTWARE)
17: CC8 (SOFTWARE)
18: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:252 , LYS A:371 , LYS A:383 , ASN A:387 , HOH A:9362
BINDING SITE FOR RESIDUE EDO A 8001
02
AC4
SOFTWARE
SER A:260 , THR A:357 , HOH A:9038
BINDING SITE FOR RESIDUE EDO A 8004
03
AC8
SOFTWARE
LEU A:294 , LYS A:295 , GLU A:296 , GLY A:297 , TYR A:298 , LYS A:317 , TYR A:449
BINDING SITE FOR RESIDUE EDO A 8008
04
AC9
SOFTWARE
ASN A:234 , ARG A:236 , TYR A:449 , HOH A:9573
BINDING SITE FOR RESIDUE EDO A 8009
05
BC1
SOFTWARE
LYS A:490 , ARG A:491 , HOH A:9164
BINDING SITE FOR RESIDUE EDO A 8010
06
BC2
SOFTWARE
LYS A:208 , PHE A:211 , THR A:213 , HOH A:9143 , HOH A:9515 , HOH A:9558
BINDING SITE FOR RESIDUE EDO A 8011
07
BC3
SOFTWARE
TYR A:259 , ASP A:365 , THR A:368 , LEU A:480 , HOH A:9177 , HOH A:9780
BINDING SITE FOR RESIDUE EDO A 8012
08
BC4
SOFTWARE
TYR A:405 , ARG A:415
BINDING SITE FOR RESIDUE EDO A 8013
09
BC5
SOFTWARE
SER A:43 , ASP A:45 , TRP A:277 , HOH A:9124
BINDING SITE FOR RESIDUE EDO A 9001
10
BC9
SOFTWARE
VAL A:210 , TYR A:265 , EDO A:9006
BINDING SITE FOR RESIDUE EDO A 9005
11
CC1
SOFTWARE
LYS A:206 , THR A:357 , GLY A:358 , LEU A:359 , EDO A:9005
BINDING SITE FOR RESIDUE EDO A 9006
12
CC2
SOFTWARE
GLU A:334 , TYR A:439 , HOH A:9126 , HOH A:9753 , HOH A:9773
BINDING SITE FOR RESIDUE EDO A 9007
13
CC3
SOFTWARE
GLN A:257 , SER A:260 , ARG A:261 , THR A:440 , GLY A:481 , HOH A:9171
BINDING SITE FOR RESIDUE EDO A 9008
14
CC5
SOFTWARE
ASP A:456 , THR A:457 , ASP A:458 , SER A:459
BINDING SITE FOR RESIDUE EDO A 9010
15
CC6
SOFTWARE
ILE A:269 , ASP A:278 , HOH A:9370 , HOH A:9518 , GLY B:111
BINDING SITE FOR RESIDUE EDO A 9011
16
CC7
SOFTWARE
HIS A:485 , GLU A:486 , GLY A:516
BINDING SITE FOR RESIDUE EDO A 9012
17
CC8
SOFTWARE
GLU A:338 , THR A:443 , ALA A:447 , HOH A:9089 , HOH A:9669 , HOH A:9672 , HOH A:9674
BINDING SITE FOR RESIDUE EDO A 9013
18
CC9
SOFTWARE
ILE A:504 , GLU A:515 , LYS A:525 , HOH A:9320
BINDING SITE FOR RESIDUE EDO A 9014
[
close Site info
]
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 A, )
2: VAR_DPOL_BPPH2_002 (A355V, chain A, )
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
A
176
R
2
UniProt
VAR_DPOL_BPPH2_002
*
A
355
V
DPOL_BPPH2
---
---
A
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 (A: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
A:454-462
-
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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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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
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
[
close SCOP info
]
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)
View:
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)
Topologies
(
)
(
)
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
[
close CATH info
]
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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]
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Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (235 KB)
Header - Asym.Unit
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