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2PYJ
Biol. Unit 2
Info
Asym.Unit (251 KB)
Biol.Unit 1 (121 KB)
Biol.Unit 2 (118 KB)
Biol.Unit 3 (16 KB)
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(1)
Title
:
PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE DNA AND INCOMING NUCLEOTIDE SUBSTRATES (TERNARY COMPLEX)
Authors
:
A. J. Berman, S. Kamtekar, J. L. Goodman, J. M. Lazaro, M. De Vega, L. Blanco, M. Salas, T. A. Steitz
Date
:
16 May 07 (Deposition) - 17 Jul 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.03
Chains
:
Asym. Unit : A,B,J,K,Q,R,X,Y
Biol. Unit 1: A,X,Y (1x)
Biol. Unit 2: B,Q,R (1x)
Biol. Unit 3: J,K (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
)
[
close entry info
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Hetero Components
(3, 19)
Info
All Hetero Components
1a: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTa)
1b: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTb)
2a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
2b: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCb)
2c: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCc)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3ab: 1,2-ETHANEDIOL (EDOab)
3ac: 1,2-ETHANEDIOL (EDOac)
3ad: 1,2-ETHANEDIOL (EDOad)
3ae: 1,2-ETHANEDIOL (EDOae)
3af: 1,2-ETHANEDIOL (EDOaf)
3ag: 1,2-ETHANEDIOL (EDOag)
3ah: 1,2-ETHANEDIOL (EDOah)
3ai: 1,2-ETHANEDIOL (EDOai)
3aj: 1,2-ETHANEDIOL (EDOaj)
3ak: 1,2-ETHANEDIOL (EDOak)
3al: 1,2-ETHANEDIOL (EDOal)
3am: 1,2-ETHANEDIOL (EDOam)
3an: 1,2-ETHANEDIOL (EDOan)
3ao: 1,2-ETHANEDIOL (EDOao)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: MANGANESE (II) ION (MNa)
5b: MANGANESE (II) ION (MNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DGT
1
Ligand/Ion
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3
EDO
17
Ligand/Ion
1,2-ETHANEDIOL
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
MN
-1
Ligand/Ion
MANGANESE (II) ION
[
close Hetero Component info
]
Sites
(26, 26)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC8 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC8 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC1 (SOFTWARE)
13: CC2 (SOFTWARE)
14: CC3 (SOFTWARE)
15: CC4 (SOFTWARE)
16: CC5 (SOFTWARE)
17: DC1 (SOFTWARE)
18: DC3 (SOFTWARE)
19: DC5 (SOFTWARE)
20: DC6 (SOFTWARE)
21: DC7 (SOFTWARE)
22: EC2 (SOFTWARE)
23: EC3 (SOFTWARE)
24: EC8 (SOFTWARE)
25: EC9 (SOFTWARE)
26: FC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP B:249 , VAL B:250 , ASP B:458 , DGT B:1589 , MG B:9002
BINDING SITE FOR RESIDUE MN B 9001
02
AC2
SOFTWARE
ASP B:249 , ASP B:458 , DGT B:1589 , MN B:9001 , HOH B:9084 , HOH B:9130 , DOC Q:10
BINDING SITE FOR RESIDUE MG B 9002
03
AC6
SOFTWARE
ASP B:249 , VAL B:250 , ASN B:251 , SER B:252 , LEU B:253 , TYR B:254 , LYS B:371 , LYS B:383 , ASN B:387 , TYR B:390 , THR B:457 , ASP B:458 , EDO B:2775 , MN B:9001 , MG B:9002 , HOH B:9013 , HOH B:9017 , HOH B:9047 , HOH B:9048 , HOH B:9065 , HOH B:9130 , HOH B:9150 , DOC Q:10 , DC R:6 , DG R:7
BINDING SITE FOR RESIDUE DGT B 1589
04
AC7
SOFTWARE
ARG B:491 , ASP B:503 , THR B:542 , PHE B:543 , HOH B:9125
BINDING SITE FOR RESIDUE EDO B 2762
05
AC8
SOFTWARE
ILE B:504 , MET B:506 , GLU B:515 , LYS B:525 , HOH B:9266
BINDING SITE FOR RESIDUE EDO B 2763
06
AC9
SOFTWARE
TYR B:265 , THR B:356
BINDING SITE FOR RESIDUE EDO B 2764
07
BC2
SOFTWARE
DA K:6 , EDO K:2767 , DC R:4
BINDING SITE FOR RESIDUE EDO K 2766
08
BC3
SOFTWARE
ASP B:104 , LYS B:114 , HIS B:116 , DC K:5 , DA K:6 , EDO K:2766 , DC R:4
BINDING SITE FOR RESIDUE EDO K 2767
09
BC4
SOFTWARE
PHE A:309 , THR B:368 , THR B:372 , LYS B:478 , LYS B:479 , LEU B:480 , HOH B:9026 , HOH B:9217 , HOH B:9296
BINDING SITE FOR RESIDUE EDO B 2769
10
BC8
SOFTWARE
ARG A:308 , EDO A:2774 , ASP B:365
BINDING SITE FOR RESIDUE EDO A 2773
11
BC9
SOFTWARE
EDO A:2773 , HOH A:9397 , TYR B:369
BINDING SITE FOR RESIDUE EDO A 2774
12
CC1
SOFTWARE
ASN B:251 , LYS B:371 , LYS B:379 , PRO B:477 , DGT B:1589 , HOH B:9008
BINDING SITE FOR RESIDUE EDO B 2775
13
CC2
SOFTWARE
GLY B:376 , LYS B:379
BINDING SITE FOR RESIDUE EDO B 2776
14
CC3
SOFTWARE
HIS A:149 , LYS A:150 , GLU A:151 , GLU B:334 , GLU B:338 , TRP B:436 , TYR B:439
BINDING SITE FOR RESIDUE EDO B 2777
15
CC4
SOFTWARE
ARG B:227 , THR B:301 , ILE B:302 , GLN B:303 , ASP B:332 , ARG B:438 , HOH B:9097 , HOH B:9122
BINDING SITE FOR RESIDUE EDO B 2778
16
CC5
SOFTWARE
GLU A:151 , PRO A:153 , PRO B:282 , HOH B:9287
BINDING SITE FOR RESIDUE EDO B 2779
17
DC1
SOFTWARE
DT Q:8 , DA Q:9 , DOC Q:10 , HOH Q:2791 , HOH Q:2796 , HOH Q:2799 , HOH Q:2800
BINDING SITE FOR RESIDUE EDO Q 2785
18
DC3
SOFTWARE
MET B:4 , GLU B:291 , HOH B:9324
BINDING SITE FOR RESIDUE EDO B 2787
19
DC5
SOFTWARE
SER A:551 , GLU B:33 , LYS B:182 , GLU B:296 , HOH B:9277
BINDING SITE FOR RESIDUE EDO B 2789
20
DC6
SOFTWARE
ARG A:552 , MET A:554 , EDO A:2803 , ASP B:34 , GLU B:296
BINDING SITE FOR RESIDUE EDO A 2790
21
DC7
SOFTWARE
TYR B:29 , SER B:36 , TYR B:38
BINDING SITE FOR RESIDUE EDO B 2791
22
EC2
SOFTWARE
HOH B:9202
BINDING SITE FOR RESIDUE EDO B 2795
23
EC3
SOFTWARE
ARG B:496 , LYS B:575 , DG R:11 , DC R:12
BINDING SITE FOR RESIDUE EDO R 2796
24
EC8
SOFTWARE
PHE A:309 , TYR A:310 , SER A:319 , GLY A:320 , THR B:372 , LYS B:478
BINDING SITE FOR RESIDUE EDO B 2802
25
EC9
SOFTWARE
GLY A:549 , PHE A:550 , SER A:551 , ARG A:552 , EDO A:2790 , HOH A:9198 , GLU B:33 , ASP B:34 , HIS B:35
BINDING SITE FOR RESIDUE EDO A 2803
26
FC2
SOFTWARE
LYS A:150 , SER B:260 , ARG B:261 , HOH B:9037
BINDING SITE FOR RESIDUE EDO B 2805
[
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 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)
[
close SNP/Variant info
]
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
View:
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Label:
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_d2pyja1 (A:5-187)
1b: SCOP_d2pyjb1 (B:3-187)
2a: SCOP_d2pyja2 (A:188-575)
2b: SCOP_d2pyjb2 (B:188-575)
View:
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Classes
(
)
(
)
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)
(
)
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(
)
(
)
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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
d2pyja1
A:5-187
1b
d2pyjb1
B:3-187
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
d2pyja2
A:188-575
2b
d2pyjb2
B:188-575
[
close SCOP info
]
CATH Domains
(6, 12)
Info
all CATH domains
1a: CATH_2pyjA01 (A:5-188)
1b: CATH_2pyjB01 (B:3-188)
2a: CATH_2pyjA03 (A:262-359)
2b: CATH_2pyjB03 (B:262-359)
3a: CATH_2pyjB02 (B:189-261,B:426-531)
3b: CATH_2pyjA02 (A:189-261,A:426-531)
4a: CATH_2pyjA05 (A:396-425)
4b: CATH_2pyjB05 (B:396-425)
5a: CATH_2pyjA06 (A:532-575)
5b: CATH_2pyjB06 (B:532-575)
6a: CATH_2pyjA04 (A:360-395)
6b: CATH_2pyjB04 (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
2pyjA01
A:5-188
1b
2pyjB01
B:3-188
Topology
:
TPR 1 domain of DNA polymerase
(8)
Homologous Superfamily
:
TPR 1 domain of DNA polymerase
(8)
[unclassified]
(6)
2a
2pyjA03
A:262-359
2b
2pyjB03
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
2pyjB02
B:189-261,B:426-531
3b
2pyjA02
A:189-261,A: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
2pyjA05
A:396-425
4b
2pyjB05
B:396-425
Homologous Superfamily
:
DNA polymerase; domain 6
(10)
[unclassified]
(6)
5a
2pyjA06
A:532-575
5b
2pyjB06
B:532-575
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(10)
[unclassified]
(7)
6a
2pyjA04
A:360-395
6b
2pyjB04
B:360-395
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_DNA_pol_B_2_2pyjB01 (B:49-488)
1b: PFAM_DNA_pol_B_2_2pyjB02 (B:49-488)
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Clans
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(
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Families
(
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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_2-2pyjB01
B:49-488
1b
DNA_pol_B_2-2pyjB02
B:49-488
[
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