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2PYL
Biol. Unit 1
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Asym.Unit (119 KB)
Biol.Unit 1 (113 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
:
2.20
Chains
:
Asym. Unit : A,X,Y
Biol. Unit 1: A,X,Y (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
(3, 8)
Info
All Hetero Components
1a: 2',3'-DIDEOXYADENOSINE-5'-MONOPHOS... (2DAa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: THYMIDINE-5'-TRIPHOSPHATE (TTPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2DA
1
Mod. Nucleotide
2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE
2
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
TTP
1
Ligand/Ion
THYMIDINE-5'-TRIPHOSPHATE
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:249 , VAL A:250 , ASP A:458 , MG A:3203 , TTP A:3204 , HOH A:3274 , HOH A:3523 , HOH A:3525
BINDING SITE FOR RESIDUE MG A 3202
2
AC2
SOFTWARE
ASP A:249 , ASP A:458 , MG A:3202 , TTP A:3204 , HOH A:3525
BINDING SITE FOR RESIDUE MG A 3203
3
AC3
SOFTWARE
LEU A:253 , TYR A:254 , LYS A:371 , LYS A:383 , ASN A:387 , ASP A:458 , MG A:3202 , MG A:3203 , HOH A:3233 , HOH A:3235 , HOH A:3265 , HOH A:3274 , HOH A:3300 , HOH A:3501 , HOH A:3523 , HOH A:3524 , HOH A:3525 , HOH A:3527 , 2DA X:11 , DA Y:6 , DT Y:7
BINDING SITE FOR RESIDUE TTP A 3204
4
AC4
SOFTWARE
ILE A:158 , GLU A:291 , EDO A:1004
BINDING SITE FOR RESIDUE EDO A 1001
5
AC5
SOFTWARE
GLN A:257 , SER A:260 , THR A:440 , GLY A:481 , HOH A:3504
BINDING SITE FOR RESIDUE EDO A 1002
6
AC6
SOFTWARE
LYS A:80 , PRO A:87 , ASN A:88
BINDING SITE FOR RESIDUE EDO A 1003
7
AC7
SOFTWARE
ILE A:40 , ASN A:42 , ILE A:158 , ASN A:344 , EDO A:1001
BINDING SITE FOR RESIDUE EDO A 1004
8
AC8
SOFTWARE
TYR A:59 , ASP A:186 , ARG A:187 , MET A:188
BINDING SITE FOR RESIDUE EDO A 1005
9
AC9
SOFTWARE
LYS A:124 , THR A:189 , GLY A:191 , HOH A:3318 , DA Y:6
BINDING SITE FOR RESIDUE EDO A 1006
[
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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 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
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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, 2)
Info
All SCOP Domains
1a: SCOP_d2pyla1 (A:5-187)
2a: SCOP_d2pyla2 (A:188-575)
View:
Select:
Label:
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
d2pyla1
A: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
d2pyla2
A:188-575
[
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]
CATH Domains
(6, 6)
Info
all CATH domains
1a: CATH_2pylA01 (A:5-188)
2a: CATH_2pylA03 (A:262-359)
3a: CATH_2pylA02 (A:189-261,A:426-531)
4a: CATH_2pylA05 (A:396-425)
5a: CATH_2pylA06 (A:532-575)
6a: CATH_2pylA04 (A:360-395)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
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
2pylA01
A:5-188
Topology
:
TPR 1 domain of DNA polymerase
(8)
Homologous Superfamily
:
TPR 1 domain of DNA polymerase
(8)
[unclassified]
(6)
2a
2pylA03
A: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
2pylA02
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
2pylA05
A:396-425
Homologous Superfamily
:
DNA polymerase; domain 6
(10)
[unclassified]
(6)
5a
2pylA06
A:532-575
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(10)
[unclassified]
(7)
6a
2pylA04
A:360-395
[
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]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_DNA_pol_B_2_2pylA01 (A:49-488)
View:
Select:
Label:
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_2-2pylA01
A: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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