PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
2PYJ
Biol. Unit 3
Info
Asym.Unit (251 KB)
Biol.Unit 1 (121 KB)
Biol.Unit 2 (118 KB)
Biol.Unit 3 (16 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(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
]
Hetero Components
(2, 4)
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
3
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
(3, 3)
Info
All Sites
1: BC1 (SOFTWARE)
2: BC2 (SOFTWARE)
3: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
BC1
SOFTWARE
DA K:6 , DA K:10 , HOH K:1218
BINDING SITE FOR RESIDUE EDO K 2765
2
BC2
SOFTWARE
DA K:6 , EDO K:2767 , DC R:4
BINDING SITE FOR RESIDUE EDO K 2766
3
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
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
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:
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
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:
Select:
Label:
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
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)
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_2-2pyjB01
B:49-488
1b
DNA_pol_B_2-2pyjB02
B:49-488
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain J
Chain K
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (251 KB)
Header - Asym.Unit
Biol.Unit 1 (121 KB)
Header - Biol.Unit 1
Biol.Unit 2 (118 KB)
Header - Biol.Unit 2
Biol.Unit 3 (16 KB)
Header - Biol.Unit 3
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2PYJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help