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.
2ZVL
Biol. Unit 1
Info
Asym.Unit (254 KB)
Biol.Unit 1 (126 KB)
Biol.Unit 2 (124 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF PCNA IN COMPLEX WITH DNA POLYMERASE KAPPA FRAGMENT
Authors
:
A. Hishiki, H. Hashimoto, T. Hanafusa, K. Kamei, E. Ohashi, T. Shimizu, M. Sato
Date
:
11 Nov 08 (Deposition) - 10 Feb 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,U,V,W,X,Y,Z
Biol. Unit 1: A,B,C,U,V,W (1x)
Biol. Unit 2: D,E,F,X,Y,Z (1x)
Keywords
:
Dna Replication, Pcna, Clamp, Translesion Synthesis, Tls, Dna Polymerase, Tls Polymerase, Complex, Pip-Box, Dna Polymerase Kappa, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Hishiki, H. Hashimoto, T. Hanafusa, K. Kamei, E. Ohashi, T. Shimizu H. Ohmori, M. Sato
Structural Basis For Novel Interactions Between Human Translesion Synthesis Polymerases And Proliferating Cell Nuclear Antigen
J. Biol. Chem. V. 284 10552 2009
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
2
Ligand/Ion
SULFATE ION
2
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC7 (SOFTWARE)
6: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS B:44 , ASP C:58 , HIS V:863 , ASP V:866
BINDING SITE FOR RESIDUE ZN V 1
2
AC2
SOFTWARE
ASP A:58 , HIS C:44 , HIS W:863 , ASP W:866
BINDING SITE FOR RESIDUE ZN W 2
3
AC5
SOFTWARE
GLU B:55 , HIS E:246 , HOH E:374
BINDING SITE FOR RESIDUE ZN E 262
4
AC6
SOFTWARE
HIS B:246 , HOH B:375 , GLU E:55
BINDING SITE FOR RESIDUE ZN B 262
5
AC7
SOFTWARE
GLU A:238 , GLY A:245 , HIS A:246
BINDING SITE FOR RESIDUE SO4 A 262
6
AC8
SOFTWARE
ARG C:53 , GLU C:238 , GLY C:245 , HIS C:246
BINDING SITE FOR RESIDUE SO4 C 262
[
close Site info
]
SAPs(SNPs)/Variants
(1, 3)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_071871 (S228I, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_071871
S
228
I
PCNA_HUMAN
Disease (ATLD2)
---
A/B/C
S
228
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: PCNA_1 (A:34-57,B:34-57,C:34-57)
2: PCNA_2 (A:61-79,B:61-79,C:61-79)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PCNA_1
PS01251
Proliferating cell nuclear antigen signature 1.
PCNA_HUMAN
34-57
3
A:34-57
B:34-57
C:34-57
-
-
-
2
PCNA_2
PS00293
Proliferating cell nuclear antigen signature 2.
PCNA_HUMAN
61-79
3
A:61-79
B:61-79
C:61-79
-
-
-
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2zvlB00 (B:1-255)
1b: CATH_2zvlA00 (A:1-255)
1c: CATH_2zvlE00 (E:1-255)
1d: CATH_2zvlF00 (F:1-255)
1e: CATH_2zvlC00 (C:1-255)
1f: CATH_2zvlD00 (D:1-255)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Box
(41)
Topology
:
Proliferating Cell Nuclear Antigen
(41)
Homologous Superfamily
:
[code=3.70.10.10, no name defined]
(41)
Human (Homo sapiens)
(10)
1a
2zvlB00
B:1-255
1b
2zvlA00
A:1-255
1c
2zvlE00
E:1-255
1d
2zvlF00
F:1-255
1e
2zvlC00
C:1-255
1f
2zvlD00
D:1-255
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_PCNA_C_2zvlF01 (F:127-254)
1b: PFAM_PCNA_C_2zvlF02 (F:127-254)
1c: PFAM_PCNA_C_2zvlF03 (F:127-254)
1d: PFAM_PCNA_C_2zvlF04 (F:127-254)
1e: PFAM_PCNA_C_2zvlF05 (F:127-254)
1f: PFAM_PCNA_C_2zvlF06 (F:127-254)
2a: PFAM_PCNA_N_2zvlF07 (F:1-125)
2b: PFAM_PCNA_N_2zvlF08 (F:1-125)
2c: PFAM_PCNA_N_2zvlF09 (F:1-125)
2d: PFAM_PCNA_N_2zvlF10 (F:1-125)
2e: PFAM_PCNA_N_2zvlF11 (F:1-125)
2f: PFAM_PCNA_N_2zvlF12 (F:1-125)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
DNA_clamp
(33)
Family
:
PCNA_C
(23)
Homo sapiens (Human)
(9)
1a
PCNA_C-2zvlF01
F:127-254
1b
PCNA_C-2zvlF02
F:127-254
1c
PCNA_C-2zvlF03
F:127-254
1d
PCNA_C-2zvlF04
F:127-254
1e
PCNA_C-2zvlF05
F:127-254
1f
PCNA_C-2zvlF06
F:127-254
Family
:
PCNA_N
(25)
Homo sapiens (Human)
(9)
2a
PCNA_N-2zvlF07
F:1-125
2b
PCNA_N-2zvlF08
F:1-125
2c
PCNA_N-2zvlF09
F:1-125
2d
PCNA_N-2zvlF10
F:1-125
2e
PCNA_N-2zvlF11
F:1-125
2f
PCNA_N-2zvlF12
F:1-125
[
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 A
Chain B
Chain C
Chain U
Chain V
Chain W
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 (254 KB)
Header - Asym.Unit
Biol.Unit 1 (126 KB)
Header - Biol.Unit 1
Biol.Unit 2 (124 KB)
Header - Biol.Unit 2
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
2ZVL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
