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.
PLEASE WAIT...
Getting 'Exon' information from database.
1VYJ
Asym. Unit
Info
Asym.Unit (268 KB)
Biol.Unit 1 (136 KB)
Biol.Unit 2 (136 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURAL AND BIOCHEMICAL STUDIES OF HUMAN PCNA COMPLEXES PROVIDE THE BASIS FOR ASSOCIATION WITH CDK/CYCLIN AND RATIONALE FOR INHIBITOR DESIGN
Authors
:
G. Kontopidis, S. Wu, D. Zheleva, P. Taylor, C. Mcinnes, D. Lane, P. Fischer, M. D. Walkinshaw
Date
:
30 Apr 04 (Deposition) - 13 Jan 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Dna, Replication, Processivity, Oncogene, Dna-Binding Protein, Dna Replication, Dna-Binding Systemic Lupus Erythematosus
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Kontopidis, S. Wu, D. Zheleva, P. Taylor, C. Mcinnes, D. Lane, P. Fischer, M. D. Walkinshaw
Structural And Biochemical Studies Of Human Proliferating Cell Nuclear Antigen Complexes Provide A Rationale For Cyclin Association And Inhibitor Design
Proc. Natl. Acad. Sci. Usa V. 102 1871 2005
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(1, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_071871 (S228I, chain A/C/E/G/I/K, )
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/C/E/G/I/K
S
228
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: PCNA_1 (A:34-57,C:34-57,E:34-57,G:34-57,I:...)
2: PCNA_2 (A:61-79,C:61-79,E:61-79,G:61-79,I:...)
;
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
6
A:34-57
C:34-57
E:34-57
G:34-57
I:34-57
K:34-57
2
PCNA_2
PS00293
Proliferating cell nuclear antigen signature 2.
PCNA_HUMAN
61-79
6
A:61-79
C:61-79
E:61-79
G:61-79
I:61-79
K:61-79
[
close PROSITE info
]
Exons
(6, 36)
Info
All Exons
Exon 1.2b (A:1-74 | C:1-74 | E:1-74 | G:1-74 ...)
Exon 1.3 (A:74-107 | C:74-107 | E:74-107 | G...)
Exon 1.4 (A:107-129 | C:107-129 | E:107-129 ...)
Exon 1.5 (A:130-194 | C:130-194 | E:130-194 ...)
Exon 1.6 (A:195-236 | C:195-236 | E:195-236 ...)
Exon 1.7 (A:236-257 | C:236-257 | E:236-257 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2b
2: Boundary 1.2b/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7
7: Boundary 1.7/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000379160
1
ENSE00001480155
chr20:
5107272-5107146
127
PCNA_HUMAN
-
0
0
-
-
1.2b
ENST00000379160
2b
ENSE00001480145
chr20:
5100560-5100224
337
PCNA_HUMAN
1-74
74
6
A:1-74
C:1-74
E:1-74
G:1-74
I:1-74
K:1-74
74
74
74
74
74
74
1.3
ENST00000379160
3
ENSE00001747465
chr20:
5099512-5099415
98
PCNA_HUMAN
74-107
34
6
A:74-107
C:74-107
E:74-107
G:74-107
I:74-107
K:74-107
34
34
34
34
34
34
1.4
ENST00000379160
4
ENSE00001693283
chr20:
5099323-5099256
68
PCNA_HUMAN
107-129
23
6
A:107-129
C:107-129
E:107-129
G:107-129
I:107-129
K:107-129
23
23
23
23
23
23
1.5
ENST00000379160
5
ENSE00000906721
chr20:
5098310-5098116
195
PCNA_HUMAN
130-194
65
6
A:130-194
C:130-194
E:130-194
G:130-194
I:130-194
K:130-194
65
65
65
65
65
65
1.6
ENST00000379160
6
ENSE00000906720
chr20:
5096218-5096095
124
PCNA_HUMAN
195-236
42
6
A:195-236
C:195-236
E:195-236
G:195-236
I:195-236
K:195-236
42
42
42
42
42
42
1.7
ENST00000379160
7
ENSE00000906719
chr20:
5096008-5095599
410
PCNA_HUMAN
236-261
26
6
A:236-257
C:236-257
E:236-257
G:236-260
I:236-257
K:236-257
22
22
22
25
22
22
[
close EXON info
]
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1vyja1 (A:1-126)
1b: SCOP_d1vyja2 (A:127-257)
1c: SCOP_d1vyjc1 (C:1-126)
1d: SCOP_d1vyjc2 (C:127-257)
1e: SCOP_d1vyje1 (E:1-126)
1f: SCOP_d1vyje2 (E:127-257)
1g: SCOP_d1vyjg1 (G:1-126)
1h: SCOP_d1vyjg2 (G:127-260)
1i: SCOP_d1vyji1 (I:1-126)
1j: SCOP_d1vyji2 (I:127-257)
1k: SCOP_d1vyjk1 (K:1-126)
1l: SCOP_d1vyjk2 (K:127-257)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DNA clamp
(88)
Superfamily
:
DNA clamp
(88)
Family
:
DNA polymerase processivity factor
(40)
Protein domain
:
Proliferating cell nuclear antigen (PCNA)
(24)
Human (Homo sapiens) [TaxId: 9606]
(9)
1a
d1vyja1
A:1-126
1b
d1vyja2
A:127-257
1c
d1vyjc1
C:1-126
1d
d1vyjc2
C:127-257
1e
d1vyje1
E:1-126
1f
d1vyje2
E:127-257
1g
d1vyjg1
G:1-126
1h
d1vyjg2
G:127-260
1i
d1vyji1
I:1-126
1j
d1vyji2
I:127-257
1k
d1vyjk1
K:1-126
1l
d1vyjk2
K:127-257
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1vyjA00 (A:1-257)
1b: CATH_1vyjC00 (C:1-257)
1c: CATH_1vyjE00 (E:1-257)
1d: CATH_1vyjI00 (I:1-257)
1e: CATH_1vyjK00 (K:1-257)
1f: CATH_1vyjG00 (G:1-260)
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
1vyjA00
A:1-257
1b
1vyjC00
C:1-257
1c
1vyjE00
E:1-257
1d
1vyjI00
I:1-257
1e
1vyjK00
K:1-257
1f
1vyjG00
G:1-260
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
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 (268 KB)
Header - Asym.Unit
Biol.Unit 1 (136 KB)
Header - Biol.Unit 1
Biol.Unit 2 (136 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
1VYJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help