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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3P83
Asym. Unit
Info
Asym.Unit (451 KB)
Biol.Unit 1 (445 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE PCNA:RNASE HII COMPLEX FROM ARCHAEOGLOBUS FULGIDUS.
Authors
:
D. Bubeck, M. A. Reijns, S. C. Graham, K. R. Astell, E. Y. Jones, A. P. Jack
Date
:
13 Oct 10 (Deposition) - 02 Feb 11 (Release) - 08 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.05
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Dna Clamp, Rnase H Fold, Cleaves Rna/Dna Hybrids, Nucleus, Hydrolase- Dna Binding Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Bubeck, M. A. Reijns, S. C. Graham, K. R. Astell, E. Y. Jones, A. P. Jackson
Pcna Directs Type 2 Rnase H Activity On Dna Replication And Repair Substrates.
Nucleic Acids Res. V. 39 3652 2011
[
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
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: PCNA_1 (A:33-56,B:33-56,C:33-56)
;
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_ARCFU
33-56
3
A:33-56
B:33-56
C:33-56
[
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.
SCOP Domains
(2, 9)
Info
All SCOP Domains
1a: SCOP_d3p83a1 (A:1-122)
1b: SCOP_d3p83a2 (A:123-244)
1c: SCOP_d3p83b1 (B:1-122)
1d: SCOP_d3p83b2 (B:123-244)
1e: SCOP_d3p83c1 (C:1-122)
1f: SCOP_d3p83c2 (C:123-243)
2a: SCOP_d3p83d_ (D:)
2b: SCOP_d3p83e_ (E:)
2c: SCOP_d3p83f_ (F:)
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
:
automated matches
(10)
Archaeoglobus fulgidus [TaxId: 2234]
(1)
1a
d3p83a1
A:1-122
1b
d3p83a2
A:123-244
1c
d3p83b1
B:1-122
1d
d3p83b2
B:123-244
1e
d3p83c1
C:1-122
1f
d3p83c2
C:123-243
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
automated matches
(127)
Protein domain
:
automated matches
(127)
Archaeoglobus fulgidus [TaxId: 2234]
(1)
2a
d3p83d_
D:
2b
d3p83e_
E:
2c
d3p83f_
F:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(3, 9)
Info
all PFAM domains
1a: PFAM_PCNA_C_3p83C01 (C:121-241)
1b: PFAM_PCNA_C_3p83C02 (C:121-241)
1c: PFAM_PCNA_C_3p83C03 (C:121-241)
2a: PFAM_PCNA_N_3p83C04 (C:1-110)
2b: PFAM_PCNA_N_3p83C05 (C:1-110)
2c: PFAM_PCNA_N_3p83C06 (C:1-110)
3a: PFAM_RNase_HII_3p83F01 (F:3-194)
3b: PFAM_RNase_HII_3p83F02 (F:3-194)
3c: PFAM_RNase_HII_3p83F03 (F:3-194)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
DNA_clamp
(33)
Family
:
PCNA_C
(23)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
(4)
1a
PCNA_C-3p83C01
C:121-241
1b
PCNA_C-3p83C02
C:121-241
1c
PCNA_C-3p83C03
C:121-241
Family
:
PCNA_N
(25)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
(4)
2a
PCNA_N-3p83C04
C:1-110
2b
PCNA_N-3p83C05
C:1-110
2c
PCNA_N-3p83C06
C:1-110
Clan
:
RNase_H
(288)
Family
:
RNase_HII
(8)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
(1)
3a
RNase_HII-3p83F01
F:3-194
3b
RNase_HII-3p83F02
F:3-194
3c
RNase_HII-3p83F03
F:3-194
[
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
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 (451 KB)
Header - Asym.Unit
Biol.Unit 1 (445 KB)
Header - Biol.Unit 1
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
3P83
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help