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.
2CB7
Theor. Model
Info
Theoretical Model (156 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
COMPUTATIONAL MODEL STRUCTURE OF HIV-2 POL POLYPROTEIN
Authors
:
C. Baruah, A. Das, S. Mahanta
Date
:
30 Dec 05 (Deposition) - 09 Jan 06 (Release) - 09 Jan 06 (Revision)
Method
:
THEORETICAL MODEL
Resolution
:
NOT APPLICABLE
Chains
:
Theor. Model : A
Keywords
:
Aspartyl Protease, Endonuclease, Hydrolase, Nuclease, Polyprotein, Transferase, Aids, Capsid Maturation, Core Protein, Dna Integration, Dna Recombination, Dna-Directed Dna Polymerase, Endonuclease, Lipoprotein, Metal-Binding, Multifunctional Enzyme, Myristate, Nucleotidyltransferase, Rna-Binding, Rna-Directed Dna Polymerase, Viral Nucleoprotein, Zinc-Finger
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Baruah, A. Das, S. Mahanta
Theoretical Model Structure Of Hiv-2 Pol Polyprotein
To Be Published
(for further references see the
PDB file header
)
[
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
(8, 9)
Info
All PROSITE Patterns/Profiles
1: ZF_CCHC (A:7-7|A:14-16)
2: ASP_PROT_RETROV (A:118-187)
3: ASP_PROTEASE (A:120-131)
4: RT_POL (A:241-431)
5: RNASE_H (A:630-753)
6: ZF_INTEGRASE (A:759-800)
7: INTEGRASE (A:809-960)
8: INTEGRASE_DBD (A:979-1026)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZF_CCHC
PS50158
Zinc finger CCHC-type profile.
POL_HV2G1
391-406
413-428
2
A:7-7
A:14-16
2
ASP_PROT_RETROV
PS50175
Aspartyl protease, retroviral-type family profile.
POL_HV2G1
533-602
1
A:118-187
3
ASP_PROTEASE
PS00141
Eukaryotic and viral aspartyl proteases active site.
POL_HV2G1
535-546
1
A:120-131
4
RT_POL
PS50878
Reverse transcriptase (RT) catalytic domain profile.
POL_HV2G1
656-846
1
A:241-431
5
RNASE_H
PS50879
RNase H domain profile.
POL_HV2G1
1045-1168
1
A:630-753
6
ZF_INTEGRASE
PS50876
Zinc finger integrase-type profile.
POL_HV2G1
1174-1215
1
A:759-800
7
INTEGRASE
PS50994
Integrase catalytic domain profile.
POL_HV2G1
1224-1375
1
A:809-960
8
INTEGRASE_DBD
PS51027
Integrase DNA binding domain profile.
POL_HV2G1
1394-1441
1
A:979-1026
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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:
Theoretical Model (156 KB)
Header - Theoretical Model
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
2CB7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
