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.
2XHU
Biol. Unit 1
Info
Asym.Unit (389 KB)
Biol.Unit 1 (195 KB)
Biol.Unit 2 (193 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HCV-J4 NS5B POLYMERASE ORTHORHOMBIC CRYSTAL FORM
Authors
:
D. Harrus, N. Ahmed-El-Sayed, P. C. Simister, S. Miller, M. Triconnet, C. H. Hagedorn, K. Mahias, F. A. Rey, T. Astier-Gin, S. Bressanelli
Date
:
21 Jun 10 (Deposition) - 04 Aug 10 (Release) - 30 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.29
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Replication, Transcription, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Harrus, N. Ahmed-El-Sayed, P. C. Simister, S. Miller, M. Triconnet C. H. Hagedorn, K. Mahias, F. A. Rey, T. Astier-Gin, S. Bressanelli
Further Insights Into The Roles Of Gtp And The C- Terminus Of The Hepatitis C Virus Polymerase In The Initiation Of Rna Synthesis
J. Biol. Chem. V. 285 32906 2010
[
close entry info
]
Hetero Components
(1, 8)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
1g: SULFATE ION (SO4g)
1h: SULFATE ION (SO4h)
1i: SULFATE ION (SO4i)
1j: SULFATE ION (SO4j)
1k: SULFATE ION (SO4k)
1l: SULFATE ION (SO4l)
1m: SULFATE ION (SO4m)
1n: SULFATE ION (SO4n)
1o: SULFATE ION (SO4o)
1p: SULFATE ION (SO4p)
1q: SULFATE ION (SO4q)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: BC6 (SOFTWARE)
10: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:141 , GLN A:446 , SER A:556 , GLY A:557 , HOH A:2298 , HOH A:2305 , HOH A:2306
BINDING SITE FOR RESIDUE SO4 A1001
02
AC2
SOFTWARE
ARG A:48 , LYS A:51 , ARG A:158 , ARG A:222 , CYS A:223 , HOH A:2046 , HOH A:2175 , HOH A:2307 , HOH A:2308
BINDING SITE FOR RESIDUE SO4 A1002
03
AC3
SOFTWARE
GLU A:143 , PHE A:145 , LYS A:155 , ARG A:158 , SER A:367 , ARG A:386 , THR A:390 , ARG A:394 , HOH A:2260 , HOH A:2309 , HOH A:2310
BINDING SITE FOR RESIDUE SO4 A1003
04
AC4
SOFTWARE
ARG A:114 , PRO B:22 , ILE B:23 , ASN B:24 , ALA B:400 , ARG B:401
BINDING SITE FOR RESIDUE SO4 A1567
05
AC5
SOFTWARE
SER A:84 , ILE A:85 , ARG A:120 , HOH A:2311
BINDING SITE FOR RESIDUE SO4 A1568
06
AC6
SOFTWARE
GLY A:516 , ARG A:517
BINDING SITE FOR RESIDUE SO4 A1569
07
AC7
SOFTWARE
ARG A:43 , HOH A:2034
BINDING SITE FOR RESIDUE SO4 A1570
08
AC8
SOFTWARE
VAL A:530 , ARG A:531 , THR A:532
BINDING SITE FOR RESIDUE SO4 A1571
09
BC6
SOFTWARE
GLU A:124 , GLU B:131 , HIS B:502 , SER B:506 , SO4 B:1567 , HOH B:2411
BINDING SITE FOR RESIDUE SO4 B1570
10
BC7
SOFTWARE
LYS A:79 , ASP A:244 , LEU B:60 , ARG B:65 , HOH B:2412 , HOH B:2413
BINDING SITE FOR RESIDUE SO4 B1571
[
close Site info
]
SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_POLG_HCVJ4_028 (C366R, chain A, )
2: VAR_POLG_HCVJ4_029 (I405V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_POLG_HCVJ4_028
*
C
2785
R
POLG_HCVJ4
---
---
A
C
366
R
2
UniProt
VAR_POLG_HCVJ4_029
*
I
2824
V
POLG_HCVJ4
---
---
A
I
405
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RDRP_SSRNA_POS (A:214-332)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RDRP_SSRNA_POS
PS50507
RdRp of positive ssRNA viruses catalytic domain profile.
POLG_HCVJ4
2633-2751
1
A:214-332
-
[
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2xhua_ (A:)
1b: SCOP_d2xhub_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
RNA-dependent RNA-polymerase
(253)
Protein domain
:
automated matches
(100)
Hepatitis C virus [TaxId: 11103]
(35)
1a
d2xhua_
A:
1b
d2xhub_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_RdRP_3_2xhuB01 (B:3-514)
1b: PFAM_RdRP_3_2xhuB02 (B:3-514)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
RdRP
(210)
Family
:
RdRP_3
(43)
Hepatitis C virus genotype 1b (strain HC-J4) (HCV)
(8)
1a
RdRP_3-2xhuB01
B:3-514
1b
RdRP_3-2xhuB02
B:3-514
[
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:
Asym.Unit (389 KB)
Header - Asym.Unit
Biol.Unit 1 (195 KB)
Header - Biol.Unit 1
Biol.Unit 2 (193 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
2XHU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help