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.
1KQR
Asym. Unit
Info
Asym.Unit (38 KB)
Biol.Unit 1 (34 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 THE RHESUS ROTAVIRUS VP4 SIALIC ACID BINDING DOMAIN IN COMPLEX WITH 2-O-METHYL-ALPHA-D-N-ACETYL NEURAMINIC ACID
Authors
:
P. R. Dormitzer, Z. -Y. J. Sun, G. Wagner, S. C. Harrison
Date
:
07 Jan 02 (Deposition) - 27 Mar 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.40
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Rotavirus, Vp4, Vp8*, Spike Protein, Outer Capsid, Sialic Acid, Hemagglutinin, Cell Attachment, Neutralization Antigen, Lectin, Galectin Fold, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. R. Dormitzer, Z. -Y. J. Sun, G. Wagner, S. C. Harrison
The Rhesus Rotavirus Vp4 Sialic Acid Binding Domain Has A Galectin Fold With A Novel Carbohydrate Binding Site
Embo J. V. 21 885 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 3)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
2a: 2-O-METHYL-5-N-ACETYL-ALPHA-D- NEU... (MNAa)
3a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
MNA
1
Ligand/Ion
2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID
3
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:134 , GLN A:135 , THR A:136 , HOH A:2080
BINDING SITE FOR RESIDUE SO4 A 3000
2
AC2
SOFTWARE
ARG A:101 , THR A:113 , ASN A:132 , ALA A:133 , THR A:146 , TYR A:155 , LYS A:187 , TYR A:188 , TYR A:189 , SER A:190 , HOH A:2003 , HOH A:2028 , HOH A:2034 , HOH A:2035 , HOH A:2038 , HOH A:2127 , HOH A:2183
BINDING SITE FOR RESIDUE MNA A 1000
3
AC3
SOFTWARE
MET A:168 , HIS A:170 , TYR A:175 , THR A:186 , ARG A:210 , GLU A:213
BINDING SITE FOR RESIDUE GOL A 4000
[
close Site info
]
SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_VP4_ROTRH_001 (T146S, chain A, )
2: VAR_VP4_ROTRH_002 (A166G, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_VP4_ROTRH_001
*
T
146
S
VP4_ROTRH
---
---
A
T
146
S
2
UniProt
VAR_VP4_ROTRH_002
*
A
166
G
VP4_ROTRH
---
---
A
A
166
G
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1kqra_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
vp4 sialic acid binding domain
(10)
Protein domain
:
vp4 sialic acid binding domain
(6)
Rhesus rotavirus [TaxId: 10969]
(6)
1a
d1kqra_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1kqrA00 (A:65-224)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Rhesus rotavirus. Organism_taxid: 10969.
(2)
1a
1kqrA00
A:65-224
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_VP4_haemagglut_1kqrA01 (A:65-224)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: VP4_haemagglut]
(5)
Family
:
VP4_haemagglut
(5)
Rotavirus A (strain Monkey/United States/RRV/1980 G3-P5B[3]-I2-R2-C3-M3-A9-Nx-T3-E3-H6) (RV-A)
(5)
1a
VP4_haemagglut-1kqrA01
A:65-224
[
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 (38 KB)
Header - Asym.Unit
Biol.Unit 1 (34 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
1KQR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
