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.
1OPO
Asym. Unit
Info
Asym.Unit (134 KB)
Biol.Unit 1, α-C (7.2 MB)
Biol.Unit 1 (7.2 MB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE STRUCTURE OF CARNATION MOTTLE VIRUS
Authors
:
E. Morgunova, Z. Dauter, E. Fry, D. Stuart, V. Stel'Mashchuk, A. M. Mikhailov, K. S. Wilson, B. K. Vainshtein
Date
:
06 Mar 03 (Deposition) - 01 Apr 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (60x)
Keywords
:
Plant Virus, Carmovirus, Virus/Viral Protein, X-Ray Diffraction, Tomato Bushy Stunt Virus, Icosahedral Virus
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Morgunova, Z. Dauter, E. Fry, D. Stuart, V. Stel'Mashchuk, A. M. Mikhailov, K. S. Wilson, B. K. Vainshtein
The Atomic Structure Of Carnation Mottle Virus Capsid Protein
Febs Lett. V. 338 267 1994
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:164 , THR A:165 , THR A:166 , GLY A:169 , LYS B:244
BINDING SITE FOR RESIDUE SO4 A 500
2
AC2
SOFTWARE
PRO B:164 , THR B:165 , THR B:166 , LYS C:244 , LYS C:281
BINDING SITE FOR RESIDUE SO4 B 501
3
AC3
SOFTWARE
LYS A:244 , PRO C:163 , PRO C:164 , THR C:165 , THR C:166 , GLY C:169
BINDING SITE FOR RESIDUE SO4 C 502
4
AC4
SOFTWARE
ASP B:158 , ASP B:161 , ASN C:128 , ASP C:200
BINDING SITE FOR RESIDUE CA B 503
[
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: ICOSAH_VIR_COAT_S (A:139-164,B:139-164,C:139-164)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ICOSAH_VIR_COAT_S
PS00555
Plant viruses icosahedral capsid proteins 'S' region signature.
CAPSD_CARMV
139-164
3
A:139-164
B:139-164
C:139-164
[
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, 3)
Info
All SCOP Domains
1a: SCOP_d1opoa_ (A:)
1b: SCOP_d1opob_ (B:)
1c: SCOP_d1opoc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Nucleoplasmin-like/VP (viral coat and capsid proteins)
(278)
Superfamily
:
Positive stranded ssRNA viruses
(163)
Family
:
Tombusviridae-like VP
(13)
Protein domain
:
Carmovirus coat protein
(1)
CarMV (Carnation mottle virus) [TaxId: 11986]
(1)
1a
d1opoa_
A:
1b
d1opob_
B:
1c
d1opoc_
C:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1opoC01 (C:81-245)
1b: CATH_1opoA01 (A:82-245)
1c: CATH_1opoB01 (B:82-245)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.20, no name defined]
(133)
CaRNAtion mottle virus. Organism_taxid: 11986
(1)
1a
1opoC01
C:81-245
1b
1opoA01
A:82-245
1c
1opoB01
B:82-245
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Viral_coat_1opoC01 (C:81-246)
1b: PFAM_Viral_coat_1opoC02 (C:81-246)
1c: PFAM_Viral_coat_1opoC03 (C:81-246)
2a: PFAM_Carmo_coat_C_1opoC04 (C:250-348)
2b: PFAM_Carmo_coat_C_1opoC05 (C:250-348)
2c: PFAM_Carmo_coat_C_1opoC06 (C:250-348)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Viral_ssRNA_CP
(106)
Family
:
Viral_coat
(12)
Carnation mottle virus (CarMV)
(1)
1a
Viral_coat-1opoC01
C:81-246
1b
Viral_coat-1opoC02
C:81-246
1c
Viral_coat-1opoC03
C:81-246
Clan
:
no clan defined [family: Carmo_coat_C]
(1)
Family
:
Carmo_coat_C
(1)
Carnation mottle virus (CarMV)
(1)
2a
Carmo_coat_C-1opoC04
C:250-348
2b
Carmo_coat_C-1opoC05
C:250-348
2c
Carmo_coat_C-1opoC06
C:250-348
[
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
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 (134 KB)
Header - Asym.Unit
Biol.Unit 1 (7.2 MB)
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
1OPO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
