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.
2OJ5
Biol. Unit 1
Info
Asym.Unit (335 KB)
Biol.Unit 1 (167 KB)
Biol.Unit 2 (167 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 REOVIRUS T3D ATTACHMENT PROTEIN SIGMA1 HEAD DOMAIN WILD-TYPE AT 1.75 A RESOLUTION
Authors
:
T. Stehle, P. Schelling, E. Kirchner, T. S. Dermody
Date
:
12 Jan 07 (Deposition) - 13 Feb 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Beta-Barrel, Beta-Spiral Repeat, Aspartic Acid Cluster, Greek Key Motif, Trimer, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Schelling, K. M. Guglielmi, E. Kirchner, B. Paetzold, T. S. Dermody T. Stehle
The Reovirus Sigma1 Aspartic Acid Sandwich: A Trimerization Motif Poised For Conformational Change.
J. Biol. Chem. V. 282 11582 2007
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
2a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
MG
-1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:2146 , HOH A:2213 , HOH A:2214 , HOH A:2215 , HOH A:2216
BINDING SITE FOR RESIDUE MG A 2001
2
AC2
SOFTWARE
ASP B:365 , GLU B:419 , ARG B:427 , ARG B:429 , HOH B:2615 , GLY E:330 , ASN E:332
BINDING SITE FOR RESIDUE GOL B 2500
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 9)
Info
All SCOP Domains
1a: SCOP_d2oj5b1 (B:293-312)
1b: SCOP_d2oj5c1 (C:293-312)
1c: SCOP_d2oj5f1 (F:293-312)
2a: SCOP_d2oj5a1 (A:313-455)
2b: SCOP_d2oj5e1 (E:313-454)
2c: SCOP_d2oj5f2 (F:313-455)
2d: SCOP_d2oj5b2 (B:313-455)
2e: SCOP_d2oj5c2 (C:313-454)
2f: SCOP_d2oj5d1 (D:313-454)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Triple beta-spiral
(6)
Superfamily
:
Fibre shaft of virus attachment proteins
(6)
Family
:
automated matches
(2)
Protein domain
:
automated matches
(2)
Reovirus sp. [TaxId: 10891]
(2)
1a
d2oj5b1
B:293-312
1b
d2oj5c1
C:293-312
1c
d2oj5f1
F:293-312
Fold
:
Virus attachment protein globular domain
(47)
Superfamily
:
Virus attachment protein globular domain
(47)
Family
:
Reovirus attachment protein sigma 1 head domain
(3)
Protein domain
:
automated matches
(2)
Reovirus sp. [TaxId: 10891]
(2)
2a
d2oj5a1
A:313-455
2b
d2oj5e1
E:313-454
2c
d2oj5f2
F:313-455
2d
d2oj5b2
B:313-455
2e
d2oj5c2
C:313-454
2f
d2oj5d1
D:313-454
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Reo_sigma1_2oj5F01 (F:293-454)
1b: PFAM_Reo_sigma1_2oj5F02 (F:293-454)
1c: PFAM_Reo_sigma1_2oj5F03 (F:293-454)
1d: PFAM_Reo_sigma1_2oj5F04 (F:293-454)
1e: PFAM_Reo_sigma1_2oj5F05 (F:293-454)
1f: PFAM_Reo_sigma1_2oj5F06 (F:293-454)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Reo_sigma
(16)
Family
:
Reo_sigma1
(3)
Reovirus type 3 (strain Dearing) (T3D) (Mammalian orthoreovirus 3)
(3)
1a
Reo_sigma1-2oj5F01
F:293-454
1b
Reo_sigma1-2oj5F02
F:293-454
1c
Reo_sigma1-2oj5F03
F:293-454
1d
Reo_sigma1-2oj5F04
F:293-454
1e
Reo_sigma1-2oj5F05
F:293-454
1f
Reo_sigma1-2oj5F06
F:293-454
[
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 (335 KB)
Header - Asym.Unit
Biol.Unit 1 (167 KB)
Header - Biol.Unit 1
Biol.Unit 2 (167 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
2OJ5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help