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.
1DUG
Asym. Unit
Info
Asym.Unit (96 KB)
Biol.Unit 1 (92 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE FIBRINOGEN G CHAIN INTEGRIN BINDING AND FACTOR XIIIA CROSSLINKING SITES OBTAINED THROUGH CARRIER PROTEIN DRIVEN CRYSTALLIZATION
Authors
:
S. Ware, J. P. Donahue, J. Hawiger, W. F. Anderson
Date
:
17 Jan 00 (Deposition) - 02 Feb 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Gamma Chain Integrin Fragment, Carrier Protein Driven Crystallization, Transferase, Blood Clotting
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Ware, J. P. Donahue, J. Hawiger, W. F. Anderson
Structure Of The Fibrinogen Gamma-Chain Integrin Binding And Factor Xiiia Cross-Linking Sites Obtained Through Carrier Protein Driven Crystallization.
Protein Sci. V. 8 2663 1999
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: GLUTATHIONE (GSHa)
1b: GLUTATHIONE (GSHb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GSH
2
Ligand/Ion
GLUTATHIONE
[
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
TYR A:6 , TRP A:7 , LEU A:12 , TRP A:40 , LYS A:44 , ASN A:53 , LEU A:54 , PRO A:55 , GLN A:66 , SER A:67 , HOH A:1243 , HOH A:1244 , HOH A:1258 , HOH A:1352 , HOH A:1363 , HOH A:1529 , HOH A:1545 , ASP B:100 , HOH B:1689 , HOH B:1711
BINDING SITE FOR RESIDUE GSH A 1239
2
AC2
SOFTWARE
ASP A:100 , HOH A:1249 , TYR B:6 , TRP B:7 , LEU B:12 , TRP B:40 , LYS B:44 , ASN B:53 , LEU B:54 , PRO B:55 , GLN B:66 , SER B:67 , HOH B:1588 , HOH B:1590 , HOH B:1605 , HOH B:1728 , HOH B:1829 , HOH B:1833 , HOH B:1840
BINDING SITE FOR RESIDUE GSH B 1587
[
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, 2)
Info
All PROSITE Patterns/Profiles
1: GST_CTER (A:84-202,B:84-202)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GST_CTER
PS50405
Soluble glutathione S-transferase C-terminal domain profile.
GST26_SCHJA
85-203
2
A:84-202
B:84-202
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1duga1 (A:81-220)
1b: SCOP_d1dugb1 (B:81-220)
2a: SCOP_d1duga2 (A:1-80)
2b: SCOP_d1dugb2 (B:1-80)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
GST C-terminal domain-like
(353)
Superfamily
:
GST C-terminal domain-like
(353)
Family
:
Glutathione S-transferase (GST), C-terminal domain
(263)
Protein domain
:
Class alpha GST
(53)
Schistosoma japonicum [TaxId: 6182]
(13)
1a
d1duga1
A:81-220
1b
d1dugb1
B:81-220
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thioredoxin fold
(994)
Superfamily
:
Thioredoxin-like
(992)
Family
:
Glutathione S-transferase (GST), N-terminal domain
(216)
Protein domain
:
Class alpha GST
(53)
Schistosoma japonicum [TaxId: 6182]
(13)
2a
d1duga2
A:1-80
2b
d1dugb2
B:1-80
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1dugA01 (A:1-80,A:186-212)
1b: CATH_1dugB01 (B:1-80,B:186-212)
2a: CATH_1dugA02 (A:81-185)
2b: CATH_1dugB02 (B:81-185)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Glutaredoxin
(620)
Homologous Superfamily
:
Glutaredoxin
(617)
Schistosoma japonicum. Organism_taxid: 6182.
(9)
1a
1dugA01
A:1-80,A:186-212
1b
1dugB01
B:1-80,B:186-212
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
(267)
Homologous Superfamily
:
[code=1.20.1050.10, no name defined]
(249)
Schistosoma japonicum. Organism_taxid: 6182.
(9)
2a
1dugA02
A:81-185
2b
1dugB02
B:81-185
[
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
Chain B
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 (96 KB)
Header - Asym.Unit
Biol.Unit 1 (92 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
1DUG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
