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.
1GYG
Asym. Unit
Info
Asym.Unit (133 KB)
Biol.Unit 1 (189 KB)
Biol.Unit 2 (189 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
R32 CLOSED FORM OF ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS STRAIN CER89L43
Authors
:
A. K. Basak, J. T. Eaton, R. W. Titball
Date
:
23 Apr 02 (Deposition) - 13 Jun 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (3x)
Biol. Unit 2: B (3x)
Keywords
:
Zinc Phospholipase C, Gangrene Determinant, C2 Domain, Ca And Membrane Binding, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. T. Eaton, C. Naylor, A. Howells, D. Moss, R. W. Titball, A. K. Basak
Crystal Structure Of The C. Perfringens Alpha-Toxin With The Active Site Closed By A Flexible Loop Region
J. Mol. Biol. V. 319 275 2002
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: ZINC ION (ZNa)
1b: ZINC ION (ZNb)
1c: ZINC ION (ZNc)
1d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ZN
4
Ligand/Ion
ZINC 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
ASP A:56 , HIS A:68 , HIS A:126 , ASP A:130 , ZN A:1372
BINDING SITE FOR RESIDUE ZN A1371
2
AC2
SOFTWARE
TRP A:1 , HIS A:11 , ASP A:130 , ZN A:1371
BINDING SITE FOR RESIDUE ZN A1372
3
AC3
SOFTWARE
ASP B:56 , HIS B:68 , HIS B:126 , ASP B:130 , ZN B:1372
BINDING SITE FOR RESIDUE ZN B1371
4
AC4
SOFTWARE
TRP B:1 , HIS B:11 , ASP B:130 , ZN B:1371
BINDING SITE FOR RESIDUE ZN B1372
[
close Site info
]
SAPs(SNPs)/Variants
(15, 30)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_PHLC1_CLOPE_007 (V15A, chain A/B, )
02: VAR_PHLC1_CLOPE_008 (V19I, chain A/B, )
03: VAR_PHLC1_CLOPE_009 (L26M, chain A/B, )
04: VAR_PHLC1_CLOPE_010 (E43D, chain A/B, )
05: VAR_PHLC1_CLOPE_011 (D63N, chain A/B, )
06: VAR_PHLC1_CLOPE_012 (D75N, chain A/B, )
07: VAR_PHLC1_CLOPE_013 (H148Y, chain A/B, )
08: VAR_PHLC1_CLOPE_014 (V167V, chain A/B, )
09: VAR_PHLC1_CLOPE_015 (D174A, chain A/B, )
10: VAR_PHLC1_CLOPE_016 (A177T, chain A/B, )
11: VAR_PHLC1_CLOPE_017 (K253N, chain A/B, )
12: VAR_PHLC1_CLOPE_018 (T301A, chain A/B, )
13: VAR_PHLC1_CLOPE_019 (P335S, chain A/B, )
14: VAR_PHLC1_CLOPE_020 (V345L, chain A/B, )
15: VAR_PHLC1_CLOPE_021 (V345V, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_PHLC1_CLOPE_007
*
V
43
A
PHLC1_CLOPE
---
---
A/B
V
15
A
02
UniProt
VAR_PHLC1_CLOPE_008
*
V
47
I
PHLC1_CLOPE
---
---
A/B
V
19
I
03
UniProt
VAR_PHLC1_CLOPE_009
*
L
54
M
PHLC1_CLOPE
---
---
A/B
L
26
M
04
UniProt
VAR_PHLC1_CLOPE_010
*
E
71
D
PHLC1_CLOPE
---
---
A/B
E
43
D
05
UniProt
VAR_PHLC1_CLOPE_011
*
D
91
N
PHLC1_CLOPE
---
---
A/B
D
63
N
06
UniProt
VAR_PHLC1_CLOPE_012
*
D
103
N
PHLC1_CLOPE
---
---
A/B
D
75
N
07
UniProt
VAR_PHLC1_CLOPE_013
*
H
176
Y
PHLC1_CLOPE
---
---
A/B
H
148
Y
08
UniProt
VAR_PHLC1_CLOPE_014
*
A
195
V
PHLC1_CLOPE
---
---
A/B
V
167
V
09
UniProt
VAR_PHLC1_CLOPE_015
*
D
202
A
PHLC1_CLOPE
---
---
A/B
D
174
A
10
UniProt
VAR_PHLC1_CLOPE_016
*
A
205
T
PHLC1_CLOPE
---
---
A/B
A
177
T
11
UniProt
VAR_PHLC1_CLOPE_017
*
K
281
N
PHLC1_CLOPE
---
---
A/B
K
253
N
12
UniProt
VAR_PHLC1_CLOPE_018
*
T
329
A
PHLC1_CLOPE
---
---
A/B
T
301
A
13
UniProt
VAR_PHLC1_CLOPE_019
*
P
363
S
PHLC1_CLOPE
---
---
A/B
P
335
S
14
UniProt
VAR_PHLC1_CLOPE_020
*
I
373
L
PHLC1_CLOPE
---
---
A/B
V
345
L
15
UniProt
VAR_PHLC1_CLOPE_021
*
I
373
V
PHLC1_CLOPE
---
---
A/B
V
345
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PROKAR_ZN_DEPEND_PLPC_1 (A:126-139,B:126-139,A:126-139,B:12...)
2: PLAT (A:256-370,B:256-370,A:256-370,B:25...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROKAR_ZN_DEPEND_PLPC_1
PS00384
Prokaryotic zinc-dependent phospholipase C signature.
PHLC_CLOP1
154-167
2
A:126-139
B:126-139
PHLC1_CLOPE
154-167
2
A:126-139
B:126-139
2
PLAT
PS50095
PLAT domain profile.
PHLC_CLOP1
284-398
2
A:256-370
B:256-370
PHLC1_CLOPE
284-398
2
A:256-370
B:256-370
[
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_d1gyga1 (A:1-249)
1b: SCOP_d1gygb1 (B:1-249)
2a: SCOP_d1gyga2 (A:250-370)
2b: SCOP_d1gygb2 (B:250-370)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Phospholipase C/P1 nuclease
(20)
Superfamily
:
Phospholipase C/P1 nuclease
(20)
Family
:
Phospholipase C
(15)
Protein domain
:
Alpha-toxin, N-terminal domain
(7)
Clostridium perfringens, different strains [TaxId: 1502]
(6)
1a
d1gyga1
A:1-249
1b
d1gygb1
B:1-249
Class
:
All beta proteins
(24004)
Fold
:
Lipase/lipooxygenase domain (PLAT/LH2 domain)
(47)
Superfamily
:
Lipase/lipooxygenase domain (PLAT/LH2 domain)
(47)
Family
:
Alpha-toxin, C-terminal domain
(7)
Protein domain
:
Alpha-toxin, C-terminal domain
(7)
Clostridium perfringens, different strains [TaxId: 1502]
(6)
2a
d1gyga2
A:250-370
2b
d1gygb2
B:250-370
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1gygA01 (A:1-250)
1b: CATH_1gygB01 (B:1-250)
2a: CATH_1gygA02 (A:251-369)
2b: CATH_1gygB02 (B:251-369)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
P1 Nuclease
(17)
Homologous Superfamily
:
P1 Nuclease
(17)
Clostridium perfringens. Organism_taxid: 1502. Strain: cer89l43
(1)
1a
1gygA01
A:1-250
1b
1gygB01
B:1-250
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Lipoxygenase-1
(46)
Homologous Superfamily
:
Lipoxygenase-1
(44)
Clostridium perfringens. Organism_taxid: 1502. Strain: cer89l43
(1)
2a
1gygA02
A:251-369
2b
1gygB02
B:251-369
[
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 (133 KB)
Header - Asym.Unit
Biol.Unit 1 (189 KB)
Header - Biol.Unit 1
Biol.Unit 2 (189 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
1GYG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
