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.
2WXU
Asym. Unit
Info
Asym.Unit (137 KB)
Biol.Unit 1 (130 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CLOSTRIDIUM PERFRINGENS ALPHA-TOXIN STRAIN NCTC8237 MUTANT T74I
Authors
:
S. G. Vachieri, C. E. Naylor, A. K. Basak
Date
:
10 Nov 09 (Deposition) - 17 Nov 09 (Release) - 27 Oct 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Cytolysis, Hydrolase, Hemolysis, Membrane Binding, Virulence, Gangrene Determinant, C2 Domain
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. G. Vachieri, G. C. Clark, A. Alape-Giron, M. Flores-Diaz, N. Justin, C. E. Naylor, R. W. Titball, A. K. Basak
Comparison Of A Nontoxic Variant Of Clostridium Perfringens [Alpha]-Toxin With The Toxic Wild-Type Strain
Acta Crystallogr. , Sect. D V. 66 1067 2010
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 13)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
2a: CADMIUM ION (CDa)
2b: CADMIUM ION (CDb)
2c: CADMIUM ION (CDc)
2d: CADMIUM ION (CDd)
2e: CADMIUM ION (CDe)
2f: CADMIUM ION (CDf)
2g: CADMIUM ION (CDg)
3a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
5
Ligand/Ion
CALCIUM ION
2
CD
7
Ligand/Ion
CADMIUM ION
3
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:46 , GLU A:47 , GLU A:359 , HOH A:2062 , HOH A:2065 , HOH A:2067
BINDING SITE FOR RESIDUE CD A1371
02
AC2
SOFTWARE
ASP A:56 , HIS A:68 , HIS A:126 , ASP A:130 , ZN A:1375 , HOH A:2107 , HOH A:2402
BINDING SITE FOR RESIDUE CD A1372
03
AC3
SOFTWARE
HIS A:136 , HIS A:148 , GLU A:152 , HOH A:2176 , HOH A:2190
BINDING SITE FOR RESIDUE CD A1373
04
AC4
SOFTWARE
CYS A:169 , GLU A:173 , ASP A:216 , HOH A:2255 , HOH A:2261
BINDING SITE FOR RESIDUE CD A1374
05
AC5
SOFTWARE
TRP A:1 , HIS A:11 , ASP A:130 , CD A:1372 , HOH A:2402
BINDING SITE FOR RESIDUE ZN A1375
06
AC6
SOFTWARE
HIS A:241 , GLU A:245 , HOH A:2130 , HOH A:2274 , HOH A:2279 , HOH A:2281
BINDING SITE FOR RESIDUE CD A1376
07
AC7
SOFTWARE
ASP A:273 , ASN A:297 , HOH A:2307 , HOH A:2339
BINDING SITE FOR RESIDUE CA A1377
08
AC8
SOFTWARE
GLU A:173 , HIS A:212 , ASP A:216 , HOH A:2249 , HOH A:2254 , HOH A:2262
BINDING SITE FOR RESIDUE CD A1378
09
AC9
SOFTWARE
GLY A:168 , CYS A:169 , HIS A:207 , HOH A:2208 , HOH A:2209 , HOH A:2251
BINDING SITE FOR RESIDUE CD A1379
10
BC1
SOFTWARE
ASP A:269 , GLY A:271 , ASP A:336 , ALA A:337 , CA A:1383 , HOH A:2305 , HOH A:2370
BINDING SITE FOR RESIDUE CA A1380
11
BC2
SOFTWARE
ASP A:293 , ASN A:294 , GLY A:296 , ASP A:298 , HOH A:2329 , HOH A:2331
BINDING SITE FOR RESIDUE CA A1381
12
BC3
SOFTWARE
GLU A:291 , ASP A:293 , HOH A:2324 , HOH A:2326
BINDING SITE FOR RESIDUE CA A1382
13
BC4
SOFTWARE
ASP A:269 , ASP A:336 , CA A:1380 , HOH A:2305 , HOH A:2368 , HOH A:2370
BINDING SITE FOR RESIDUE CA A1383
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROKAR_ZN_DEPEND_PLPC_1 (A:126-139)
2: PLAT (A:256-370)
;
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
1
A:126-139
2
PLAT
PS50095
PLAT domain profile.
PHLC_CLOP1
284-398
1
A: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, 2)
Info
All SCOP Domains
1a: SCOP_d2wxua1 (A:1-249)
2a: SCOP_d2wxua2 (A: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
:
automated matches
(1)
Clostridium perfringens [TaxId: 1502]
(1)
1a
d2wxua1
A:1-249
Class
:
All beta proteins
(24004)
Fold
:
Lipase/lipooxygenase domain (PLAT/LH2 domain)
(47)
Superfamily
:
Lipase/lipooxygenase domain (PLAT/LH2 domain)
(47)
Family
:
automated matches
(8)
Protein domain
:
automated matches
(8)
Clostridium perfringens [TaxId: 1502]
(1)
2a
d2wxua2
A:250-370
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2wxuA01 (A:1-250)
2a: CATH_2wxuA02 (A:251-370)
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: nctc8237. Variant: t74i.
(1)
1a
2wxuA01
A:1-250
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Lipoxygenase-1
(46)
Homologous Superfamily
:
Lipoxygenase-1
(44)
Clostridium perfringens. Organism_taxid: 1502. Strain: nctc8237. Variant: t74i.
(1)
2a
2wxuA02
A:251-370
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_PLAT_2wxuA01 (A:258-370)
2a: PFAM_Zn_dep_PLPC_2wxuA02 (A:10-227)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PLAT
(25)
Family
:
PLAT
(25)
Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A)
(4)
1a
PLAT-2wxuA01
A:258-370
Clan
:
PhosC-NucP1
(7)
Family
:
Zn_dep_PLPC
(7)
Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A)
(4)
2a
Zn_dep_PLPC-2wxuA02
A:10-227
[
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 (137 KB)
Header - Asym.Unit
Biol.Unit 1 (130 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
2WXU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help