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.
2WGV
Biol. Unit 1
Info
Asym.Unit (96 KB)
Biol.Unit 1 (88 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 THE OXA-10 V117T MUTANT AT PH 6.5 INHIBITED BY A CHLORIDE ION
Authors
:
L. Vercheval, F. Kerff, C. Bauvois, E. Sauvage, R. Guiet, P. Charlier,
Date
:
27 Apr 09 (Deposition) - 19 May 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Antibiotic Resistance, Plasmid Encoded, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Vercheval, C. Bauvois, A. Di Paolo, F. Borel, J. L. Ferrer, E. Sauvage, A. Matagne, J. M. Frere, P. Charlier, M. Galleni, F. Kerff
Three Factors That Modulate The Activity Of Class D Beta-Lactamases And Interfere With The Post- Translational Carboxylation Of Lys70.
Biochem. J. V. 432 495 2010
[
close entry info
]
Hetero Components
(3, 5)
Info
All Hetero Components
1a: CITRIC ACID (CITa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
4a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CIT
1
Ligand/Ion
CITRIC ACID
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
GOL
3
Ligand/Ion
GLYCEROL
4
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:107 , ARG A:109 , GLY A:110 , HOH A:2225 , ALA B:197 , PRO B:198 , GLU B:199 , TYR B:200 , GLU B:227 , GLU B:229 , HOH B:2106
BINDING SITE FOR RESIDUE GOL A1265
02
AC2
SOFTWARE
ALA A:197 , PRO A:198 , GLU A:199 , TYR A:200 , GLU A:227 , GLU A:229 , HOH A:2190 , THR B:107 , ARG B:109
BINDING SITE FOR RESIDUE GOL A1266
03
AC3
SOFTWARE
LYS A:138 , SER A:140 , SER A:172 , HOH A:2226
BINDING SITE FOR RESIDUE GOL A1267
04
AC4
SOFTWARE
LYS A:70 , TRP A:154 , HOH A:2053
BINDING SITE FOR RESIDUE CL A1268
05
AC5
SOFTWARE
LYS B:70 , TRP B:154 , HOH B:2030
BINDING SITE FOR RESIDUE CL B1266
06
AC6
SOFTWARE
ALA A:98 , HOH A:2122
BINDING SITE FOR RESIDUE CL A1269
07
AC7
SOFTWARE
ARG A:250 , HOH A:2215
BINDING SITE FOR RESIDUE CL A1270
08
AC8
SOFTWARE
ARG A:131 , LYS A:152 , HOH A:2120
BINDING SITE FOR RESIDUE CL A1271
09
AC9
SOFTWARE
SER B:67 , SER B:115 , LYS B:205 , THR B:206 , GLY B:207 , PHE B:208 , ARG B:250 , HOH B:2124
BINDING SITE FOR RESIDUE SO4 B1267
10
BC1
SOFTWARE
ALA A:66 , SER A:67 , SER A:115 , LYS A:205 , THR A:206 , GLY A:207 , PHE A:208 , ARG A:250 , HOH A:2099 , HOH A:2227 , HOH A:2228
BINDING SITE FOR RESIDUE CIT A1272
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: BETA_LACTAMASE_D (A:65-75,B:65-75)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BETA_LACTAMASE_D
PS00337
Beta-lactamase class-D active site.
BLO10_PSEAI
65-75
2
A:65-75
B:65-75
[
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2wgva_ (A:)
1b: SCOP_d2wgvb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
beta-lactamase/transpeptidase-like
(515)
Superfamily
:
beta-lactamase/transpeptidase-like
(515)
Family
:
beta-Lactamase/D-ala carboxypeptidase
(411)
Protein domain
:
Class D beta-lactamase
(32)
Pseudomonas aeruginosa, OXA-10 [TaxId: 287]
(25)
1a
d2wgva_
A:
1b
d2wgvb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2wgvB00 (B:19-265)
1b: CATH_2wgvA00 (A:19-264)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Beta-lactamase
(339)
Homologous Superfamily
:
DD-peptidase/beta-lactamase superfamily
(335)
Pseudomonas aeruginosa. Organism_taxid: 287.
(17)
1a
2wgvB00
B:19-265
1b
2wgvA00
A:19-264
[
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 (88 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
2WGV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
