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.
3G32
Asym. Unit
Info
Asym.Unit (193 KB)
Biol.Unit 1 (97 KB)
Biol.Unit 2 (95 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CTX-M-9 CLASS A BETA-LACTAMASE COMPLEXED WITH COMPOUND 6 (3G3)
Authors
:
Y. Chen, B. K. Shoichet
Date
:
01 Feb 09 (Deposition) - 24 Mar 09 (Release) - 05 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.31
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Ctx-M, Beta-Lactamase, Molecular Docking, Fragment, Inhibitor, Antibiotic Resistance, Hydrolase, Plasmid, Hydrolase/Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Chen, B. K. Shoichet
Molecular Docking And Ligand Specificity In Fragment-Based Inhibitor Discovery
Nat. Chem. Biol. V. 5 358 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 10)
Info
All Hetero Components
1a: 2-[2-(1H-TETRAZOL-5-YL)ETHYL]-1H-I... (3G3a)
1b: 2-[2-(1H-TETRAZOL-5-YL)ETHYL]-1H-I... (3G3b)
1c: 2-[2-(1H-TETRAZOL-5-YL)ETHYL]-1H-I... (3G3c)
2a: DIMETHYL SULFOXIDE (DMSa)
2b: DIMETHYL SULFOXIDE (DMSb)
2c: DIMETHYL SULFOXIDE (DMSc)
2d: DIMETHYL SULFOXIDE (DMSd)
2e: DIMETHYL SULFOXIDE (DMSe)
2f: DIMETHYL SULFOXIDE (DMSf)
3a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3G3
3
Ligand/Ion
2-[2-(1H-TETRAZOL-5-YL)ETHYL]-1H-ISOINDOLE-1,3(2H)-DIONE
2
DMS
6
Ligand/Ion
DIMETHYL SULFOXIDE
3
PO4
1
Ligand/Ion
PHOSPHATE 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
DMS A:10 , SER A:70 , TYR A:105 , SER A:130 , ASN A:132 , THR A:235 , GLY A:236 , SER A:237 , HOH A:379 , HOH A:430 , HOH A:483 , HOH A:569
BINDING SITE FOR RESIDUE 3G3 A 1
02
AC2
SOFTWARE
ARG A:222 , PRO A:226 , THR A:227 , TRP A:229 , HOH A:559
BINDING SITE FOR RESIDUE DMS A 9
03
AC3
SOFTWARE
3G3 A:1 , TYR A:105 , THR A:216 , HOH A:557 , HOH A:563
BINDING SITE FOR RESIDUE DMS A 10
04
AC4
SOFTWARE
PO4 B:4 , SER B:70 , ASN B:104 , TYR B:105 , SER B:130 , ASN B:132 , THR B:235 , GLY B:236 , SER B:237 , HOH B:353 , HOH B:370 , HOH B:413 , HOH B:571 , HOH B:572 , HOH B:584
BINDING SITE FOR RESIDUE 3G3 B 2
05
AC5
SOFTWARE
LYS A:38 , ALA A:150 , HOH A:544 , DMS B:5 , DMS B:8 , ASN B:54 , GLN B:188 , ARG B:191 , GLY B:196 , HOH B:406
BINDING SITE FOR RESIDUE 3G3 B 3
06
AC6
SOFTWARE
3G3 B:2 , SER B:70 , SER B:130 , THR B:235 , GLY B:236 , SER B:237 , HOH B:353 , HOH B:370 , HOH B:401 , HOH B:571 , HOH B:584
BINDING SITE FOR RESIDUE PO4 B 4
07
AC7
SOFTWARE
ARG A:61 , HOH A:513 , 3G3 B:3 , ILE B:49 , ASN B:54 , GLN B:56 , ARG B:191 , HOH B:557
BINDING SITE FOR RESIDUE DMS B 5
08
AC8
SOFTWARE
GLU A:37 , ARG A:61 , GLN B:56 , ARG B:184
BINDING SITE FOR RESIDUE DMS B 6
09
AC9
SOFTWARE
ARG B:222 , PRO B:226 , THR B:227 , TRP B:229 , HOH B:345
BINDING SITE FOR RESIDUE DMS B 7
10
BC1
SOFTWARE
GLY A:143 , GLY A:147 , 3G3 B:3 , GLN B:192 , ALA B:198 , HOH B:406
BINDING SITE FOR RESIDUE DMS B 8
[
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
(0, 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.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3g32a_ (A:)
1b: SCOP_d3g32b_ (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
:
automated matches
(81)
Escherichia coli [TaxId: 562]
(40)
1a
d3g32a_
A:
1b
d3g32b_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3g32A00 (A:26-290)
1b: CATH_3g32B00 (B:26-290)
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)
Escherichia coli. Organism_taxid: 562.
(91)
1a
3g32A00
A:26-290
1b
3g32B00
B:26-290
[
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 (193 KB)
Header - Asym.Unit
Biol.Unit 1 (97 KB)
Header - Biol.Unit 1
Biol.Unit 2 (95 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
3G32
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help