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.
3IME
Asym. Unit
Info
Asym.Unit (95 KB)
Biol.Unit 1 (90 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 MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE SYNTHETASE AT 2.40 ANG RESOLUTION IN COMPLEX WITH FRAGMENT COMPOUND 1-BENZOFURAN-2-CARBOXYLIC ACID
Authors
:
A. Ciulli, A. W. Hung, H. L. Silvestre, S. Wen, T. L. Blundell, C. Abell
Date
:
10 Aug 09 (Deposition) - 13 Oct 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.39
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Mycobacterium Tuberculosis, Pantothenate Biosynthesis, Enzymes, Ligase, Drug Design, Fragment-Based, Atp-Binding, Magnesium, Metal- Binding, Nucleotide-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. W. Hung, H. L. Silvestre, S. Wen, A. Ciulli, T. L. Blundell, C. Abell
Application Of Fragment Growing And Fragment Linking To The Discovery Of Inhibitors Of Mycobacterium Tuberculosis Pantothenate Synthetase.
Angew. Chem. Int. Ed. Engl. V. 48 8452 2009
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: 1-BENZOFURAN-2-CARBOXYLIC ACID (BZ2a)
1b: 1-BENZOFURAN-2-CARBOXYLIC ACID (BZ2b)
2a: ETHANOL (EOHa)
2b: ETHANOL (EOHb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BZ2
2
Ligand/Ion
1-BENZOFURAN-2-CARBOXYLIC ACID
2
EOH
2
Ligand/Ion
ETHANOL
3
GOL
2
Ligand/Ion
GLYCEROL
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:38 , THR A:39 , MET A:40 , HIS A:47 , VAL A:143 , GLN A:164 , HOH A:518
BINDING SITE FOR RESIDUE BZ2 A 301
2
AC2
SOFTWARE
MET A:109 , TYR A:110 , PRO A:111 , ASP A:112 , GLY A:113 , ARG A:115 , THR A:116 , LYS A:145 , ASP B:174
BINDING SITE FOR RESIDUE GOL A 701
3
AC3
SOFTWARE
PRO A:111 , ASP A:112
BINDING SITE FOR RESIDUE GOL A 702
4
AC4
SOFTWARE
ARG A:115 , THR A:117 , GLN B:119 , PRO B:120
BINDING SITE FOR RESIDUE EOH A 703
5
AC5
SOFTWARE
THR A:218 , HIS B:222 , THR B:225
BINDING SITE FOR RESIDUE EOH A 704
6
AC6
SOFTWARE
PRO B:38 , THR B:39 , MET B:40 , HIS B:47 , VAL B:143 , GLN B:164
BINDING SITE FOR RESIDUE BZ2 B 302
[
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_d3imea_ (A:)
1b: SCOP_d3imeb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Adenine nucleotide alpha hydrolase-like
(440)
Superfamily
:
Nucleotidylyl transferase
(325)
Family
:
Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)
(46)
Protein domain
:
Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)
(44)
Mycobacterium tuberculosis [TaxId: 1773]
(39)
1a
d3imea_
A:
1b
d3imeb_
B:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3imeB02 (B:186-288)
1b: CATH_3imeA02 (A:186-289)
2a: CATH_3imeA01 (A:4-185)
2b: CATH_3imeB01 (B:2-185)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Pantoate--beta-alanine Ligase; Chain: A,domain 2
(43)
Homologous Superfamily
:
[code=3.30.1300.10, no name defined]
(36)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(19)
1a
3imeB02
B:186-288
1b
3imeA02
A:186-289
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(20)
2a
3imeA01
A:4-185
2b
3imeB01
B:2-185
[
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 (95 KB)
Header - Asym.Unit
Biol.Unit 1 (90 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
3IME
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
