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.
2QMX
Biol. Unit 2
Info
Asym.Unit (98 KB)
Biol.Unit 1 (91 KB)
Biol.Unit 2 (180 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE CRYSTAL STRUCTURE OF L-PHE INHIBITED PREPHENATE DEHYDRATASE FROM CHLOROBIUM TEPIDUM TLS
Authors
:
K. Tan, H. Li, S. Clancy, A. Joachimiak, Midwest Center For Structur Genomics (Mcsg)
Date
:
17 Jul 07 (Deposition) - 07 Aug 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (2x)
Keywords
:
Apc86053, L-Phe Inhibition, Prephenate Dehydratase, Pdt, Chlorobium Tepidum Tls, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Lyase, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Tan, H. Li, R. Zhang, M. Gu, S. T. Clancy, A. Joachimiak
Structures Of Open (R) And Close (T) States Of Prephenate Dehydratase (Pdt) - Implication Of Allosteric Regulation By L-Phenylalanine.
J. Struct. Biol. V. 162 94 2008
[
close entry info
]
Hetero Components
(4, 42)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
4a: PHENYLALANINE (PHEa)
4b: PHENYLALANINE (PHEb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
4
Ligand/Ion
ACETATE ION
2
EDO
22
Ligand/Ion
1,2-ETHANEDIOL
3
MSE
12
Mod. Amino Acid
SELENOMETHIONINE
4
PHE
4
Mod. Amino Acid
PHENYLALANINE
[
close Hetero Component info
]
Sites
(14, 14)
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)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:14 , TYR A:15 , SER A:16 , HOH A:315
BINDING SITE FOR RESIDUE ACT A 301
02
AC2
SOFTWARE
ARG A:263 , GLU A:264 , ALA A:266 , EDO A:308
BINDING SITE FOR RESIDUE ACT A 302
03
AC3
SOFTWARE
ASP A:224 , LEU A:225 , THR A:226 , LYS A:227 , ASN B:206 , GLU B:207 , GLY B:209 , SER B:210 , LEU B:211 , SER B:230 , TYR B:240
BINDING SITE FOR RESIDUE PHE A 303
04
AC4
SOFTWARE
ASN A:206 , GLU A:207 , GLY A:209 , SER A:210 , LEU A:211 , SER A:230 , TYR A:240 , ASP B:224 , LEU B:225 , THR B:226 , LYS B:227
BINDING SITE FOR RESIDUE PHE A 304
05
AC5
SOFTWARE
ARG A:195 , ASP A:224 , ASN B:206
BINDING SITE FOR RESIDUE EDO A 306
06
AC6
SOFTWARE
GLU A:152
BINDING SITE FOR RESIDUE EDO A 307
07
AC7
SOFTWARE
ARG A:263 , ALA A:266 , ACT A:302
BINDING SITE FOR RESIDUE EDO A 308
08
AC8
SOFTWARE
ARG B:213
BINDING SITE FOR RESIDUE EDO A 309
09
AC9
SOFTWARE
ARG A:221 , GLY A:222
BINDING SITE FOR RESIDUE EDO A 310
10
BC1
SOFTWARE
THR A:40 , GLU A:41 , GLN A:42 , PRO B:280
BINDING SITE FOR RESIDUE EDO A 311
11
BC2
SOFTWARE
LYS A:98
BINDING SITE FOR RESIDUE EDO A 312
12
BC3
SOFTWARE
LYS B:98 , MSE B:100
BINDING SITE FOR RESIDUE EDO B 281
13
BC4
SOFTWARE
ILE B:223 , ASP B:224 , ILE B:247
BINDING SITE FOR RESIDUE EDO B 282
14
BC5
SOFTWARE
ARG B:263 , MSE B:268 , VAL B:269
BINDING SITE FOR RESIDUE EDO B 283
[
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
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2qmxA03 (A:190-280)
1b: CATH_2qmxB03 (B:190-280)
2a: CATH_2qmxA01 (A:3-81,A:168-178)
2b: CATH_2qmxB01 (B:3-81,B:168-178)
2c: CATH_2qmxA02 (A:82-167)
2d: CATH_2qmxB02 (B:82-167)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.260, no name defined]
(34)
Chlorobium tepidum tls. Organism_taxid: 194439. Strain: tls, dsm 12025.
(1)
1a
2qmxA03
A:190-280
1b
2qmxB03
B:190-280
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
D-Maltodextrin-Binding Protein; domain 2
(600)
Homologous Superfamily
:
Periplasmic binding protein-like II
(486)
Chlorobium tepidum tls. Organism_taxid: 194439. Strain: tls, dsm 12025.
(1)
2a
2qmxA01
A:3-81,A:168-178
2b
2qmxB01
B:3-81,B:168-178
2c
2qmxA02
A:82-167
2d
2qmxB02
B:82-167
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_ACT_2qmxB01 (B:198-265)
1b: PFAM_ACT_2qmxB02 (B:198-265)
2a: PFAM_PDT_2qmxB03 (B:6-181)
2b: PFAM_PDT_2qmxB04 (B:6-181)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ACT
(34)
Family
:
ACT
(19)
Chlorobium tepidum
(1)
1a
ACT-2qmxB01
B:198-265
1b
ACT-2qmxB02
B:198-265
Clan
:
no clan defined [family: PDT]
(2)
Family
:
PDT
(2)
Chlorobium tepidum
(1)
2a
PDT-2qmxB03
B:6-181
2b
PDT-2qmxB04
B:6-181
[
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
Asymmetric Unit 2
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 (98 KB)
Header - Asym.Unit
Biol.Unit 1 (91 KB)
Header - Biol.Unit 1
Biol.Unit 2 (180 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
2QMX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help