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.
2UXQ
Biol. Unit 1
Info
Asym.Unit (311 KB)
Biol.Unit 1 (153 KB)
Biol.Unit 2 (154 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ISOCITRATE DEHYDROGENASE FROM THE PSYCHROPHILIC BACTERIUM DESULFOTALEA PSYCHROPHILA: BIOCHEMICAL PROPERTIES AND CRYSTAL STRUCTURE ANALYSIS
Authors
:
A. -E. Fedoy, N. Yang, A. Martinez, H. -K. S. Leiros, I. H. Steen
Date
:
29 Mar 07 (Deposition) - 05 Feb 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Psychrophilic, Cold Adaptation, Thermal Stability, Isocitrate Dehydrogenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. -E. Fedoy, N. Yang, A. Martinez, H. -K. S. Leiros, I. H. Steen
Structural And Functional Properties Of Isocitrate Dehydrogenase From The Psychrophilic Bacterium Desulfotalea Psychrophila Reveal A Cold -Active Enzyme With An Unusual High Thermal
J. Mol. Biol. V. 372 130 2007
[
close entry info
]
Hetero Components
(3, 13)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
2a: MAGNESIUM ION (MGa)
3a: DI(HYDROXYETHYL)ETHER (PEGa)
3b: DI(HYDROXYETHYL)ETHER (PEGb)
3c: DI(HYDROXYETHYL)ETHER (PEGc)
3d: DI(HYDROXYETHYL)ETHER (PEGd)
3e: DI(HYDROXYETHYL)ETHER (PEGe)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
PEG
3
Ligand/Ion
DI(HYDROXYETHYL)ETHER
4
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC2 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC6 (SOFTWARE)
08: BC7 (SOFTWARE)
09: BC8 (SOFTWARE)
10: CC2 (SOFTWARE)
11: CC3 (SOFTWARE)
12: CC4 (SOFTWARE)
13: CC5 (SOFTWARE)
14: CC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
ASN B:324 , HOH B:2497 , HOH B:2498
BINDING SITE FOR RESIDUE GOL B1402
02
AC3
SOFTWARE
SER A:284 , LEU A:285 , ALA A:286 , ASN A:324 , HOH A:2427 , HOH A:2464 , HOH A:2465 , HOH A:2466
BINDING SITE FOR RESIDUE GOL A1403
03
AC6
SOFTWARE
ASP A:15 , GLU A:16 , GLY A:44 , ILE A:45 , GLU A:46 , TYR A:85 , HOH A:2467
BINDING SITE FOR RESIDUE GOL A1404
04
AC8
SOFTWARE
ARG A:99 , ARG A:131 , ASP A:272 , GLU A:302 , SO4 A:1406 , MG A:1407 , HOH A:2468
BINDING SITE FOR RESIDUE GOL A1405
05
BC2
SOFTWARE
GLN A:218 , LYS A:221 , ASN B:78 , GLN B:79 , GLN B:90 , HOH B:2500 , HOH B:2501 , HOH B:2502
BINDING SITE FOR RESIDUE SO4 B1403
06
BC3
SOFTWARE
HIS B:311 , GLN B:314 , SER B:322 , HOH B:2404 , HOH B:2503
BINDING SITE FOR RESIDUE SO4 B1404
07
BC6
SOFTWARE
ASN B:95 , ARG B:99 , GLU B:302 , SO4 B:1406 , HOH B:2164
BINDING SITE FOR RESIDUE SO4 B1405
08
BC7
SOFTWARE
LYS A:209 , HOH A:2282 , THR B:76 , SER B:93 , ASN B:95 , SO4 B:1405 , HOH B:2223 , HOH B:2504
BINDING SITE FOR RESIDUE SO4 B1406
09
BC8
SOFTWARE
THR A:76 , SER A:93 , ASN A:95 , GOL A:1405 , HOH A:2468 , HOH A:2469 , HOH A:2470 , HOH B:2306
BINDING SITE FOR RESIDUE SO4 A1406
10
CC2
SOFTWARE
GLY B:306 , THR B:307 , VAL B:308 , GLN B:309 , HOH B:2505 , HOH B:2506 , HOH B:2507 , HOH B:2508
BINDING SITE FOR RESIDUE SO4 B1407
11
CC3
SOFTWARE
ASP A:272 , ASP A:276 , GOL A:1405 , HOH A:2345 , ASP B:249
BINDING SITE FOR RESIDUE MG A1407
12
CC4
SOFTWARE
GLU A:46 , GLU A:84 , TYR A:85 , TYR A:313 , LEU A:316 , HOH A:2471 , HOH A:2472 , HOH A:2473
BINDING SITE FOR RESIDUE PEG A1408
13
CC5
SOFTWARE
TYR B:85 , TYR B:313 , LEU B:316 , HOH B:2509
BINDING SITE FOR RESIDUE PEG B1408
14
CC8
SOFTWARE
GLU B:39 , TYR B:40 , TYR B:41 , HOH B:2512
BINDING SITE FOR RESIDUE PEG B1409
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2uxqa_ (A:)
1b: SCOP_d2uxqb_ (B:)
1c: SCOP_d2uxqc_ (C:)
1d: SCOP_d2uxqd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Isocitrate/Isopropylmalate dehydrogenase-like
(143)
Superfamily
:
Isocitrate/Isopropylmalate dehydrogenase-like
(143)
Family
:
automated matches
(22)
Protein domain
:
automated matches
(22)
Desulfotalea psychrophila [TaxId: 84980]
(3)
1a
d2uxqa_
A:
1b
d2uxqb_
B:
1c
d2uxqc_
C:
1d
d2uxqd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2uxqB00 (B:1-401)
1b: CATH_2uxqA00 (A:1-402)
1c: CATH_2uxqC00 (C:1-402)
1d: CATH_2uxqD00 (D:1-402)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Isopropylmalate Dehydrogenase
(91)
Homologous Superfamily
:
Isopropylmalate Dehydrogenase
(91)
Desulfotalea psychrophila. Organism_taxid: 84980.
(2)
1a
2uxqB00
B:1-401
1b
2uxqA00
A:1-402
1c
2uxqC00
C:1-402
1d
2uxqD00
D:1-402
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Iso_dh_2uxqD01 (D:4-393)
1b: PFAM_Iso_dh_2uxqD02 (D:4-393)
1c: PFAM_Iso_dh_2uxqD03 (D:4-393)
1d: PFAM_Iso_dh_2uxqD04 (D:4-393)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Iso_DH
(49)
Family
:
Iso_dh
(38)
Desulfotalea psychrophila
(2)
1a
Iso_dh-2uxqD01
D:4-393
1b
Iso_dh-2uxqD02
D:4-393
1c
Iso_dh-2uxqD03
D:4-393
1d
Iso_dh-2uxqD04
D:4-393
[
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 (311 KB)
Header - Asym.Unit
Biol.Unit 1 (153 KB)
Header - Biol.Unit 1
Biol.Unit 2 (154 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
2UXQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help