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.
2HK9
Asym. Unit
Info
Asym.Unit (188 KB)
Biol.Unit 1 (49 KB)
Biol.Unit 2 (49 KB)
Biol.Unit 3 (49 KB)
Biol.Unit 4 (49 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 SHIKIMATE DEHYDROGENASE FROM AQUIFEX AEOLICUS IN COMPLEX WITH SHIKIMATE AND NADP+ AT 2.2 ANGSTROM RESOLUTION
Authors
:
J. H. Gan, P. Prabakaran, Y. J. Gu, M. Andrykovitch, Y. Li, H. H. Liu, H. Yan, X. Ji
Date
:
03 Jul 06 (Deposition) - 19 Jun 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Shikimate Pathway, Shikimate Dehydrogenase, Drug Design, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Gan, Y. Wu, P. Prabakaran, Y. Gu, Y. Li, M. Andrykovitch, H. Liu, Y. Gong, H. Yan, X. Ji
Structural And Biochemical Analyses Of Shikimate Dehydrogenase Aroe From Aquifex Aeolicus: Implications For The Catalytic Mechanism.
Biochemistry V. 46 9513 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 8)
Info
All Hetero Components
1a: 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSP... (ATRa)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
2c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
3a: (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHE... (SKMa)
3b: (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHE... (SKMb)
3c: (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHE... (SKMc)
3d: (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHE... (SKMd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATR
1
Ligand/Ion
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
2
NAP
3
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3
SKM
4
Ligand/Ion
(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:67 , ALA A:131 , GLY A:132 , GLY A:133 , ALA A:134 , ASN A:153 , ARG A:154 , THR A:155 , LYS A:158 , THR A:187 , THR A:188 , SER A:189 , VAL A:190 , HOH A:1123 , HOH A:1147
BINDING SITE FOR RESIDUE ATR A 1101
2
AC2
SOFTWARE
SER A:19 , SER A:21 , ASN A:64 , THR A:66 , LYS A:70 , ASN A:91 , ASP A:106 , TYR A:216 , LEU A:239 , GLN A:242
BINDING SITE FOR RESIDUE SKM A 1102
3
AC3
SOFTWARE
VAL B:67 , LYS B:70 , ASP B:106 , GLY B:130 , ALA B:131 , GLY B:132 , GLY B:133 , ALA B:134 , ASN B:153 , ARG B:154 , THR B:155 , LYS B:158 , THR B:187 , THR B:188 , SER B:189 , VAL B:190 , LEU B:192 , ILE B:214 , GLY B:235 , MET B:238 , LEU B:239 , GLN B:242 , SKM B:1202 , HOH B:1239 , HOH B:1245
BINDING SITE FOR RESIDUE NAP B 1201
4
AC4
SOFTWARE
SER B:19 , SER B:21 , ASN B:64 , THR B:66 , LYS B:70 , ASN B:91 , ASP B:106 , TYR B:216 , LEU B:239 , GLN B:242 , NAP B:1201
BINDING SITE FOR RESIDUE SKM B 1202
5
AC5
SOFTWARE
VAL C:67 , LYS C:70 , ASP C:106 , GLY C:130 , ALA C:131 , GLY C:132 , GLY C:133 , ALA C:134 , ASN C:153 , ARG C:154 , THR C:155 , LYS C:158 , THR C:187 , THR C:188 , SER C:189 , VAL C:190 , ILE C:214 , GLY C:235 , MET C:238 , LEU C:239 , SKM C:1302 , HOH C:1341 , HOH C:1348 , HOH C:1350 , HOH C:1351
BINDING SITE FOR RESIDUE NAP C 1301
6
AC6
SOFTWARE
SER C:19 , SER C:21 , ASN C:64 , THR C:66 , LYS C:70 , ASN C:91 , ASP C:106 , TYR C:216 , LEU C:239 , GLN C:242 , NAP C:1301 , HOH C:1341
BINDING SITE FOR RESIDUE SKM C 1302
7
AC7
SOFTWARE
ASP A:82 , VAL D:67 , LYS D:70 , ASP D:106 , GLY D:130 , ALA D:131 , GLY D:132 , GLY D:133 , ALA D:134 , ASN D:153 , ARG D:154 , THR D:155 , LYS D:158 , THR D:187 , THR D:188 , SER D:189 , VAL D:190 , ILE D:214 , GLY D:235 , MET D:238 , LEU D:239 , SKM D:1402 , HOH D:1438 , HOH D:1441 , HOH D:1442 , HOH D:1443 , HOH D:1447
BINDING SITE FOR RESIDUE NAP D 1401
8
AC8
SOFTWARE
SER D:19 , SER D:21 , ASN D:64 , THR D:66 , LYS D:70 , ASN D:91 , ASP D:106 , TYR D:216 , LEU D:239 , GLN D:242 , NAP D:1401 , HOH D:1442
BINDING SITE FOR RESIDUE SKM D 1402
[
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2hk9a1 (A:1-105)
1b: SCOP_d2hk9b1 (B:1-105)
1c: SCOP_d2hk9c1 (C:1-105)
1d: SCOP_d2hk9d1 (D:1-105)
2a: SCOP_d2hk9a2 (A:106-269)
2b: SCOP_d2hk9b2 (B:106-267)
2c: SCOP_d2hk9c2 (C:106-266)
2d: SCOP_d2hk9d2 (D:106-266)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Family
:
Shikimate dehydrogenase-like
(14)
Protein domain
:
Shikimate 5-dehydrogenase AroE
(10)
Aquifex aeolicus [TaxId: 63363]
(3)
1a
d2hk9a1
A:1-105
1b
d2hk9b1
B:1-105
1c
d2hk9c1
C:1-105
1d
d2hk9d1
D:1-105
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Aminoacid dehydrogenase-like, C-terminal domain
(67)
Protein domain
:
Shikimate 5-dehydrogenase AroE
(10)
Aquifex aeolicus [TaxId: 63363]
(3)
2a
d2hk9a2
A:106-269
2b
d2hk9b2
B:106-267
2c
d2hk9c2
C:106-266
2d
d2hk9d2
D:106-266
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2hk9A01 (A:1-104,A:235-269)
1b: CATH_2hk9B01 (B:1-104,B:235-267)
1c: CATH_2hk9C01 (C:1-104,C:235-266)
1d: CATH_2hk9D01 (D:1-104,D:235-266)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Leucine Dehydrogenase; Chain A, domain 1
(52)
Homologous Superfamily
:
Leucine Dehydrogenase, chain A, domain 1
(52)
Aquifex aeolicus. Organism_taxid: 63363.
(3)
1a
2hk9A01
A:1-104,A:235-269
1b
2hk9B01
B:1-104,B:235-267
1c
2hk9C01
C:1-104,C:235-266
1d
2hk9D01
D:1-104,D:235-266
[
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
Chain C
Chain D
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 (188 KB)
Header - Asym.Unit
Biol.Unit 1 (49 KB)
Header - Biol.Unit 1
Biol.Unit 2 (49 KB)
Header - Biol.Unit 2
Biol.Unit 3 (49 KB)
Header - Biol.Unit 3
Biol.Unit 4 (49 KB)
Header - Biol.Unit 4
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
2HK9
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
