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.
2IYO
Biol. Unit 1
Info
Asym.Unit (85 KB)
Biol.Unit 1 (160 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURAL CHARACTERIZATION OF A BACTERIAL 6PDH REVEALS ASPECTS OF SPECIFICITY, MECHANISM AND MODE OF INHIBITION
Authors
:
R. Sundaramoorthy, J. Iulek, W. N. Hunter
Date
:
21 Jul 06 (Deposition) - 23 Jan 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Oxidoreductase, 6-Phosphogluconate Dehydrogenase, Nadp, Pentose Shunt, Gluconate Utilization
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Sundaramoorthy, J. Iulek, M. P. Barrett, O. Bidet, G. F. Ruda, I. H. Gilbert, W. N. Hunter
Crystal Structures Of A Bacterial 6- Phosphogluconate Dehydrogenase Reveal Aspects Of Specificity, Mechanism And Mode Of Inhibition By Analogues Of High-Energy Reaction Intermediates.
Febs J. V. 274 275 2007
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: 6-PHOSPHOGLUCONIC ACID (6PGa)
2a: CACODYLATE ION (CACa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6PG
2
Ligand/Ion
6-PHOSPHOGLUCONIC ACID
2
CAC
2
Ligand/Ion
CACODYLATE ION
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:102 , SER A:128 , GLY A:129 , GLY A:130 , LYS A:184 , HIS A:187 , ASN A:188 , GLU A:191 , TYR A:192 , LYS A:262 , ARG A:289 , ILE A:367 , ARG A:447 , PHE A:450 , HIS A:453 , HOH A:2115 , HOH A:2311 , HOH A:2312 , HOH A:2313
BINDING SITE FOR RESIDUE 6PG A1471
2
AC2
SOFTWARE
LYS A:262 , GLY A:451 , ALA A:452 , HIS A:453
BINDING SITE FOR RESIDUE CAC A1472
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: 6PGD (A:255-267)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
6PGD
PS00461
6-phosphogluconate dehydrogenase signature.
6PGD_LACLM
255-267
2
A:255-267
[
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2iyoa2 (A:178-470)
2a: SCOP_d2iyoa1 (A:1-177)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
automated matches
(50)
Protein domain
:
automated matches
(50)
Lactococcus lactis [TaxId: 1358]
(4)
1a
d2iyoa2
A:178-470
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Lactococcus lactis [TaxId: 1358]
(4)
2a
d2iyoa1
A:1-177
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2iyoA01 (A:1-181)
2a: CATH_2iyoA02 (A:182-436)
3a: CATH_2iyoA03 (A:437-470)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Lactococcus lactis. Organism_taxid: 1358. Strain: mg1363.
(4)
1a
2iyoA01
A:1-181
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
(60)
Homologous Superfamily
:
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
(59)
Lactococcus lactis. Organism_taxid: 1358. Strain: mg1363.
(4)
2a
2iyoA02
A:182-436
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
6-Phosphogluconate Dehydrogenase, domain 3
(20)
Lactococcus lactis. Organism_taxid: 1358. Strain: mg1363.
(4)
3a
2iyoA03
A:437-470
[
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
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 (85 KB)
Header - Asym.Unit
Biol.Unit 1 (160 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
2IYO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
