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.
2IZ1
Asym. Unit
Info
Asym.Unit (277 KB)
Biol.Unit 1 (181 KB)
Biol.Unit 2 (181 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
6PDH COMPLEXED WITH PEX INHIBITOR SYNCHROTRON DATA
Authors
:
R. Sundaramoorthy, J. Iulek, W. N. Hunter
Date
:
23 Jul 06 (Deposition) - 23 Jan 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C (2x)
Keywords
:
Pentose Shunt, Oxidoreductase, 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
(5, 11)
Info
All Hetero Components
1a: 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSP... (ATRa)
1b: 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSP... (ATRb)
1c: 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSP... (ATRc)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20... (P33a)
3b: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20... (P33b)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
5a: 4-PHOSPHO-D-ERYTHRONOHYDROXAMIC AC... (RESa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATR
3
Ligand/Ion
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
2
CL
4
Ligand/Ion
CHLORIDE ION
3
P33
2
Ligand/Ion
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
4
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
RES
1
Ligand/Ion
4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER B:128 , GLY B:129 , HIS B:187 , CYS B:366 , ILE B:367 , HOH B:2337
BINDING SITE FOR RESIDUE CL B1471
02
AC2
SOFTWARE
ASN B:112 , GLY B:144 , GLN B:145 , ASN B:177 , HOH B:2126 , HOH B:2333
BINDING SITE FOR RESIDUE CL B1472
03
AC3
SOFTWARE
SER C:128 , GLY C:129 , ILE C:367 , PHE C:450
BINDING SITE FOR RESIDUE CL C1471
04
AC4
SOFTWARE
ASN C:112 , GLY C:144 , GLN C:145 , ASN C:177 , HOH C:2108 , HOH C:2307
BINDING SITE FOR RESIDUE CL C1472
05
AC5
SOFTWARE
ALA A:12 , ASN A:33 , ARG A:34 , THR A:35 , VAL A:74 , GLN A:75 , ALA A:79 , LYS A:262 , HOH A:2556 , HOH A:2557 , HOH A:2558 , HOH A:2559 , HOH A:2560
BINDING SITE FOR RESIDUE ATR A1470
06
AC6
SOFTWARE
ASN A:102 , LYS A:184 , ASN A:188 , GLU A:191 , TYR A:192 , LYS A:262 , ARG A:289 , ILE A:367 , HOH A:2189 , HOH A:2562 , HOH A:2563 , HOH A:2564 , HOH A:2565 , HOH A:2566 , ARG B:447 , PHE B:450 , HIS B:453
BINDING SITE FOR RESIDUE RES A1471
07
AC7
SOFTWARE
GLN A:165 , ASP A:229 , GLU A:371 , PEG A:1473 , HOH A:2567 , HOH A:2568 , HOH A:2569 , HOH A:2570 , HOH A:2572 , GLN C:47 , P33 C:1473 , HOH C:2668 , HOH C:2670
BINDING SITE FOR RESIDUE P33 A1472
08
AC8
SOFTWARE
ALA B:12 , ASN B:33 , ARG B:34 , THR B:35 , LYS B:38 , VAL B:74 , GLN B:75 , ALA B:79 , THR B:83 , HOH B:2083 , HOH B:2084 , HOH B:2650 , HOH B:2651 , HOH B:2652 , HOH B:2653 , HOH B:2655
BINDING SITE FOR RESIDUE ATR B1470
09
AC9
SOFTWARE
ALA C:12 , ASN C:33 , ARG C:34 , THR C:35 , LYS C:38 , VAL C:74 , GLN C:75 , ALA C:79 , THR C:83 , HOH C:2077 , HOH C:2147 , HOH C:2658 , HOH C:2660 , HOH C:2661 , HOH C:2663
BINDING SITE FOR RESIDUE ATR C1470
10
BC1
SOFTWARE
PRO A:164 , P33 A:1472 , PHE C:43 , GLN C:47 , LYS C:49 , LEU C:51 , HOH C:2106 , HOH C:2665 , HOH C:2667 , HOH C:2668 , HOH C:2669 , HOH C:2670
BINDING SITE FOR RESIDUE P33 C1473
11
BC2
SOFTWARE
P33 A:1472 , HOH A:2572 , HOH A:2573 , HOH C:2669
BINDING SITE FOR RESIDUE PEG A1473
[
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
(1, 3)
Info
All PROSITE Patterns/Profiles
1: 6PGD (A:255-267,B:255-267,C: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
3
A:255-267
B:255-267
C: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.
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d2iz1a2 (A:178-470)
1b: SCOP_d2iz1b2 (B:178-470)
1c: SCOP_d2iz1c2 (C:178-470)
2a: SCOP_d2iz1a1 (A:1-177)
2b: SCOP_d2iz1b1 (B:-1-177)
2c: SCOP_d2iz1c1 (C:2-177)
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
d2iz1a2
A:178-470
1b
d2iz1b2
B:178-470
1c
d2iz1c2
C: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
d2iz1a1
A:1-177
2b
d2iz1b1
B:-1-177
2c
d2iz1c1
C:2-177
[
close SCOP info
]
CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_2iz1B01 (B:-1-181)
1b: CATH_2iz1A01 (A:1-181)
1c: CATH_2iz1C01 (C:2-181)
2a: CATH_2iz1A02 (A:182-436)
2b: CATH_2iz1B02 (B:182-436)
2c: CATH_2iz1C02 (C:182-436)
3a: CATH_2iz1A03 (A:437-470)
3b: CATH_2iz1B03 (B:437-470)
3c: CATH_2iz1C03 (C: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
2iz1B01
B:-1-181
1b
2iz1A01
A:1-181
1c
2iz1C01
C:2-181
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
2iz1A02
A:182-436
2b
2iz1B02
B:182-436
2c
2iz1C02
C: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
2iz1A03
A:437-470
3b
2iz1B03
B:437-470
3c
2iz1C03
C: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
Chain B
Chain C
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 (277 KB)
Header - Asym.Unit
Biol.Unit 1 (181 KB)
Header - Biol.Unit 1
Biol.Unit 2 (181 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
2IZ1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help