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.
1XEA
Asym. Unit
Info
Asym.Unit (214 KB)
Biol.Unit 1 (206 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 A GFO/IDH/MOCA FAMILY OXIDOREDUCTASE FROM VIBRIO CHOLERAE
Authors
:
K. R Rajashankar, J. A. Reynes, R. Kniewel, C. D. Lima, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date
:
09 Sep 04 (Deposition) - 28 Sep 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.65
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Structural Genomics; Protein Structure Initiative; Nysgxrc; T1536; Vca1048; Gfo/Idh/Moca Family Oxidoreductase, Psi, New York Sgx Research Center For Structural Genomics
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. R Rajashankar, J. A. Reynes, R. Kniewel, C. D. Lima
Crystal Structure Of A Gfo/Idh/Moca Family Oxidoreductase From Vibrio Cholerae
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 29)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1aa: SELENOMETHIONINE (MSEaa)
1ab: SELENOMETHIONINE (MSEab)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
1s: SELENOMETHIONINE (MSEs)
1t: SELENOMETHIONINE (MSEt)
1u: SELENOMETHIONINE (MSEu)
1v: SELENOMETHIONINE (MSEv)
1w: SELENOMETHIONINE (MSEw)
1x: SELENOMETHIONINE (MSEx)
1y: SELENOMETHIONINE (MSEy)
1z: SELENOMETHIONINE (MSEz)
2a: NICKEL (II) ION (NIa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
28
Mod. Amino Acid
SELENOMETHIONINE
2
NI
1
Ligand/Ion
NICKEL (II) ION
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:134 , HOH A:1032 , HOH A:1046 , HOH A:1066
BINDING SITE FOR RESIDUE NI A 1001
[
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_d1xeaa2 (A:123-266)
1b: SCOP_d1xeab2 (B:123-266)
1c: SCOP_d1xeac2 (C:123-266)
1d: SCOP_d1xead2 (D:123-266)
2a: SCOP_d1xeaa1 (A:2-122,A:267-312)
2b: SCOP_d1xeab1 (B:2-122,B:267-312)
2c: SCOP_d1xeac1 (C:2-122,C:267-312)
2d: SCOP_d1xead1 (D:2-122,D:267-312)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
(179)
Family
:
Glucose 6-phosphate dehydrogenase-like
(25)
Protein domain
:
Putative oxidoreductase VCA1048
(1)
Vibrio cholerae [TaxId: 666]
(1)
1a
d1xeaa2
A:123-266
1b
d1xeab2
B:123-266
1c
d1xeac2
C:123-266
1d
d1xead2
D:123-266
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
:
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
(179)
Protein domain
:
Putative oxidoreductase VCA1048
(1)
Vibrio cholerae [TaxId: 666]
(1)
2a
d1xeaa1
A:2-122,A:267-312
2b
d1xeab1
B:2-122,B:267-312
2c
d1xeac1
C:2-122,C:267-312
2d
d1xead1
D:2-122,D:267-312
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1xeaA02 (A:121-312)
1b: CATH_1xeaB02 (B:121-312)
1c: CATH_1xeaC02 (C:121-312)
1d: CATH_1xeaD02 (D:121-312)
2a: CATH_1xeaA01 (A:2-120)
2b: CATH_1xeaB01 (B:2-120)
2c: CATH_1xeaC01 (C:2-120)
2d: CATH_1xeaD01 (D:2-120)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Vibrio cholerae. Organism_taxid: 666.
(3)
1a
1xeaA02
A:121-312
1b
1xeaB02
B:121-312
1c
1xeaC02
C:121-312
1d
1xeaD02
D:121-312
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Vibrio cholerae. Organism_taxid: 666.
(3)
2a
1xeaA01
A:2-120
2b
1xeaB01
B:2-120
2c
1xeaC01
C:2-120
2d
1xeaD01
D:2-120
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_GFO_IDH_MocA_1xeaD01 (D:4-121)
1b: PFAM_GFO_IDH_MocA_1xeaD02 (D:4-121)
1c: PFAM_GFO_IDH_MocA_1xeaD03 (D:4-121)
1d: PFAM_GFO_IDH_MocA_1xeaD04 (D:4-121)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
GFO_IDH_MocA
(25)
Vibrio cholerae
(1)
1a
GFO_IDH_MocA-1xeaD01
D:4-121
1b
GFO_IDH_MocA-1xeaD02
D:4-121
1c
GFO_IDH_MocA-1xeaD03
D:4-121
1d
GFO_IDH_MocA-1xeaD04
D:4-121
[
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 (214 KB)
Header - Asym.Unit
Biol.Unit 1 (206 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
1XEA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help