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.
1B3B
Asym. Unit
Info
Asym.Unit (359 KB)
Biol.Unit 1 (353 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THERMOTOGA MARITIMA GLUTAMATE DEHYDROGENASE MUTANT N97D, G376K
Authors
:
S. Knapp, J. H. G. Lebbink, J. Van Der Oost, W. M. Devos, D. Rice, R. Ladenstein
Date
:
07 Dec 98 (Deposition) - 08 Dec 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Metabolic Role, Glutamate, Dehydrogenase, Mutant, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. H. Lebbink, S. Knapp, J. Van Der Oost, D. Rice, R. Ladenstein, W. M. De Vos
Engineering Activity And Stability Of Thermotoga Maritima Glutamate Dehydrogenase. I. Introduction Of A Six-Residue Ion-Pair Network In The Hinge Region.
J. Mol. Biol. V. 280 287 1998
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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, 6)
Info
All PROSITE Patterns/Profiles
1: GLFV_DEHYDROGENASE (A:98-111,B:98-111,C:98-111,D:98-11...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLFV_DEHYDROGENASE
PS00074
Glu / Leu / Phe / Val dehydrogenases active site.
DHE3_THEMA
99-112
6
A:98-111
B:98-111
C:98-111
D:98-111
E:98-111
F:98-111
[
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, 12)
Info
All SCOP Domains
1a: SCOP_d1b3ba2 (A:4-178)
1b: SCOP_d1b3bb2 (B:4-178)
1c: SCOP_d1b3bc2 (C:4-178)
1d: SCOP_d1b3bd2 (D:4-178)
1e: SCOP_d1b3be2 (E:4-178)
1f: SCOP_d1b3bf2 (F:4-178)
2a: SCOP_d1b3ba1 (A:179-412)
2b: SCOP_d1b3bb1 (B:179-412)
2c: SCOP_d1b3bc1 (C:179-412)
2d: SCOP_d1b3bd1 (D:179-412)
2e: SCOP_d1b3be1 (E:179-412)
2f: SCOP_d1b3bf1 (F:179-412)
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
:
Aminoacid dehydrogenases
(28)
Protein domain
:
Glutamate dehydrogenase
(19)
Thermotoga maritima [TaxId: 2336]
(3)
1a
d1b3ba2
A:4-178
1b
d1b3bb2
B:4-178
1c
d1b3bc2
C:4-178
1d
d1b3bd2
D:4-178
1e
d1b3be2
E:4-178
1f
d1b3bf2
F:4-178
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
:
Glutamate dehydrogenase
(19)
Thermotoga maritima [TaxId: 2336]
(3)
2a
d1b3ba1
A:179-412
2b
d1b3bb1
B:179-412
2c
d1b3bc1
C:179-412
2d
d1b3bd1
D:179-412
2e
d1b3be1
E:179-412
2f
d1b3bf1
F:179-412
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1b3bA01 (A:35-178)
1b: CATH_1b3bB01 (B:35-178)
1c: CATH_1b3bC01 (C:35-178)
1d: CATH_1b3bD01 (D:35-178)
1e: CATH_1b3bE01 (E:35-178)
1f: CATH_1b3bF01 (F:35-178)
2a: CATH_1b3bA02 (A:179-412)
2b: CATH_1b3bB02 (B:179-412)
2c: CATH_1b3bC02 (C:179-412)
2d: CATH_1b3bD02 (D:179-412)
2e: CATH_1b3bE02 (E:179-412)
2f: CATH_1b3bF02 (F:179-412)
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)
Thermotoga maritima. Organism_taxid: 2336.
(3)
1a
1b3bA01
A:35-178
1b
1b3bB01
B:35-178
1c
1b3bC01
C:35-178
1d
1b3bD01
D:35-178
1e
1b3bE01
E:35-178
1f
1b3bF01
F:35-178
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Thermotoga maritima. Organism_taxid: 2336.
(10)
2a
1b3bA02
A:179-412
2b
1b3bB02
B:179-412
2c
1b3bC02
C:179-412
2d
1b3bD02
D:179-412
2e
1b3bE02
E:179-412
2f
1b3bF02
F:179-412
[
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
Chain E
Chain F
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 (359 KB)
Header - Asym.Unit
Biol.Unit 1 (353 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
1B3B
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help