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.
1OFD
Asym. Unit
Info
Asym.Unit (492 KB)
Biol.Unit 1 (247 KB)
Biol.Unit 2 (245 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
GLUTAMATE SYNTHASE FROM SYNECHOCYSTIS SP IN COMPLEX WITH 2-OXOGLUTARATE AT 2.0 ANGSTROM RESOLUTION
Authors
:
R. H. H. Van Den Heuvel, A. Mattevi
Date
:
14 Apr 03 (Deposition) - 11 Jun 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Oxidoreductase, Complex Enzyme, Substrate Channeling, Amidotransferase, Flavoprotein, Iron-Sulphur, Fd-Gogat
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. H. H. Van Den Heuvel, D. I. Svergun, M. V. Petoukhov, A. Coda, B. Curti, S. Ravasio, M. A. Vanoni, A. Mattevi
The Active Conformation Of Glutamate Synthase And Its Binding To Ferredoxin
J. Mol. Biol. V. 330 113 2003
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: 2-OXOGLUTARIC ACID (AKGa)
1b: 2-OXOGLUTARIC ACID (AKGb)
2a: FE3-S4 CLUSTER (F3Sa)
2b: FE3-S4 CLUSTER (F3Sb)
3a: FLAVIN MONONUCLEOTIDE (FMNa)
3b: FLAVIN MONONUCLEOTIDE (FMNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AKG
2
Ligand/Ion
2-OXOGLUTARIC ACID
2
F3S
2
Ligand/Ion
FE3-S4 CLUSTER
3
FMN
2
Ligand/Ion
FLAVIN MONONUCLEOTIDE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:874 , MET A:875 , SER A:876 , GLY A:902 , GLU A:903 , GLN A:944 , LYS A:966 , GLN A:969 , LYS A:1034 , GLY A:1063 , GLY A:1064 , THR A:1065 , GLY A:1066 , ASP A:1105 , GLY A:1106 , GLY A:1107 , GLY A:1128 , SER A:1129 , ILE A:1130 , MET A:1132 , HOH A:2703 , HOH A:2704 , HOH A:2705 , AKG A:3510
BINDING SITE FOR RESIDUE FMN A3508
2
AC2
SOFTWARE
MET A:1132 , CYS A:1137 , ILE A:1138 , MET A:1139 , ALA A:1140 , ARG A:1141 , VAL A:1142 , CYS A:1143 , CYS A:1148 , ALA A:1153
BINDING SITE FOR RESIDUE F3S A3509
3
AC3
SOFTWARE
SER A:876 , ALA A:879 , GLU A:903 , GLN A:969 , LYS A:972 , GLY A:977 , GLN A:978 , ARG A:992 , THR A:1065 , GLY A:1066 , HOH A:2463 , HOH A:2487 , FMN A:3508
BINDING SITE FOR RESIDUE AKG A3510
4
AC4
SOFTWARE
GLY B:874 , MET B:875 , SER B:876 , GLY B:902 , GLU B:903 , GLN B:944 , LYS B:966 , GLN B:969 , LYS B:1034 , GLY B:1063 , GLY B:1064 , THR B:1065 , GLY B:1066 , ASP B:1105 , GLY B:1106 , GLY B:1107 , GLY B:1128 , SER B:1129 , ILE B:1130 , HOH B:2535 , HOH B:2716 , HOH B:2717 , AKG B:3510
BINDING SITE FOR RESIDUE FMN B3508
5
AC5
SOFTWARE
MET B:1132 , CYS B:1137 , ILE B:1138 , MET B:1139 , ALA B:1140 , ARG B:1141 , VAL B:1142 , CYS B:1143 , CYS B:1148 , ALA B:1153
BINDING SITE FOR RESIDUE F3S B3509
6
AC6
SOFTWARE
SER B:876 , ALA B:879 , GLU B:903 , GLN B:969 , LYS B:972 , GLY B:977 , GLN B:978 , ARG B:992 , THR B:1065 , GLY B:1066 , ALA B:1067 , HOH B:2718 , HOH B:2719 , FMN B:3508
BINDING SITE FOR RESIDUE AKG B3510
[
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, 2)
Info
All PROSITE Patterns/Profiles
1: GATASE_TYPE_2 (A:1-395,B:1-395)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GATASE_TYPE_2
PS51278
Glutamine amidotransferase type 2 domain profile.
GLTS_SYNY3
37-431
2
A:1-395
B:1-395
[
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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1ofda1 (A:1240-1507)
1b: SCOP_d1ofdb1 (B:1240-1507)
2a: SCOP_d1ofda3 (A:1-430)
2b: SCOP_d1ofdb3 (B:1-430)
3a: SCOP_d1ofda2 (A:431-1239)
3b: SCOP_d1ofdb2 (B:431-1239)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Single-stranded right-handed beta-helix
(140)
Superfamily
:
Alpha subunit of glutamate synthase, C-terminal domain
(7)
Family
:
Alpha subunit of glutamate synthase, C-terminal domain
(7)
Protein domain
:
Alpha subunit of glutamate synthase, C-terminal domain
(7)
Synechocystis sp. [TaxId: 1143]
(5)
1a
d1ofda1
A:1240-1507
1b
d1ofdb1
B:1240-1507
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ntn hydrolase-like
(356)
Superfamily
:
N-terminal nucleophile aminohydrolases (Ntn hydrolases)
(352)
Family
:
Class II glutamine amidotransferases
(27)
Protein domain
:
Alpha subunit of glutamate synthase, N-terminal domain
(7)
Synechocystis sp. [TaxId: 1143]
(5)
2a
d1ofda3
A:1-430
2b
d1ofdb3
B:1-430
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
FMN-linked oxidoreductases
(290)
Family
:
FMN-linked oxidoreductases
(242)
Protein domain
:
Alpha subunit of glutamate synthase, central and FMN domains
(7)
Synechocystis sp. [TaxId: 1143]
(5)
3a
d1ofda2
A:431-1239
3b
d1ofdb2
B:431-1239
[
close SCOP info
]
CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_1ofdA01 (A:1-421,A:525-533)
1b: CATH_1ofdB01 (B:1-421,B:525-533)
2a: CATH_1ofdA02 (A:422-470,A:482-524,A:534-786)
2b: CATH_1ofdB02 (B:422-470,B:482-524,B:534-786)
2c: CATH_1ofdA03 (A:471-481,A:787-1244)
2d: CATH_1ofdB03 (B:471-481,B:787-1244)
3a: CATH_1ofdA04 (A:1245-1507)
3b: CATH_1ofdB04 (B:1245-1507)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
(128)
Homologous Superfamily
:
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
(124)
Synechocystis sp.. Organism_taxid: 1148. Strain: pcc6803.
(2)
1a
1ofdA01
A:1-421,A:525-533
1b
1ofdB01
B:1-421,B:525-533
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Synechocystis sp.. Organism_taxid: 1148. Strain: pcc6803.
(2)
2a
1ofdA02
A:422-470,A:482-524,A:534-786
2b
1ofdB02
B:422-470,B:482-524,B:534-786
2c
1ofdA03
A:471-481,A:787-1244
2d
1ofdB03
B:471-481,B:787-1244
Class
:
Mainly Beta
(13760)
Architecture
:
3 Solenoid
(196)
Topology
:
Pectate Lyase C-like
(105)
Homologous Superfamily
:
[code=2.160.20.60, no name defined]
(6)
Synechocystis sp.. Organism_taxid: 1148. Strain: pcc6803.
(2)
3a
1ofdA04
A:1245-1507
3b
1ofdB04
B:1245-1507
[
close CATH info
]
Pfam Domains
(4, 8)
Info
all PFAM domains
1a: PFAM_GATase_2_1ofdB01 (B:1-368)
1b: PFAM_GATase_2_1ofdB02 (B:1-368)
2a: PFAM_Glu_syn_central_1ofdB03 (B:443-739)
2b: PFAM_Glu_syn_central_1ofdB04 (B:443-739)
3a: PFAM_Glu_synthase_1ofdB05 (B:795-1191)
3b: PFAM_Glu_synthase_1ofdB06 (B:795-1191)
4a: PFAM_GXGXG_1ofdB07 (B:1269-1464)
4b: PFAM_GXGXG_1ofdB08 (B:1269-1464)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NTN
(93)
Family
:
GATase_2
(9)
Synechocystis sp. (strain ATCC 27184 / PCC 6803 / N-1)
(5)
1a
GATase_2-1ofdB01
B:1-368
1b
GATase_2-1ofdB02
B:1-368
Clan
:
TIM_barrel
(694)
Family
:
Glu_syn_central
(5)
Synechocystis sp. (strain ATCC 27184 / PCC 6803 / N-1)
(5)
2a
Glu_syn_central-1ofdB03
B:443-739
2b
Glu_syn_central-1ofdB04
B:443-739
Family
:
Glu_synthase
(5)
Synechocystis sp. (strain ATCC 27184 / PCC 6803 / N-1)
(5)
3a
Glu_synthase-1ofdB05
B:795-1191
3b
Glu_synthase-1ofdB06
B:795-1191
Clan
:
no clan defined [family: GXGXG]
(5)
Family
:
GXGXG
(5)
Synechocystis sp. (strain ATCC 27184 / PCC 6803 / N-1)
(5)
4a
GXGXG-1ofdB07
B:1269-1464
4b
GXGXG-1ofdB08
B:1269-1464
[
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
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 (492 KB)
Header - Asym.Unit
Biol.Unit 1 (247 KB)
Header - Biol.Unit 1
Biol.Unit 2 (245 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
1OFD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
