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.
1SIJ
Asym. Unit
Info
Asym.Unit (155 KB)
Biol.Unit 1 (150 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 THE ALDEHYDE DEHYDROGENASE (A.K.A. AOR OR MOP) OF DESULFOVIBRIO GIGAS COVALENTLY BOUND TO [ASO3]-
Authors
:
D. R. Boer, A. Thapper, C. D. Brondino, M. J. Romao, J. J. G. Moura
Date
:
01 Mar 04 (Deposition) - 27 Jul 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Aldehyde Oxidoreductase; Xanthine Oxidase Family; Arsenite Inhibition
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. R. Boer, A. Thapper, C. D. Brondino, M. J. Romao, J. J. G. Moura
X-Ray Crystal Structure And Epr Spectra Of "Arsenite-Inhibited" Desulfovibriogigas Aldehyde Dehydrogenase: A Member Of The Xanthine Oxidase Family
J. Am. Chem. Soc. V. 126 8614 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 9)
Info
All Hetero Components
1a: ARSENITE (ASTa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTI... (PCDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AST
1
Ligand/Ion
ARSENITE
2
CL
3
Ligand/Ion
CHLORIDE ION
3
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
MG
2
Ligand/Ion
MAGNESIUM ION
5
PCD
1
Ligand/Ion
(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:460 , TYR A:535 , GLN A:539
BINDING SITE FOR RESIDUE CL A 916
2
AC2
SOFTWARE
TYR A:892 , ARG A:893
BINDING SITE FOR RESIDUE CL A 918
3
AC3
SOFTWARE
LYS A:248 , PRO A:898 , GLU A:899
BINDING SITE FOR RESIDUE CL A 920
4
AC4
SOFTWARE
ASP A:263 , GLU A:899 , GLU A:903 , HOH A:923 , HOH A:924 , HOH A:925
BINDING SITE FOR RESIDUE MG A 917
5
AC5
SOFTWARE
GLN A:99 , CYS A:139 , GLY A:419 , THR A:420 , PHE A:421 , GLY A:422 , ALA A:531 , PHE A:532 , ARG A:533 , TRP A:650 , HIS A:653 , GLY A:654 , GLN A:655 , GLY A:656 , GLY A:660 , SER A:695 , GLY A:696 , GLY A:697 , SER A:698 , ARG A:699 , GLN A:700 , GLN A:701 , LEU A:795 , SER A:797 , CYS A:799 , ASN A:800 , THR A:804 , GLN A:807 , ALA A:864 , SER A:865 , GLY A:866 , VAL A:867 , GLY A:868 , AST A:922 , HOH A:926
BINDING SITE FOR RESIDUE PCD A 921
6
AC6
SOFTWARE
TYR A:535 , TYR A:622 , GLY A:696 , GLY A:697 , GLU A:869 , PCD A:921 , HOH A:1244
BINDING SITE FOR RESIDUE AST A 922
7
AC7
SOFTWARE
GLN A:99 , CYS A:100 , GLY A:101 , CYS A:103 , CYS A:137 , ARG A:138 , CYS A:139 , ILE A:368
BINDING SITE FOR RESIDUE FES A 908
8
AC8
SOFTWARE
GLY A:39 , CYS A:40 , GLU A:41 , GLY A:43 , GLN A:44 , CYS A:45 , GLY A:46 , CYS A:48 , CYS A:60
BINDING SITE FOR RESIDUE FES A 909
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (A:2-79)
2: 2FE2S_FER_1 (A:40-48)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
2FE2S_FER_2
PS51085
2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
MOP_DESGI
2-79
1
A:2-79
2
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
MOP_DESGI
40-48
1
A:40-48
[
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
(4, 4)
Info
All SCOP Domains
1a: SCOP_d1sija1 (A:81-193)
2a: SCOP_d1sija3 (A:194-310)
3a: SCOP_d1sija2 (A:1-80)
4a: SCOP_d1sija4 (A:311-907)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
CO dehydrogenase ISP C-domain like
(45)
Superfamily
:
CO dehydrogenase ISP C-domain like
(45)
Family
:
CO dehydrogenase ISP C-domain like
(42)
Protein domain
:
Aldehyde oxidoreductase, domain 2
(9)
Desulfovibrio gigas [TaxId: 879]
(8)
1a
d1sija1
A:81-193
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
CO dehydrogenase molybdoprotein N-domain-like
(44)
Family
:
CO dehydrogenase molybdoprotein N-domain-like
(34)
Protein domain
:
Aldehyde oxidoreductase, domain 3
(9)
Desulfovibrio gigas [TaxId: 879]
(8)
2a
d1sija3
A:194-310
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
2Fe-2S ferredoxin domains from multidomain proteins
(82)
Protein domain
:
Aldehyde oxidoreductase, N-terminal domain
(9)
Desulfovibrio gigas [TaxId: 879]
(8)
3a
d1sija2
A:1-80
Fold
:
Molybdenum cofactor-binding domain
(44)
Superfamily
:
Molybdenum cofactor-binding domain
(44)
Family
:
Molybdenum cofactor-binding domain
(44)
Protein domain
:
Aldehyde oxidoreductase
(9)
Desulfovibrio gigas [TaxId: 879]
(8)
4a
d1sija4
A:311-907
[
close SCOP info
]
CATH Domains
(4, 7)
Info
all CATH domains
1a: CATH_1sijA04 (A:331-364,A:458-580)
1b: CATH_1sijA07 (A:581-624,A:751-907)
1c: CATH_1sijA05 (A:365-457)
1d: CATH_1sijA06 (A:625-750)
2a: CATH_1sijA03 (A:208-308)
3a: CATH_1sijA01 (A:1-74)
4a: CATH_1sijA02 (A:75-193)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Aldehyde Oxidoreductase; domain 4
(20)
Homologous Superfamily
:
Aldehyde Oxidoreductase; domain 4
(20)
Desulfovibrio gigas. Organism_taxid: 879
(5)
1a
1sijA04
A:331-364,A:458-580
1b
1sijA07
A:581-624,A:751-907
1c
1sijA05
A:365-457
1d
1sijA06
A:625-750
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aldehyde Oxidoreductase; domain 3
(111)
Homologous Superfamily
:
[code=3.90.1170.50, no name defined]
(20)
Desulfovibrio gigas. Organism_taxid: 879
(5)
2a
1sijA03
A:208-308
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Desulfovibrio gigas. Organism_taxid: 879
(5)
3a
1sijA01
A:1-74
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.120, no name defined]
(29)
Desulfovibrio gigas. Organism_taxid: 879
(5)
4a
1sijA02
A:75-193
[
close CATH info
]
Pfam Domains
(4, 4)
Info
all PFAM domains
1a: PFAM_Fer2_1sijA01 (A:6-73)
2a: PFAM_Fer2_2_1sijA02 (A:75-151)
3a: PFAM_Ald_Xan_dh_C2_1sijA03 (A:315-845)
4a: PFAM_Ald_Xan_dh_C_1sijA04 (A:190-308)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Fer2
(69)
Family
:
Fer2
(60)
Desulfovibrio gigas
(2)
1a
Fer2-1sijA01
A:6-73
Family
:
Fer2_2
(24)
Desulfovibrio gigas
(2)
2a
Fer2_2-1sijA02
A:75-151
Clan
:
no clan defined [family: Ald_Xan_dh_C2]
(24)
Family
:
Ald_Xan_dh_C2
(24)
Desulfovibrio gigas
(2)
3a
Ald_Xan_dh_C2-1sijA03
A:315-845
Clan
:
no clan defined [family: Ald_Xan_dh_C]
(24)
Family
:
Ald_Xan_dh_C
(24)
Desulfovibrio gigas
(2)
4a
Ald_Xan_dh_C-1sijA04
A:190-308
[
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
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 (155 KB)
Header - Asym.Unit
Biol.Unit 1 (150 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
1SIJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
