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3FC4
Biol. Unit 2
Info
Asym.Unit (172 KB)
Biol.Unit 1 (166 KB)
Biol.Unit 2 (327 KB)
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(1)
Title
:
ETHYLENE GLYCOL INHIBITED FORM OF ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO GIGAS
Authors
:
T. Santos-Silva, M. J. Romao
Date
:
21 Nov 08 (Deposition) - 06 Oct 09 (Release) - 06 Oct 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.79
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (2x)
Keywords
:
Mo-Ethylene Glycol Adduct, 2Fe-2S, Fad, Flavoprotein, Iron, Iron-Sulfur, Metal-Binding, Molybdenum, Nad, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Santos-Silva, F. Ferroni, A. Thapper, J. Marangon, P. J. Gonzalez, A. C. Rizzi, I. Moura, J. J. Moura, M. J. Romao, C. D. Brondino
Kinetic, Structural, And Epr Studies Reveal That Aldehyde Oxidoreductase From Desulfovibrio Gigas Does Not Need A Sulfido Ligand For Catalysis And Give Evidence For A Direct Mo-C Interaction In A Biological System.
J. Am. Chem. Soc. V. 131 7990 2009
(for further references see the
PDB file header
)
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
5a: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTI... (PCDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
3
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
PCD
2
Ligand/Ion
(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
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Sites
(12, 12)
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)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:1148 , HOH A:1620 , HOH A:1798 , HOH A:1862 , HOH A:1944 , HOH A:2063
BINDING SITE FOR RESIDUE MG A 919
02
AC2
SOFTWARE
LYS A:248 , PRO A:898 , GLU A:899 , HOH A:1097
BINDING SITE FOR RESIDUE CL A 920
03
AC3
SOFTWARE
ARG A:460 , TYR A:535 , GLN A:539
BINDING SITE FOR RESIDUE CL A 916
04
AC4
SOFTWARE
ASP A:263 , GLU A:899 , GLU A:903 , HOH A:1379 , HOH A:1442 , HOH A:1520
BINDING SITE FOR RESIDUE MG A 917
05
AC5
SOFTWARE
TYR A:892 , ARG A:893 , HOH A:1867
BINDING SITE FOR RESIDUE CL A 918
06
AC6
SOFTWARE
HOH A:927 , HOH A:928 , HOH A:929 , HOH A:1144 , HOH A:1145 , HOH A:1183
BINDING SITE FOR RESIDUE MG A 915
07
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
08
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
09
AC9
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 , 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 , GLU A:869 , EDO A:912 , HOH A:1199 , HOH A:1361
BINDING SITE FOR RESIDUE PCD A 921
10
BC1
SOFTWARE
LYS A:472 , LYS A:473 , ASP A:474
BINDING SITE FOR RESIDUE EDO A 910
11
BC2
SOFTWARE
LEU A:254 , ILE A:255 , THR A:256 , ALA A:780 , THR A:781 , LEU A:902 , HOH A:932 , HOH A:1396 , HOH A:1729 , HOH A:1781
BINDING SITE FOR RESIDUE EDO A 911
12
BC3
SOFTWARE
PHE A:425 , ALA A:531 , TYR A:535 , TYR A:622 , GLY A:696 , GLY A:697 , GLU A:869 , PCD A:921 , HOH A:1335
BINDING SITE FOR RESIDUE EDO A 912
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (A:2-79)
2: 2FE2S_FER_1 (A:40-48)
;
View:
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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
2
A:2-79
2
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
MOP_DESGI
40-48
2
A:40-48
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 4)
Info
All SCOP Domains
1a: SCOP_d3fc4a2 (A:81-193)
2a: SCOP_d3fc4a3 (A:194-310)
3a: SCOP_d3fc4a1 (A:1-80)
4a: SCOP_d3fc4a4 (A:311-907)
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Classes
(
)
(
)
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(
)
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)
(
)
Families
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)
(
)
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
d3fc4a2
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
d3fc4a3
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
d3fc4a1
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
d3fc4a4
A:311-907
[
close SCOP info
]
CATH Domains
(4, 7)
Info
all CATH domains
1a: CATH_3fc4A04 (A:331-364,A:458-580)
1b: CATH_3fc4A06 (A:581-624,A:751-907)
1c: CATH_3fc4A05 (A:365-457)
1d: CATH_3fc4A07 (A:625-750)
2a: CATH_3fc4A03 (A:208-308)
3a: CATH_3fc4A01 (A:1-74)
4a: CATH_3fc4A02 (A:75-193)
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(
)
(
)
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
3fc4A04
A:331-364,A:458-580
1b
3fc4A06
A:581-624,A:751-907
1c
3fc4A05
A:365-457
1d
3fc4A07
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
3fc4A03
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
3fc4A01
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
3fc4A02
A:75-193
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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