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3L4P
Biol. Unit 1
Info
Asym.Unit (326 KB)
Biol.Unit 1 (318 KB)
Biol.Unit 2 (632 KB)
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(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, M. J. Romao
Date
:
21 Dec 09 (Deposition) - 16 Feb 10 (Release) - 16 Feb 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.45
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (2x)
Keywords
:
Molybdenum-Containing Enzymes, Aldehyde Oxidoreductase, Xanthine Oxidase Family, Reduced Form, Arsenite Inhibition, 2Fe-2S, Fad, Flavoprotein, Iron, Iron-Sulfur, Metal- Binding, Molybdenum, Nad, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Thapper, D. R. Boer, C. D. Brondino, J. J. Moura, M. J. Romao
Correlating Epr And X-Ray Structural Analysis Of Arsenite-Inhibited Forms Of Aldehyde Oxidoreductase.
J. Biol. Inorg. Chem. V. 12 353 2007
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Hetero Components
(5, 8)
Info
All Hetero Components
1a: ARSENITE (ASTa)
2a: CALCIUM ION (CAa)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
3f: CHLORIDE ION (CLf)
3g: CHLORIDE ION (CLg)
3h: CHLORIDE ION (CLh)
3i: CHLORIDE ION (CLi)
4a: FE2/S2 (INORGANIC) CLUSTER (FESa)
4b: FE2/S2 (INORGANIC) CLUSTER (FESb)
5a: ISOPROPYL ALCOHOL (IPAa)
5b: ISOPROPYL ALCOHOL (IPAb)
5c: ISOPROPYL ALCOHOL (IPAc)
6a: LITHIUM ION (LIa)
7a: MAGNESIUM ION (MGa)
7b: MAGNESIUM ION (MGb)
7c: MAGNESIUM ION (MGc)
7d: MAGNESIUM ION (MGd)
7e: MAGNESIUM ION (MGe)
8a: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTI... (PCDa)
9a: UREA (UREa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AST
1
Ligand/Ion
ARSENITE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
IPA
3
Ligand/Ion
ISOPROPYL ALCOHOL
6
LI
-1
Ligand/Ion
LITHIUM ION
7
MG
-1
Ligand/Ion
MAGNESIUM ION
8
PCD
1
Ligand/Ion
(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
9
URE
1
Ligand/Ion
UREA
[
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Sites
(24, 24)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
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
02
AC2
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 , ARG A:58 , CYS A:60
BINDING SITE FOR RESIDUE FES A 909
03
AC3
SOFTWARE
HOH A:1391 , HOH A:1568 , HOH A:1760 , HOH A:1937 , HOH A:1938 , HOH A:2272
BINDING SITE FOR RESIDUE MG A 910
04
AC4
SOFTWARE
HOH A:1260 , HOH A:1750 , HOH A:1831 , HOH A:1843 , HOH A:1983 , HOH A:1984
BINDING SITE FOR RESIDUE MG A 911
05
AC5
SOFTWARE
HOH A:1395 , HOH A:1677 , HOH A:1708 , HOH A:1710 , HOH A:1828 , HOH A:1900
BINDING SITE FOR RESIDUE MG A 912
06
AC6
SOFTWARE
ASP A:263 , GLU A:899 , GLU A:903 , HOH A:1723 , HOH A:1727 , HOH A:2813
BINDING SITE FOR RESIDUE MG A 913
07
AC7
SOFTWARE
HOH A:1337 , HOH A:1467 , HOH A:1647 , HOH A:1721 , HOH A:2611 , HOH A:2612
BINDING SITE FOR RESIDUE MG A 914
08
AC8
SOFTWARE
ALA A:649 , GLU A:651 , GLY A:693 , HOH A:1243
BINDING SITE FOR RESIDUE LI A 915
09
AC9
SOFTWARE
PRO A:258 , THR A:259 , ALA A:755 , HOH A:1438 , HOH A:2296
BINDING SITE FOR RESIDUE CL A 916
10
BC1
SOFTWARE
PHE A:167 , SER A:178 , LYS A:179 , HOH A:1331 , HOH A:1765
BINDING SITE FOR RESIDUE CL A 917
11
BC2
SOFTWARE
ARG A:123 , LYS A:605
BINDING SITE FOR RESIDUE CL A 918
12
BC3
SOFTWARE
TYR A:892 , ARG A:893 , HOH A:1664
BINDING SITE FOR RESIDUE CL A 919
13
BC4
SOFTWARE
LYS A:248 , PRO A:898 , GLU A:899
BINDING SITE FOR RESIDUE CL A 920
14
BC5
SOFTWARE
LYS A:473 , ASP A:474
BINDING SITE FOR RESIDUE CL A 921
15
BC6
SOFTWARE
MET A:1 , ALA A:19
BINDING SITE FOR RESIDUE CL A 923
16
BC7
SOFTWARE
ASP A:342 , THR A:343 , GLY A:344
BINDING SITE FOR RESIDUE CL A 925
17
BC8
SOFTWARE
ARG A:460 , SER A:461 , LEU A:498 , ALA A:531 , PHE A:532 , TYR A:535 , GLY A:536 , GLN A:539 , HOH A:957
BINDING SITE FOR RESIDUE URE A 926
18
BC9
SOFTWARE
ASP A:826 , ILE A:827 , LYS A:828 , LYS A:829 , HOH A:2595 , HOH A:2596
BINDING SITE FOR RESIDUE CL A 930
19
CC1
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 , AST A:932 , IPA A:933 , HOH A:1409 , HOH A:2814
BINDING SITE FOR RESIDUE PCD A 931
20
CC2
SOFTWARE
TYR A:535 , TYR A:622 , GLY A:696 , GLY A:697 , GLU A:869 , PCD A:931 , HOH A:1236
BINDING SITE FOR RESIDUE AST A 932
21
CC3
SOFTWARE
TYR A:535 , LEU A:626 , GLY A:697 , PCD A:931 , HOH A:1236
BINDING SITE FOR RESIDUE IPA A 933
22
CC4
SOFTWARE
ASN A:691 , HOH A:1012
BINDING SITE FOR RESIDUE IPA A 934
23
CC5
SOFTWARE
LEU A:626
BINDING SITE FOR RESIDUE IPA A 935
24
CC6
SOFTWARE
ASP A:288 , HOH A:1935
BINDING SITE FOR RESIDUE CA A 1457
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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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
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 4)
Info
All SCOP Domains
1a: SCOP_d3l4pa1 (A:81-193)
2a: SCOP_d3l4pa3 (A:194-310)
3a: SCOP_d3l4pa2 (A:1-80)
4a: SCOP_d3l4pa4 (A:311-907)
View:
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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
d3l4pa1
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
d3l4pa3
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
d3l4pa2
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
d3l4pa4
A:311-907
[
close SCOP info
]
CATH Domains
(4, 7)
Info
all CATH domains
1a: CATH_3l4pA04 (A:331-364,A:458-580)
1b: CATH_3l4pA06 (A:581-624,A:751-907)
1c: CATH_3l4pA05 (A:365-457)
1d: CATH_3l4pA07 (A:625-750)
2a: CATH_3l4pA03 (A:208-308)
3a: CATH_3l4pA01 (A:1-74)
4a: CATH_3l4pA02 (A:75-193)
View:
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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
3l4pA04
A:331-364,A:458-580
1b
3l4pA06
A:581-624,A:751-907
1c
3l4pA05
A:365-457
1d
3l4pA07
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
3l4pA03
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
3l4pA01
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
3l4pA02
A:75-193
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Protein & NOT PROSITE
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Asymmetric Unit 1
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Asym.Unit (326 KB)
Header - Asym.Unit
Biol.Unit 1 (318 KB)
Header - Biol.Unit 1
Biol.Unit 2 (632 KB)
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