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1H0H
Biol. Unit 1
Info
Asym.Unit (435 KB)
Biol.Unit 1 (218 KB)
Biol.Unit 2 (214 KB)
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(1)
Title
:
TUNGSTEN CONTAINING FORMATE DEHYDROGENASE FROM DESULFOVIBRIO GIGAS
Authors
:
H. C. A. Raaijmakers
Date
:
19 Jun 02 (Deposition) - 20 Feb 03 (Release) - 28 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,K,L
Biol. Unit 1: A,B (1x)
Biol. Unit 2: K,L (1x)
Keywords
:
Electron Transport, Tungsten Selenium Formate Dehydrogenase, Selenocysteine, Molybdopterin, Mgd, Iron-Sulphur Cluster, Periplasmic
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. C. A. Raaijmakers, S. Macieira, J. Dias, S. Teixeira, S. Bursakov, R. Huber, J. Moura, I. Moura, M. Romao
Gene Sequence And The 1. 8 A Crystal Structure Of The Tungsten-Containing Formate Dehydrogenase From Desulfovibri Gigas
Structure V. 10 1261 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 8)
Info
All Hetero Components
1a: GUANYLATE-O'-PHOSPHORIC ACID MONO-... (2MDa)
1b: GUANYLATE-O'-PHOSPHORIC ACID MONO-... (2MDb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
3b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
4a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDa)
4b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDb)
5a: (SECa)
5b: (SECb)
6a: IRON/SULFUR CLUSTER (SF4a)
6b: IRON/SULFUR CLUSTER (SF4b)
6c: IRON/SULFUR CLUSTER (SF4c)
6d: IRON/SULFUR CLUSTER (SF4d)
6e: IRON/SULFUR CLUSTER (SF4e)
6f: IRON/SULFUR CLUSTER (SF4f)
6g: IRON/SULFUR CLUSTER (SF4g)
6h: IRON/SULFUR CLUSTER (SF4h)
7a: UNKNOWN ATOM OR ION (UNXa)
7b: UNKNOWN ATOM OR ION (UNXb)
8a: TUNGSTEN ION (Wa)
8b: TUNGSTEN ION (Wb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2MD
1
Ligand/Ion
GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER
2
CA
-1
Ligand/Ion
CALCIUM ION
3
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
MGD
1
Ligand/Ion
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINEDINUCLEOTIDE
5
SEC
-1
Mod. Amino Acid
6
SF4
4
Ligand/Ion
IRON/SULFUR CLUSTER
7
UNX
1
Ligand/Ion
UNKNOWN ATOM OR ION
8
W
-1
Ligand/Ion
TUNGSTEN ION
[
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]
Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:358 , LYS A:360 , LYS A:363 , LEU A:393 , GLY A:394 , ASN A:395 , HOH A:2328
BINDING SITE FOR RESIDUE CA A 1100
02
AC3
SOFTWARE
SEC A:158 , 2MD A:1001 , MGD A:1002 , UNX A:1003
BINDING SITE FOR RESIDUE W A 1000
03
AC5
SOFTWARE
ALA A:130 , GLN A:154 , ILE A:157 , SEC A:158 , MET A:371 , GLU A:409 , GLY A:516 , GLN A:517 , ASN A:518 , SER A:522 , VAL A:542 , ASN A:543 , ILE A:544 , CYS A:572 , ALA A:573 , LYS A:578 , ASP A:605 , THR A:854 , ARG A:856 , GLN A:862 , THR A:863 , LEU A:865 , MET A:866 , TRP A:936 , ASN A:951 , THR A:967 , W A:1000 , MGD A:1002 , UNX A:1003 , HOH A:2646 , HOH A:2692 , HOH A:2697
BINDING SITE FOR RESIDUE 2MD A 1001
04
AC6
SOFTWARE
LYS A:56 , SEC A:158 , GLY A:192 , SER A:193 , ASN A:194 , GLU A:197 , ASN A:198 , VAL A:219 , ASP A:220 , PRO A:221 , ARG A:222 , SER A:238 , GLY A:239 , ASP A:241 , ALA A:370 , MET A:371 , TRP A:373 , GLY A:408 , TYR A:855 , ARG A:856 , VAL A:857 , THR A:858 , HIS A:860 , TRP A:861 , GLN A:862 , HIS A:937 , LYS A:968 , W A:1000 , 2MD A:1001 , UNX A:1003 , HOH A:2053 , HOH A:2317 , HOH A:2700 , HOH A:2701
BINDING SITE FOR RESIDUE MGD A 1002
05
AC7
SOFTWARE
SEC A:158 , GLU A:409 , VAL A:412 , W A:1000 , 2MD A:1001 , MGD A:1002
BINDING SITE FOR RESIDUE UNX A 1003
06
AC8
SOFTWARE
CYS A:17 , TYR A:19 , CYS A:20 , CYS A:24 , LEU A:53 , CYS A:54 , GLY A:57 , PRO A:200 , ILE A:201
BINDING SITE FOR RESIDUE SF4 A 1010
07
AC9
SOFTWARE
HOH A:2702 , HOH A:2703 , HOH A:2704 , PRO B:42 , ASP B:43 , ASP B:123 , ARG B:126 , TYR B:211
BINDING SITE FOR RESIDUE EPE A 1200
08
BC1
SOFTWARE
CYS B:11 , THR B:12 , ALA B:13 , CYS B:14 , ARG B:15 , CYS B:17 , CYS B:156 , THR B:158 , MET B:161
BINDING SITE FOR RESIDUE SF4 B 1011
09
BC2
SOFTWARE
PHE B:4 , CYS B:21 , HIS B:25 , GLN B:71 , CYS B:137 , ASP B:138 , MET B:139 , CYS B:140 , PRO B:150 , CYS B:152
BINDING SITE FOR RESIDUE SF4 B 1012
10
BC3
SOFTWARE
CYS B:72 , ARG B:73 , CYS B:75 , PRO B:79 , CYS B:80 , CYS B:120 , TYR B:122 , PRO B:125 , LYS B:136
BINDING SITE FOR RESIDUE SF4 B 1013
[
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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
(3, 3)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_MOW_BIS_MGD (A:10-68)
2: MOLYBDOPTERIN_PROK_1 (A:15-33)
3: MOLYBDOPTERIN_PROK_3 (A:889-916)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_MOW_BIS_MGD
PS51669
Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
FDHA_DESGI
45-103
1
A:10-68
-
2
MOLYBDOPTERIN_PROK_1
PS00551
Prokaryotic molybdopterin oxidoreductases signature 1.
FDHA_DESGI
50-68
1
A:15-33
-
3
MOLYBDOPTERIN_PROK_3
PS00932
Prokaryotic molybdopterin oxidoreductases signature 3.
FDHA_DESGI
924-951
1
A:889-916
-
[
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Exons
(0, 0)
Info
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1h0ha1 (A:813-977)
1b: SCOP_d1h0hk1 (K:813-977)
2a: SCOP_d1h0hb_ (B:)
2b: SCOP_d1h0hl_ (L:)
3a: SCOP_d1h0ha2 (A:1-812)
3b: SCOP_d1h0hk2 (K:1-812)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double psi beta-barrel
(111)
Superfamily
:
ADC-like
(88)
Family
:
Formate dehydrogenase/DMSO reductase, C-terminal domain
(41)
Protein domain
:
Tungsten containing formate dehydrogenase, large subunit
(1)
Desulfovibrio gigas [TaxId: 879]
(1)
1a
d1h0ha1
A:813-977
1b
d1h0hk1
K:813-977
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
4Fe-4S ferredoxins
(143)
Family
:
Ferredoxin domains from multidomain proteins
(69)
Protein domain
:
Tungsten containing formate dehydrogenase, small subunit
(1)
Desulfovibrio gigas [TaxId: 879]
(1)
2a
d1h0hb_
B:
2b
d1h0hl_
L:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Superfamily
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Family
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Protein domain
:
Tungsten containing formate dehydrogenase, large subunit
(1)
Desulfovibrio gigas [TaxId: 879]
(1)
3a
d1h0ha2
A:1-812
3b
d1h0hk2
K:1-812
[
close SCOP info
]
CATH Domains
(4, 10)
Info
all CATH domains
1a: CATH_1h0hB02 (B:74-137)
1b: CATH_1h0hL02 (L:74-137)
1c: CATH_1h0hB01 (B:1-73,B:138-214)
1d: CATH_1h0hL01 (L:1-73,L:138-214)
2a: CATH_1h0hA03 (A:157-268,A:321-410,A:735-801)
2b: CATH_1h0hK03 (K:157-268,K:321-410,K:735-801)
3a: CATH_1h0hA02 (A:69-156,A:490-640)
3b: CATH_1h0hK02 (K:69-156,K:490-640)
4a: CATH_1h0hA04 (A:802-977)
4b: CATH_1h0hK04 (K:802-977)
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)
(
)
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.20, no name defined]
(120)
Desulfovibrio gigas. Organism_taxid: 879. Strain: ncib 9332.
(1)
1a
1h0hB02
B:74-137
1b
1h0hL02
L:74-137
1c
1h0hB01
B:1-73,B:138-214
1d
1h0hL01
L:1-73,L:138-214
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Dimethylsulfoxide Reductase; domain 2
(37)
Homologous Superfamily
:
Dimethylsulfoxide Reductase, domain 2
(37)
Desulfovibrio gigas. Organism_taxid: 879. Strain: ncib 9332.
(1)
2a
1h0hA03
A:157-268,A:321-410,A:735-801
2b
1h0hK03
K:157-268,K:321-410,K:735-801
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.740, no name defined]
(37)
Desulfovibrio gigas. Organism_taxid: 879. Strain: ncib 9332.
(1)
3a
1h0hA02
A:69-156,A:490-640
3b
1h0hK02
K:69-156,K:490-640
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Barwin-like endoglucanases
(75)
Homologous Superfamily
:
[code=2.40.40.20, no name defined]
(63)
Desulfovibrio gigas. Organism_taxid: 879. Strain: ncib 9332.
(1)
4a
1h0hA04
A:802-977
4b
1h0hK04
K:802-977
[
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]
Pfam Domains
(0, 0)
Info
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