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3C8Y
Asym. Unit
Info
Asym.Unit (219 KB)
Biol.Unit 1 (213 KB)
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(1)
Title
:
1.39 ANGSTROM CRYSTAL STRUCTURE OF FE-ONLY HYDROGENASE
Authors
:
A. S. Pandey, B. J. Lemon, J. W. Peters
Date
:
14 Feb 08 (Deposition) - 22 Apr 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.39
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Dithiomethylether, H-Cluster, Hydrogenase, Iron, Iron-Sulfur, Metal- Binding, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. S. Pandey, T. V. Harris, L. J. Giles, J. W. Peters, R. K. Szilagyi
Dithiomethylether As A Ligand In The Hydrogenase H-Cluster.
J. Am. Chem. Soc. V. 130 4533 2008
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Hetero Components
(4, 9)
Info
All Hetero Components
1a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: 2 IRON/2 SULFUR/3 CARBONYL/2 CYANI... (HCNa)
4a: IRON/SULFUR CLUSTER (SF4a)
4b: IRON/SULFUR CLUSTER (SF4b)
4c: IRON/SULFUR CLUSTER (SF4c)
4d: IRON/SULFUR CLUSTER (SF4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
2
GOL
3
Ligand/Ion
GLYCEROL
3
HCN
1
Ligand/Ion
2 IRON/2 SULFUR/3 CARBONYL/2 CYANIDE/WATER/METHYLETHERCLUSTER
4
SF4
4
Ligand/Ion
IRON/SULFUR CLUSTER
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Sites
(9, 9)
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)
9: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:230 , PRO A:231 , SER A:232 , ILE A:268 , ALA A:272 , CYS A:299 , PRO A:324 , GLN A:325 , MET A:353 , PRO A:354 , CYS A:355 , LYS A:358 , PHE A:417 , MET A:497 , CYS A:503
BINDING SITE FOR RESIDUE HCN A 575
2
AC2
SOFTWARE
CYS A:300 , PRO A:301 , CYS A:355 , CYS A:499 , CYS A:503 , GLY A:506
BINDING SITE FOR RESIDUE SF4 A 576
3
AC3
SOFTWARE
CYS A:157 , THR A:163 , MET A:166 , CYS A:190 , LEU A:191 , LEU A:192 , CYS A:193 , GLY A:194 , CYS A:196
BINDING SITE FOR RESIDUE SF4 A 577
4
AC4
SOFTWARE
CYS A:147 , LEU A:148 , LEU A:149 , CYS A:150 , GLY A:151 , CYS A:153 , CYS A:200 , PRO A:201 , ALA A:204 , LEU A:205
BINDING SITE FOR RESIDUE SF4 A 578
5
AC5
SOFTWARE
HIS A:94 , GLU A:95 , PHE A:96 , LYS A:97 , CYS A:98 , CYS A:101 , CYS A:107 , LYS A:146 , ALA A:203
BINDING SITE FOR RESIDUE SF4 A 579
6
AC6
SOFTWARE
LEU A:33 , CYS A:34 , PHE A:35 , CYS A:46 , GLU A:47 , CYS A:49 , CYS A:62
BINDING SITE FOR RESIDUE FES A 580
7
AC7
SOFTWARE
LYS A:223 , LYS A:333 , LYS A:345 , PHE A:348 , ARG A:373 , ASP A:376 , HOH A:1087
BINDING SITE FOR RESIDUE GOL A 581
8
AC8
SOFTWARE
ARG A:104 , ASN A:106 , CYS A:107 , LEU A:110 , LYS A:111 , ASN A:437 , HOH A:795 , HOH A:1008
BINDING SITE FOR RESIDUE GOL A 582
9
AC9
SOFTWARE
LYS A:223 , PHE A:348 , HOH A:701 , HOH A:846 , HOH A:855
BINDING SITE FOR RESIDUE GOL A 583
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 5)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (A:1-78)
2: 4FE4S_FER_2 (A:138-167|A:181-210)
3: 4FE4S_FER_1 (A:147-158|A:190-201)
;
View:
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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.
PHF1_CLOPA
1-78
1
A:1-78
2
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
PHF1_CLOPA
138-167
181-210
2
A:138-167
A:181-210
3
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
PHF1_CLOPA
147-158
190-201
2
A:147-158
A:190-201
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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.
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d3c8ya2 (A:1-126)
2a: SCOP_d3c8ya3 (A:127-209)
3a: SCOP_d3c8ya1 (A:210-574)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
2Fe-2S ferredoxin domains from multidomain proteins
(82)
Protein domain
:
Fe-only hydrogenase, N-terminal domain
(4)
Clostridium pasteurianum [TaxId: 1501]
(4)
1a
d3c8ya2
A:1-126
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
4Fe-4S ferredoxins
(143)
Family
:
Ferredoxin domains from multidomain proteins
(69)
Protein domain
:
Fe-only hydrogenase, second domain
(4)
Clostridium pasteurianum [TaxId: 1501]
(4)
2a
d3c8ya3
A:127-209
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Fe-only hydrogenase
(5)
Superfamily
:
Fe-only hydrogenase
(5)
Family
:
Fe-only hydrogenase
(5)
Protein domain
:
Fe-only hydrogenase, catalytic domain
(4)
Clostridium pasteurianum [TaxId: 1501]
(4)
3a
d3c8ya1
A:210-574
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3c8yA02 (A:125-208)
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)
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)
Clostridium pasteurianum
(1)
1a
3c8yA02
A:125-208
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Pfam Domains
(0, 0)
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Chain A
Asymmetric Unit 1
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Asym.Unit (219 KB)
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