5JSK
The 3D structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough in the reduced state at 0.95 Angstrom resolution
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d5jska_ | Multi-domain proteins (alpha and beta) | HydA/Nqo6-like | HydA/Nqo6-like | Nickel-iron hydrogenase, small subunit | automated matches | (Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | PF01058 | e5jskA1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: CheY-like | F: PF01058 | ECOD (1.6) |
A | PF14720 | e5jskA2 | A: few secondary structure elements | X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology) | H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology) | T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit | F: PF14720 | ECOD (1.6) |
B | PF00374 | e5jskB1 | A: beta meanders | X: all-beta domain in nickel-iron hydrogenase large subunit (From Topology) | H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology) | T: all-beta domain in nickel-iron hydrogenase large subunit | F: PF00374 | ECOD (1.6) |
B | PF00374 | e5jskB4 | A: alpha complex topology | X: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology) | H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology) | T: alpha-helical domain in nickel-iron hydrogenase, large subunit | F: PF00374 | ECOD (1.6) |
B | PF00374 | e5jskB2 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: PF00374 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.40.50.700 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | NADH:ubiquinone oxidoreductase-like, 20kDa subunit | CATH (4.3.0) |
A | 4.10.480.10 | Few Secondary Structures | Irregular | Cytochrome-c3 Hydrogenase | Chain A, domain 2 | CATH (4.3.0) |
B | 1.10.645.10 | Mainly Alpha | Orthogonal Bundle | Cytochrome-c3 Hydrogenase | chain B | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF14720 | NiFe/NiFeSe hydrogenase small subunit C-terminal (NiFe_hyd_SSU_C) | NiFe/NiFeSe hydrogenase small subunit C-terminal | - | Family | |
PF01058 | NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6) | NADH ubiquinone oxidoreductase, 20 Kd subunit | - | Family | |
PF00374 | Nickel-dependent hydrogenase (NiFeSe_Hases) | Nickel-dependent hydrogenase | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR006311 | Twin-arginine translocation pathway, signal sequence | Conserved Site | |
IPR001821 | [NiFe]-hydrogenase, small subunit | Family | |
IPR027394 | Cytochrome-c3 hydrogenase, C-terminal | Domain | |
IPR006137 | NADH:ubiquinone oxidoreductase-like, 20kDa subunit | Domain | |
IPR053622 | NiFe/NiFeSe hydrogenase small subunit | Family | |
IPR037024 | [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily | Homologous Superfamily | |
IPR019546 | Twin-arginine translocation pathway, signal sequence, bacterial/archaeal | Conserved Site | |
IPR037148 | [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily | Homologous Superfamily | |
IPR001501 | Nickel-dependent hydrogenase, large subunit | Family | |
IPR029014 | [NiFe]-hydrogenase, large subunit | Homologous Superfamily | |
IPR018194 | Nickel-dependent hydrogenase, large subunit, nickel binding site | Binding Site | |
IPR050867 | [NiFe]/[NiFeSe] hydrogenase large subunit | Family |