1E08 | pdb_00001e08

Structural model of the [Fe]-Hydrogenase/cytochrome c553 complex combining NMR and soft-docking

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1e08a_	Low resolution protein structures	Electron transport chains	Electron transport chains	Electron transport chains	[Fe]-hydrogenase/cytochrome c553 complex	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
B [auth D]	d1e08d_	Low resolution protein structures	Electron transport chains	Electron transport chains	Electron transport chains	[Fe]-hydrogenase/cytochrome c553 complex	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
C [auth E]	d1e08e_	Low resolution protein structures	Electron transport chains	Electron transport chains	Electron transport chains	[Fe]-hydrogenase/cytochrome c553 complex	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Fe-only hydrogenase	8033441	3001826	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Fe-only hydrogenase smaller subunit	8039092	3001779	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Cytochrome c	8036386	3000815	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Fer4_21_1	e1e08A2	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
A	Fe_hyd_lg_C	e1e08A3	A: a/b three-layered sandwiches	X: Fe-only hydrogenase (From Topology)	H: Fe-only hydrogenase (From Topology)	T: Fe-only hydrogenase	F: Fe_hyd_lg_C	ECOD (1.6)
B [auth D]	Fe_hyd_SSU	e1e08D1	A: extended segments	X: Fe-only hydrogenase smaller subunit (From Topology)	H: Fe-only hydrogenase smaller subunit (From Topology)	T: Fe-only hydrogenase smaller subunit	F: Fe_hyd_SSU	ECOD (1.6)
C [auth E]	Cytochrome_CBB3	e1e08E1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02906	Iron only hydrogenase large subunit, C-terminal domain (Fe_hyd_lg_C)	Iron only hydrogenase large subunit, C-terminal domain		Domain
A	PF00037	4Fe-4S binding domain (Fer4)	4Fe-4S binding domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich.	Domain
B [auth D]	PF02256	Iron hydrogenase small subunit (Fe_hyd_SSU)	Iron hydrogenase small subunit	This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold [1].	Domain
C [auth E]	PF00034	Cytochrome c (Cytochrom_C)	Cytochrome c	The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, Pfam:PF06181, has now been merged into this family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	[FE]-HYDROGENASE (LARGE SUBUNIT)	oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding	-	cellular anatomical structure periplasmic space
B [auth D]	[FE]-HYDROGENASE (SMALL SUBUNIT)	iron-sulfur cluster binding binding metal cluster binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity electron transfer activity cation binding transition metal ion binding iron ion binding ion binding iron-sulfur cluster binding binding metal cluster binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding	-	cellular anatomical structure periplasmic space
C [auth E]	CYTOCHROME C553	binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	cellular anatomical structure periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A	IPR004108	Iron hydrogenase, large subunit, C-terminal	Domain
A	IPR050340	Cytosolic Fe-S Cluster Assembly Factor	Family
A	IPR009016	Iron hydrogenase	Homologous Superfamily
A	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A	IPR013352	Iron hydrogenase, subset	Domain
B [auth D]	IPR036991	Iron hydrogenase, small subunit superfamily	Homologous Superfamily
B [auth D]	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
B [auth D]	IPR003149	Iron hydrogenase, small subunit	Domain
B [auth D]	IPR008953	Iron hydrogenase, small subunit HydB-type	Homologous Superfamily
B [auth D]	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site
C [auth E]	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
C [auth E]	IPR009056	Cytochrome c-like domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.