6QGR

The F420-reducing [NiFe] hydrogenase complex from Methanosarcina barkeri at the Nia-S state

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B [auth A]	d6qgra_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Methanosarcina barkeri MS ) [TaxId: 1434108 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth B]	SCOP2B Superfamily	FrhB/FdhB-like	8095209	3002602	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 [auth G]	Fer4_21_1	e6qgrG1	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 [auth G]	Oxidored_q6	e6qgrG2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
B [auth A]	NiFeSe_Hases_1st	e6qgrA4	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: NiFeSe_Hases_1st	ECOD (1.6)
B [auth A]	NiFeSe_Hases_3rd_1	e6qgrA2	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: NiFeSe_Hases_3rd_1	ECOD (1.6)
C [auth B]	FrhB_FdhB_C	e6qgrB1	A: alpha arrays	X: F420-reducing hydrogenase subunit beta (From Topology)	H: F420-reducing hydrogenase subunit beta (From Topology)	T: F420-reducing hydrogenase subunit beta	F: FrhB_FdhB_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth G]	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (utative)
A [auth G]	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
B [auth A]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (utative)
C [auth B]	3.10.450.750	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth G]	PF13187	4Fe-4S dicluster domain (Fer4_9)	4Fe-4S dicluster domain	-	Family
A [auth G]	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit	-	Family
B [auth A]	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family
C [auth B]	PF04422	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term (FrhB_FdhB_N)	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term	-	Family
C [auth B]	PF04432	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus (FrhB_FdhB_C)	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus	Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum fo ...	Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2, Swiss:P06130) is also a member of this family [3]. This region is often found in association with the 4Fe-4S binding domain, fer4 (Pfam:PF00037).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G]	Coenzyme F420 hydrogenase subunit gamma	oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity coenzyme F420 hydrogenase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity coenzyme F420 hydrogenase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding metal cluster binding 4 iron, 4 sulfur cluster binding flavin adenine dinucleotide binding nucleoside phosphate binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding	-	-
B [auth A]	Coenzyme F420 hydrogenase subunit alpha	oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity coenzyme F420 hydrogenase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor ferredoxin hydrogenase activity	-	-
C [auth B]	Coenzyme F420 hydrogenase subunit beta	oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity coenzyme F420 hydrogenase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity coenzyme F420 hydrogenase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding flavin adenine dinucleotide binding nucleoside phosphate binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A [auth G]	IPR017681	Coenzyme F420 hydrogenase, subunit gamma	Family
A [auth G]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A [auth G]	IPR051349	Hydrogenase complex-associated protein	Family
A [auth G]	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
A [auth G]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
B [auth A]	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
B [auth A]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
B [auth A]	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
C [auth B]	IPR045220	Oxidoreductase FRHB/FDHB/HCAR-like	Family
C [auth B]	IPR007516	Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal	Domain
C [auth B]	IPR017679	Coenzyme F420 hydrogenase subunit beta, archaea	Family
C [auth B]	IPR007525	Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal	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.