5XF9 | pdb_00005xf9

Crystal structure of NAD+-reducing [NiFe]-hydrogenase in the air-oxidized state

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
H	d5xf9h_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Hydrogenophilus thermoluteolus ) [TaxId: 297 ],	SCOPe (2.08)
D	d5xf9d_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Hydrogenophilus thermoluteolus ) [TaxId: 297 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	Fz	e5xf9H1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Fz	ECOD (develop294)
D	Fz	e5xf9D1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Fz	ECOD (develop294)
G	Oxidored_q6	e5xf9G1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Oxidored_q6	ECOD (develop294)
C	Oxidored_q6	e5xf9C1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Oxidored_q6	ECOD (develop294)
F	Oxidored_q6	e5xf9F1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Oxidored_q6	ECOD (develop294)
B	Oxidored_q6	e5xf9B1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Oxidored_q6	ECOD (develop294)
E	2Fe-2S_thioredx	e5xf9E1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: 2Fe-2S_thioredx	ECOD (develop294)
E	Tudor_2	e5xf9E5	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Tudor_2	ECOD (develop294)
A	PHD	e5xf9A1	A: alpha bundles	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
E	3.40.50.11540	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH-ubiquinone oxidoreductase 51kDa subunit	CATH (utative)
E	3.10.20.600	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
E	1.20.1440.230	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	CATH (utative)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
A	3.40.50.11540	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH-ubiquinone oxidoreductase 51kDa subunit	CATH (utative)
A	3.10.20.600	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
A	1.20.1440.230	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, H	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family
C, G	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit		Domain
B, F	PF13459	4Fe-4S single cluster domain (Fer4_15)	4Fe-4S single cluster domain		Domain
B, F	PF13510	2Fe-2S iron-sulfur cluster binding domain (Fer2_4)	2Fe-2S iron-sulfur cluster binding domain	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. Th ...	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins.	Domain
B, F	PF10588	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3)	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region		Domain
A, E	PF01512	Nuo51 FMN-binding domain (Complex1_51K)	Nuo51 FMN-binding domain	This entry represents the FMN-binding domain of NADH-ubiquinone oxidoreductase 51kDa subunit from NADH:ubiquinone oxidoreductase.	Domain
A, E	PF10589	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S)	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, H	NAD-reducing hydrogenase	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion 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	-	-
C, G	NAD-reducing hydrogenase	oxidoreductase activity catalytic activity iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding 4 iron, 4 sulfur cluster binding cation binding ion binding metal ion binding	-	-
B, F	NAD-reducing hydrogenase	oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity 4 iron, 4 sulfur cluster binding cation binding ion binding metal ion binding	aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain ATP synthesis coupled electron transport electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane
A, E	NAD-reducing hydrogenase	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, H	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
D, H	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
D, H	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
C, G	IPR051349	Hydrogenase complex-associated protein	Family
C, G	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
C, G	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
B, F	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
B, F	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
B, F	IPR000283	NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site	Conserved Site
B, F	IPR016214	NAD-reducing hydrogenase, HoxS gamma subunit	Family
B, F	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, F	IPR019574	NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding	Domain
A, E	IPR019575	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	Domain
A, E	IPR001949	NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site	Conserved Site
A, E	IPR037225	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily	Homologous Superfamily
A, E	IPR037207	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily	Homologous Superfamily
A, E	IPR011538	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain	Domain
A, E	IPR041921	NADH-quinone oxidoreductase subunit E, N-terminal	Homologous Superfamily
A, E	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.