7XK4 | pdb_00007xk4

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 2

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	SufE/NifU	8053868	3000436	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)
F	FAD_binding_6	e7xk4F2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: FAD_binding_6	ECOD (1.6)
F	Fer2	e7xk4F1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)
F	NAD_binding_1	e7xk4F3	A: a/b three-layered sandwiches	X: Ferredoxin reductase-like, C-terminal NADP-linked domain (From Topology)	H: Ferredoxin reductase-like, C-terminal NADP-linked domain (From Topology)	T: Ferredoxin reductase-like, C-terminal NADP-linked domain	F: NAD_binding_1	ECOD (1.6)
E	Rnf-Nqr	e7xk4E1	A: alpha complex topology	X: Na(+)-translocating NADH-quinone reductase subunit D (From Topology)	H: Na(+)-translocating NADH-quinone reductase subunit D (From Topology)	T: Na(+)-translocating NADH-quinone reductase subunit D	F: Rnf-Nqr	ECOD (1.6)
D	Rnf-Nqr	e7xk4D1	A: alpha complex topology	X: Na(+)-translocating NADH-quinone reductase subunit D (From Topology)	H: Na(+)-translocating NADH-quinone reductase subunit D (From Topology)	T: Na(+)-translocating NADH-quinone reductase subunit D	F: Rnf-Nqr	ECOD (1.6)
C	FMN_bind	e7xk4C1	A: a+b two layers	X: putative RnfG subunit of electron transport complex (From Homology)	H: putative RnfG subunit of electron transport complex	T: putative RnfG subunit of electron transport complex	F: FMN_bind	ECOD (1.6)
B	NQR2_RnfD_RnfE	e7xk4B1	A: alpha complex topology	X: Ammonium transporter-related (From Homology)	H: Ammonium transporter-related	T: Na(+)-translocating NADH-quinone reductase subunit B	F: NQR2_RnfD_RnfE	ECOD (1.6)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F	Na(+)-translocating NADH-quinone reductase subunit F	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding electron transfer activity cation binding iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding electron transfer activity cation binding metal ion binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor catalytic activity	localization transport monoatomic ion transport monoatomic cation transport establishment of localization sodium ion transport metal ion transport	cell periphery cellular anatomical structure plasma membrane membrane
E	Na(+)-translocating NADH-quinone reductase subunit E	oxidoreductase activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor catalytic activity	cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy localization transport monoatomic ion transport monoatomic cation transport establishment of localization sodium ion transport metal ion transport	cell periphery cellular anatomical structure plasma membrane membrane Gram-negative-bacterium-type cell wall external encapsulating structure cell envelope cell wall peptidoglycan-based cell wall
D	Na(+)-translocating NADH-quinone reductase subunit D	oxidoreductase activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor catalytic activity	localization transport monoatomic ion transport monoatomic cation transport establishment of localization sodium ion transport metal ion transport	cell periphery cellular anatomical structure plasma membrane membrane
C	Na(+)-translocating NADH-quinone reductase subunit C	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor catalytic activity	localization transport monoatomic ion transport monoatomic cation transport establishment of localization sodium ion transport metal ion transport	cell periphery cellular anatomical structure plasma membrane membrane
B	Na(+)-translocating NADH-quinone reductase subunit B	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding riboflavin binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding riboflavin binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor catalytic activity	cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy transmembrane transport localization transport establishment of localization monoatomic ion transport monoatomic cation transport sodium ion transport cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy transmembrane transport localization transport establishment of localization monoatomic ion transport monoatomic cation transport sodium ion transport metal ion transport	cell periphery cellular anatomical structure plasma membrane membrane
A	Na(+)-translocating NADH-quinone reductase subunit A	oxidoreductase activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor catalytic activity	localization transport monoatomic ion transport monoatomic cation transport establishment of localization sodium ion transport metal ion transport	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F	IPR010205	Na(+)-translocating NADH-quinone reductase subunit F	Family
F	IPR001433	Oxidoreductase FAD/NAD(P)-binding	Domain
F	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
F	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
F	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain	Homologous Superfamily
F	IPR008333	Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain	Domain
F	IPR017938	Riboflavin synthase-like beta-barrel	Homologous Superfamily
F	IPR017927	FAD-binding domain, ferredoxin reductase-type	Domain
F	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily
E	IPR050133	Ion-translocating oxidoreductase complex subunit A/E	Family
E	IPR010967	Na(+)-translocating NADH-quinone reductase subunit E	Family
E	IPR003667	NqrDE/RnfAE	Family
D	IPR003667	NqrDE/RnfAE	Family
D	IPR011292	Na(+)-translocating NADH-quinone reductase subunit D	Family
C	IPR010204	Na(+)-translocating NADH-quinone reductase subunit C	Family
C	IPR007329	FMN-binding	Domain
B	IPR010966	Na(+)-translocating NADH-quinone reductase subunit B	Family
B	IPR004338	Ion-translocating oxidoreductase NqrB/RnfD	Family
A	IPR056148	NqrA, second alpha/beta domain	Domain
A	IPR056147	NqrA, N-terminal barrel-sandwich hybrid domain	Domain
A	IPR022615	Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain	Domain
A	IPR008703	Na(+)-translocating NADH-quinone reductase subunit A	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
B, C, D, E, F	OPM	Transmembrane	Alpha-helical polytopic	Ammonia/urea transporters/Na+ exporter	Na(+)-translocating NADH-quinone reductase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
B, C, D, E, F	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
B, C, D, E, F	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex I	Na⁺-pumping NADH-ubiquinone oxidoreductase, State 1