3VR5 | pdb_00003vr5

Crystal structure of nucleotide-free Enterococcus hirae V1-ATPase [eV1(L)]

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8093379	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Single hybrid motif	8093375	3001880	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ATP synthase alpha/beta N-terminal domain-like	8093377	3001034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ATP synthase alpha/beta C-terminal domain-like	8093380	3000684	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ATP synthase alpha/beta N-terminal domain-like	8093377	3001034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Single hybrid motif	8093375	3001880	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ATP synthase alpha/beta C-terminal domain-like	8093380	3000684	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8093379	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8093379	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ATP synthase alpha/beta N-terminal domain-like	8093377	3001034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Single hybrid motif	8093375	3001880	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ATP synthase alpha/beta C-terminal domain-like	8093380	3000684	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)
H	Glyco_hydro_19	e3vr5H1	A: alpha bundles	X: Globin-like	H: Ring-building motif I in type III secretion system	T: Ring-building motif I in type III secretion system	F: Glyco_hydro_19	ECOD (develop294)
F	V-set	e3vr5F4	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (develop294)
E	V-set	e3vr5E4	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (develop294)
D	V-set	e3vr5D4	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (develop294)
C	14-3-3	e3vr5C1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
C	AAA_16	e3vr5C3	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_16	ECOD (develop294)
B	14-3-3	e3vr5B1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
B	AAA_16	e3vr5B3	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_16	ECOD (develop294)
A	14-3-3	e3vr5A1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
A	RNA_pol_Rpb1_5	e3vr5A3	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: RNA_pol_Rpb1_5	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.40.50.10580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	ATPase, V1 complex, subunit F	CATH (4.3.0)
F	3.40.50.12240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
E	3.40.50.12240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.40.50.12240	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
C	1.10.1140.10	Mainly Alpha	Orthogonal Bundle	Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain	Chain D, domain3	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
B	1.10.1140.10	Mainly Alpha	Orthogonal Bundle	Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain	Chain D, domain3	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
A	1.10.1140.10	Mainly Alpha	Orthogonal Bundle	Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain	Chain D, domain3	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H	V-type sodium ATPase subunit G	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity proton-transporting ATPase activity, rotational mechanism ATPase-coupled monoatomic cation transmembrane transporter activity ATP-dependent activity active monoatomic ion transmembrane transporter activity ATPase-coupled ion transmembrane transporter activity active transmembrane transporter activity ATPase activity, coupled to transmembrane movement of ions, rotational mechanism monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic ion channel activity proton channel activity proton-transporting ATP synthase activity, rotational mechanism monoatomic cation channel activity passive transmembrane transporter activity channel activity catalytic activity ligase activity	ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process proton motive force-driven plasma membrane ATP synthesis primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process localization transport monoatomic ion transport monoatomic cation transport establishment of localization sodium ion transport metal ion transport	-
G	V-type sodium ATPase subunit D	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity proton-transporting ATPase activity, rotational mechanism ATPase-coupled monoatomic cation transmembrane transporter activity ATP-dependent activity active monoatomic ion transmembrane transporter activity ATPase-coupled ion transmembrane transporter activity active transmembrane transporter activity ATPase activity, coupled to transmembrane movement of ions, rotational mechanism monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic ion channel activity proton channel activity proton-transporting ATP synthase activity, rotational mechanism monoatomic cation channel activity passive transmembrane transporter activity channel activity catalytic activity ligase activity	ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process proton motive force-driven plasma membrane ATP synthesis primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process localization transport monoatomic ion transport monoatomic cation transport establishment of localization sodium ion transport metal ion transport	-
D, E, F	V-type sodium ATPase subunit B	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity monoatomic ion channel activity proton channel activity proton-transporting ATP synthase activity, rotational mechanism monoatomic cation channel activity passive transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity ligase activity	ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process proton motive force-driven plasma membrane ATP synthesis primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process localization transport monoatomic ion transport monoatomic cation transport establishment of localization sodium ion transport metal ion transport	-
A, B, C	V-type sodium ATPase catalytic subunit A	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity proton-transporting ATPase activity, rotational mechanism ATPase-coupled monoatomic cation transmembrane transporter activity ATP-dependent activity active monoatomic ion transmembrane transporter activity ATPase-coupled ion transmembrane transporter activity active transmembrane transporter activity ATPase activity, coupled to transmembrane movement of ions, rotational mechanism monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity sodium ion transmembrane transporter activity sodium-transporting ATPase activity, rotational mechanism metal ion transmembrane transporter activity monoatomic ion channel activity proton channel activity proton-transporting ATP synthase activity, rotational mechanism monoatomic cation channel activity passive transmembrane transporter activity channel activity catalytic activity ligase activity	ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process proton motive force-driven plasma membrane ATP synthesis primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process	respiratory chain complex protein-containing complex catalytic complex proton-transporting ATP synthase complex membrane membrane protein complex cation channel complex transporter complex cellular anatomical structure proton-transporting two-sector ATPase complex transmembrane transporter complex monoatomic ion channel complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H	IPR022944	ATPase, V1 complex, subunit F, bacterial/archaeal	Family
H	IPR036906	ATPase, V1 complex, subunit F superfamily	Homologous Superfamily
H	IPR008218	ATPase, V1 complex, subunit F	Family
G	IPR002699	ATPase, V1 complex, subunit D	Family
D, E, F	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	Active Site
D, E, F	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Domain
D, E, F	IPR055190	ATP synthase A/B type, C-terminal domain	Domain
D, E, F	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	Domain
D, E, F	IPR022879	V-type ATP synthase regulatory subunit B/beta	Family
D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	Domain
A, B, C	IPR022878	V-type ATP synthase catalytic alpha chain	Family
A, B, C	IPR024034	ATPase, F1/V1 complex, beta/alpha subunit, C-terminal	Homologous Superfamily
A, B, C	IPR036121	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily	Homologous Superfamily
A, B, C	IPR031686	ATPsynthase alpha/beta subunit, barrel-sandwich domain	Domain
A, B, C	IPR023366	ATP synthase subunit alpha, N-terminal domain-like superfamily	Homologous Superfamily
A, B, C	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	Active Site
A, B, C	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Domain
A, B, C	IPR055190	ATP synthase A/B type, C-terminal domain	Domain
A, B, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily