3K5B | pdb_00003k5b

Crystal structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase

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)
D [auth A]	d3k5ba1	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	V-type ATPase subunit E-like	V-type ATPase subunit E C-terminal domain	V-type ATPase subunit E C-terminal domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
D [auth A]	d3k5ba2	Coiled coil proteins	Parallel coiled-coil	V-type ATPase peripheral stalk subunit E coiled coil	V-type ATPase peripheral stalk subunit E coiled coil	V-type ATPase peripheral stalk subunit E coiled coil	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B [auth E]	d3k5be1	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	V-type ATPase subunit E-like	V-type ATPase subunit E C-terminal domain	V-type ATPase subunit E C-terminal domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B [auth E]	d3k5be2	Coiled coil proteins	Parallel coiled-coil	V-type ATPase peripheral stalk subunit E coiled coil	V-type ATPase peripheral stalk subunit E coiled coil	V-type ATPase peripheral stalk subunit E coiled coil	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C [auth B]	d3k5bb_	Coiled coil proteins	Parallel coiled-coil	V-type ATPase peripheral stalk subunit G coiled coil	V-type ATPase peripheral stalk subunit G coiled coil	V-type ATPase peripheral stalk subunit G coiled coil	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A [auth G]	d3k5bg_	Coiled coil proteins	Parallel coiled-coil	V-type ATPase peripheral stalk subunit G coiled coil	V-type ATPase peripheral stalk subunit G coiled coil	V-type ATPase peripheral stalk subunit G coiled coil	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	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	VAPG-like	8101875	3002722	SCOP2B (2022-06-29)
A [auth G]	SCOP2B Superfamily	VAPG-like	8101875	3002722	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)
D [auth A]	LRR_1,LRR_8,Island	e3k5bA1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: LRR_1,LRR_8,Island	ECOD (v294.1)
B [auth E]	LRR_1,LRR_8,Island	e3k5bE1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: LRR_1,LRR_8,Island	ECOD (v294.1)
C [auth B]	Sigma70_r2,Sigma70_ner	e3k5bB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Sigma70_r2,Sigma70_ner	ECOD (v294.1)
A [auth G]	Sigma70_r2,Sigma70_ner	e3k5bG1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Sigma70_r2,Sigma70_ner	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth A]	1.20.5.620	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	F1F0 ATP synthase subunit B, membrane domain	CATH (4.3.0)
D [auth A]	3.30.2320.30	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold	ATP synthase, E subunit, C-terminal	CATH (4.3.0)
B [auth E]	1.20.5.620	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	F1F0 ATP synthase subunit B, membrane domain	CATH (4.3.0)
B [auth E]	3.30.2320.30	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold	ATP synthase, E subunit, C-terminal	CATH (4.3.0)
C [auth B]	1.20.5.2950	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A [auth G]	1.20.5.2950	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth E], D [auth A]	PF01991	ATP synthase (E/31 kDa) subunit (vATP-synt_E)	ATP synthase (E/31 kDa) subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth E], D [auth A]	V-type ATP synthase subunit E	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	protein-containing complex cellular anatomical structure proton-transporting two-sector ATPase complex, catalytic domain proton-transporting two-sector ATPase complex membrane membrane protein complex
A [auth G], C [auth B]	V-type ATP synthase, subunit (VAPC-THERM)	cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth E], D [auth A]	IPR002842	V-type ATPase subunit E	Family
B [auth E], D [auth A]	IPR038495	V-type ATPase subunit E, C-terminal domain 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.