5YLU | pdb_00005ylu

Crystal structure of the gastric proton pump complexed with vonoprazan

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	V-set	e5yluB1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (develop294)
A	V-set	e5yluA2	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (develop294)
A	DNA_gyraseB_C,Toprim	e5yluA5	A: alpha bundles	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: DNA_gyraseB_C,Toprim	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.70.150.10	Mainly Beta	Distorted Sandwich	Calcium-transporting ATPase, cytoplasmic transduction domain A	Calcium-transporting ATPase, cytoplasmic transduction domain A	CATH (4.3.0)
A	1.20.1110.10	Mainly Alpha	Up-down Bundle	Calcium-transporting ATPase, transmembrane domain	Calcium-transporting ATPase, transmembrane domain	CATH (4.3.0)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	3.40.1110.10	Alpha Beta	3-Layer(aba) Sandwich	Calcium-transporting ATPase, cytoplasmic domain N	Calcium-transporting ATPase, cytoplasmic domain N	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00689	Cation transporting ATPase, C-terminus (Cation_ATPase_C)	Cation transporting ATPase, C-terminus	-	Family
A	PF00690	Cation transporter/ATPase, N-terminus (Cation_ATPase_N)	Cation transporter/ATPase, N-terminus	Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport.	Domain
A	PF08282	haloacid dehalogenase-like hydrolase (Hydrolase_3)	haloacid dehalogenase-like hydrolase	This family contains haloacid dehalogenase-like hydrolase enzymes.	Domain
A	PF00122	P-type ATPase actuator domain (E1-E2_ATPase)	P-type ATPase actuator domain	This entry describes the actuator (A) domain found in P-type ATPases (also known as E1-E2 ATPases). The A domain serves as a built-in protein phosphatase that functions to dephosphorylate the phosphorylated P domain. The A domain is the smallest of t ...	This entry describes the actuator (A) domain found in P-type ATPases (also known as E1-E2 ATPases). The A domain serves as a built-in protein phosphatase that functions to dephosphorylate the phosphorylated P domain. The A domain is the smallest of the three cytoplasmic domains. It consists of a distorted jellyroll structure and two short helices [1-2].	Domain
A	PF13246	P-type ATPase, cytoplasmic domain N (Cation_ATPase)	P-type ATPase, cytoplasmic domain N	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Potassium-transporting ATPase subunit beta	ATPase activator activity molecular function activator activity molecular function regulator activity ATPase regulator activity	potassium ion homeostasis inorganic ion homeostasis homeostatic process cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis intracellular potassium ion homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis sodium ion homeostasis intracellular sodium ion homeostasis monoatomic cation transmembrane transport potassium ion homeostasis inorganic ion homeostasis homeostatic process cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis intracellular potassium ion homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis sodium ion homeostasis intracellular sodium ion homeostasis monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization potassium ion transmembrane transport metal ion transport potassium ion transport cell adhesion sodium ion export across plasma membrane sodium ion transmembrane transport export from cell export across plasma membrane sodium ion transport import into cell import across plasma membrane inorganic cation import across plasma membrane inorganic ion import across plasma membrane potassium ion import across plasma membrane	cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane protein complex sodium:potassium-exchanging ATPase complex transporter complex cation-transporting ATPase complex cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane protein complex sodium:potassium-exchanging ATPase complex transporter complex cation-transporting ATPase complex transmembrane transporter complex potassium:proton exchanging ATPase complex
A	Potassium-transporting ATPase alpha chain 1	cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity P-type transmembrane transporter activity P-type sodium transporter activity potassium ion transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity P-type sodium:potassium-exchanging transporter activity cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity P-type transmembrane transporter activity P-type sodium transporter activity potassium ion transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity P-type sodium:potassium-exchanging transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity sodium ion transmembrane transporter activity ATP-dependent activity P-type potassium transmembrane transporter activity P-type ion transporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity magnesium ion binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity proton transmembrane transporter activity P-type potassium:proton transporter activity P-type proton-exporting transporter activity	potassium ion homeostasis inorganic ion homeostasis homeostatic process cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis intracellular potassium ion homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis sodium ion homeostasis intracellular sodium ion homeostasis monoatomic cation transmembrane transport potassium ion homeostasis inorganic ion homeostasis homeostatic process cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis intracellular potassium ion homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis sodium ion homeostasis intracellular sodium ion homeostasis monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization potassium ion transmembrane transport metal ion transport potassium ion transport sodium ion export across plasma membrane sodium ion transmembrane transport export from cell export across plasma membrane sodium ion transport import into cell import across plasma membrane inorganic cation import across plasma membrane inorganic ion import across plasma membrane potassium ion import across plasma membrane	cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane ATPase dependent transmembrane transport complex potassium:proton exchanging ATPase complex protein-containing complex plasma membrane protein complex membrane protein complex transporter complex cation-transporting ATPase complex cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane ATPase dependent transmembrane transport complex potassium:proton exchanging ATPase complex protein-containing complex plasma membrane protein complex membrane protein complex transporter complex cation-transporting ATPase complex transmembrane transporter complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR000402	Sodium/potassium-transporting ATPase subunit beta	Family
B	IPR038702	Sodium/potassium-transporting ATPase subunit beta superfamily	Homologous Superfamily
A	IPR005775	P-type ATPase subfamily IIC, subunit alpha	Family
A	IPR004014	Cation-transporting P-type ATPase, N-terminal	Domain
A	IPR001757	P-type ATPase	Family
A	IPR044492	P-type ATPase, haloacid dehalogenase domain	Domain
A	IPR006068	Cation-transporting P-type ATPase, C-terminal	Domain
A	IPR018303	P-type ATPase, phosphorylation site	PTM
A	IPR059000	P-type ATPase, A domain	Domain
A	IPR023298	P-type ATPase, transmembrane domain superfamily	Homologous Superfamily
A	IPR015127	Gastric H+/K+-transporter P-type ATPase, N-terminal	Domain
A	IPR050510	Cation transport ATPase (P-type)	Family
A	IPR023214	HAD superfamily	Homologous Superfamily
A	IPR008250	P-type ATPase, A domain superfamily	Homologous Superfamily
A	IPR036412	HAD-like superfamily	Homologous Superfamily
A	IPR023299	P-type ATPase, cytoplasmic domain N	Homologous Superfamily

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	P-type ATPase	gastric H⁺,K⁺-ATPase with bound vonoprazan

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.

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