4RET | pdb_00004ret

Crystal structure of the Na,K-ATPase E2P-digoxin complex with bound magnesium

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
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth E]		e4retE1	A: P-loop domains-like	X: P-loop domains-related	H: P-loop containing nucleoside triphosphate hydrolases	T: TsaD	F:	ECOD (20:10:01)
C [auth G]		e4retG1	A: P-loop domains-like	X: P-loop domains-related	H: P-loop containing nucleoside triphosphate hydrolases	T: TsaD	F:	ECOD (20:10:01)
B		e4retB1	A: P-loop domains-like	X: P-loop domains-related	H: P-loop containing nucleoside triphosphate hydrolases	T: TsaD	F:	ECOD (20:10:01)
E [auth D]		e4retD1	A: P-loop domains-like	X: P-loop domains-related	H: P-loop containing nucleoside triphosphate hydrolases	T: TsaD	F:	ECOD (20:10:01)
A		e4retA1	A: P-loop domains-like	X: P-loop domains-related	H: P-loop containing nucleoside triphosphate hydrolases	T: TsaD	F:	ECOD (20:10:01)
D [auth C]		e4retC1	A: P-loop domains-like	X: P-loop domains-related	H: P-loop containing nucleoside triphosphate hydrolases	T: TsaD	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.1660	Mainly Beta	Sandwich	Immunoglobulin-like	Na, k-atpase alpha subunit.	CATH (4.3.0)
E [auth D]	1.20.5.170	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
E [auth D]	2.60.40.1660	Mainly Beta	Sandwich	Immunoglobulin-like	Na, k-atpase alpha subunit.	CATH (4.3.0)
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)
D [auth C]	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)
D [auth C]	1.20.1110.10	Mainly Alpha	Up-down Bundle	Calcium-transporting ATPase, transmembrane domain	Calcium-transporting ATPase, transmembrane domain	CATH (4.3.0)
D [auth C]	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
D [auth C]	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, D [auth C]	PF00689	Cation transporting ATPase, C-terminus (Cation_ATPase_C)	Cation transporting ATPase, C-terminus	-	Family
A, D [auth C]	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, D [auth C]	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, D [auth C]	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
C [auth G], F [auth E]	Na+/K+ ATPase gamma subunit transcript variant a	channel regulator activity ion channel regulator activity molecular function regulator activity transporter regulator activity ATPase activator activity molecular function activator activity ATPase regulator activity protein-macromolecule adaptor activity molecular adaptor 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 regulation of localization regulation of biological process regulation of transport regulation of monoatomic ion transport biological regulation establishment or maintenance of transmembrane electrochemical gradient sodium ion export across plasma membrane sodium ion transmembrane transport export from cell export across plasma membrane metal ion transport sodium ion transport import into cell import across plasma membrane potassium ion transmembrane transport inorganic cation import across plasma membrane inorganic ion import across plasma membrane potassium ion transport potassium ion import across plasma membrane	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex sodium:potassium-exchanging ATPase complex transporter complex cation-transporting ATPase complex cell periphery cellular anatomical structure transmembrane transporter complex
B, E [auth D]	Sodium/potassium-transporting ATPase subunit beta-1	ATPase activator activity molecular function activator activity molecular function regulator activity ATPase regulator activity 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 ATPase activator activity molecular function activator activity molecular function regulator activity ATPase regulator activity 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 protein-macromolecule adaptor activity molecular adaptor activity protein binding binding kinase binding enzyme binding protein kinase binding transporter activator activity transporter regulator activity ATPase binding	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 multicellular organismal process system process relaxation of cardiac muscle muscle system process relaxation of muscle nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process primary metabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process metabolic process small molecule metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process phosphorus metabolic process regulation of protein stability biological regulation regulation of biological quality protein stabilization establishment or maintenance of transmembrane electrochemical gradient membrane repolarization regulation of membrane potential regulation of localization positive regulation of cation transmembrane transport regulation of cellular process positive regulation of biological process sodium ion transmembrane transport regulation of monoatomic ion transmembrane transport regulation of sodium ion transport metal ion transport regulation of sodium ion transmembrane transport positive regulation of sodium ion transport positive regulation of monoatomic ion transport positive regulation of sodium ion transmembrane transport positive regulation of transmembrane transport positive regulation of monoatomic ion transmembrane transport regulation of metal ion transport positive regulation of cellular process regulation of biological process regulation of transport regulation of monoatomic ion transport regulation of transmembrane transport positive regulation of transport regulation of monoatomic cation transmembrane transport sodium ion transport regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process import into cell positive regulation of potassium ion import across plasma membrane regulation of potassium ion transport potassium ion transmembrane transport potassium ion import across plasma membrane import across plasma membrane regulation of potassium ion transmembrane transport inorganic cation import across plasma membrane positive regulation of potassium ion transport positive regulation of potassium ion transmembrane transport inorganic ion import across plasma membrane potassium ion transport regulation of potassium ion import sodium ion export across plasma membrane export from cell export across plasma membrane biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane intracellular calcium ion homeostasis calcium ion homeostasis regulation of sodium ion export across plasma membrane positive regulation of sodium ion export across plasma membrane cell adhesion heart process circulatory system process cardiac muscle contraction heart contraction muscle contraction blood circulation striated muscle contraction regulation of calcium ion transport calcium ion transport regulation of calcium ion transmembrane transport calcium ion transmembrane transport cellular response to stimulus signaling regulation of heart contraction regulation of system process intracellular signal transduction cell communication intracellular signaling cassette regulation of multicellular organismal process signal transduction regulation of cardiac muscle contraction by calcium ion signaling regulation of cardiac muscle contraction regulation of muscle system process regulation of blood circulation regulation of striated muscle contraction calcium-mediated signaling regulation of muscle contraction	cell periphery cellular anatomical structure sarcolemma plasma membrane membrane T-tubule membrane-bounded organelle organelle organelle membrane apical part of cell plasma membrane region apical plasma membrane cell projection cilium cell periphery cellular anatomical structure sarcolemma plasma membrane membrane T-tubule membrane-bounded organelle organelle organelle membrane apical part of cell plasma membrane region apical plasma membrane cell projection cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection basal part of cell basal plasma membrane basolateral 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 lateral plasma membrane cell-cell junction intercalated disc anchoring junction cell junction cell-cell contact zone
A, D [auth C]	Sodium/potassium-transporting ATPase subunit alpha-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 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 sodium ion binding ATPase binding protein binding enzyme binding	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 establishment or maintenance of transmembrane electrochemical gradient membrane repolarization biological regulation regulation of biological quality regulation of membrane potential sodium ion export across plasma membrane sodium ion transmembrane transport export from cell export across plasma membrane metal ion transport sodium ion transport import into cell import across plasma membrane potassium ion transmembrane transport inorganic cation import across plasma membrane inorganic ion import across plasma membrane potassium ion transport potassium ion import across plasma membrane regulation of localization regulation of biological process regulation of transport regulation of monoatomic ion transport regulation of sodium ion transport regulation of metal ion transport	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle cell periphery cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle cell periphery sarcolemma plasma membrane basal part of cell basal plasma membrane plasma membrane region basolateral 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 axon cell projection neuron projection plasma membrane bounded cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth G], F [auth E]	IPR047297	Ion-transport regulator, FXYD motif	Conserved Site
C [auth G], F [auth E]	IPR000272	Ion-transport regulator, FXYD family	Family
C [auth G], F [auth E]	IPR047282	Sodium/potassium-transporting ATPase subunit gamma	Family
B, E [auth D]	IPR000402	Sodium/potassium-transporting ATPase subunit beta	Family
B, E [auth D]	IPR038702	Sodium/potassium-transporting ATPase subunit beta superfamily	Homologous Superfamily
A, D [auth C]	IPR005775	P-type ATPase subfamily IIC, subunit alpha	Family
A, D [auth C]	IPR004014	Cation-transporting P-type ATPase, N-terminal	Domain
A, D [auth C]	IPR001757	P-type ATPase	Family
A, D [auth C]	IPR044492	P-type ATPase, haloacid dehalogenase domain	Domain
A, D [auth C]	IPR006068	Cation-transporting P-type ATPase, C-terminal	Domain
A, D [auth C]	IPR018303	P-type ATPase, phosphorylation site	PTM
A, D [auth C]	IPR059000	P-type ATPase, A domain	Domain
A, D [auth C]	IPR023298	P-type ATPase, transmembrane domain superfamily	Homologous Superfamily
A, D [auth C]	IPR050510	Cation transport ATPase (P-type)	Family
A, D [auth C]	IPR023214	HAD superfamily	Homologous Superfamily
A, D [auth C]	IPR008250	P-type ATPase, A domain superfamily	Homologous Superfamily
A, D [auth C]	IPR036412	HAD-like superfamily	Homologous Superfamily
A, D [auth C]	IPR023299	P-type ATPase, cytoplasmic domain N	Homologous Superfamily

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C [auth G], D [auth C], E [auth D] A, B, C [auth G], D [auth C], E [auth D], F [auth E]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C [auth G], D [auth C], E [auth D] A, B, C [auth G], D [auth C], E [auth D], F [auth E]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C [auth G], D [auth C], E [auth D] A, B, C [auth G], D [auth C], E [auth D], F [auth E]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	P-type ATPase	Na,K-ATPase, phosphorylated form in complex with bufalin

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, D [auth C]	PHD	Parent Component: ASP RESID: AA0033 PSI-MOD : L-aspartic 4-phosphoric anhydride MOD:00042

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.