7ZRG | pdb_00007zrg

Cryo-EM map of the WT KdpFABC complex in the E1_ATPearly conformation, under turnover conditions

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth B]	SCOP2B Superfamily	Metal cation-transporting ATPase, ATP-binding domain N	8036482	3000981	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)
A	F_UNCLASSIFIED	e7zrgA2	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: F_UNCLASSIFIED	ECOD (1.6)
A	TrkH_3rd	e7zrgA4	A: alpha complex topology	X: Voltage-gated ion channels (From Topology)	H: Voltage-gated ion channels (From Topology)	T: Voltage-gated ion channels	F: TrkH_3rd	ECOD (1.6)
B [auth C]	F_UNCLASSIFIED	e7zrgC1	A: alpha arrays	X: Potassium-transporting ATPase KdpC subunit (From Topology)	H: Potassium-transporting ATPase KdpC subunit (From Topology)	T: Potassium-transporting ATPase KdpC subunit	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth B]	E1-E2_ATPase_N	e7zrgB3	A: beta sandwiches	X: jelly-roll	H: Calcium ATPase, transduction domain A (From Topology)	T: Calcium ATPase, transduction domain A	F: E1-E2_ATPase_N	ECOD (1.6)
D [auth B]	F_UNCLASSIFIED	e7zrgB1	A: alpha bundles	X: Calcium ATPase transmembrane domain-related (From Homology)	H: Calcium ATPase transmembrane domain-related	T: Potassium-transporting ATPase subunit KdpB transmembrane domain	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth B]	PRK01122	e7zrgB2	A: a+b complex topology	X: Metal cation-transporting ATPase, ATP-binding domain (From Topology)	H: Metal cation-transporting ATPase, ATP-binding domain (From Topology)	T: Metal cation-transporting ATPase, ATP-binding domain	F: PRK01122	ECOD (1.6)
D [auth B]	Hydrolase_3_1	e7zrgB4	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	3.40.1110.10	Alpha Beta	3-Layer(aba) Sandwich	Calcium-transporting ATPase, cytoplasmic domain N	Calcium-transporting ATPase, cytoplasmic domain N	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03814	Potassium-transporting ATPase A subunit (KdpA)	Potassium-transporting ATPase A subunit	-	Family
B [auth C]	PF02669	K+-transporting ATPase, c chain (KdpC)	K+-transporting ATPase, c chain	-	Family
C [auth D]	PF09604	F subunit of K+-transporting ATPase (Potass_KdpF) (Potass_KdpF)	F subunit of K+-transporting ATPase (Potass_KdpF)	-	Family
D [auth B]	PF00702	haloacid dehalogenase-like hydrolase (Hydrolase)	haloacid dehalogenase-like hydrolase	This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted fo ...	This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain [1]. Those members with the characteristic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria [2].	Domain
D [auth B]	PF00122	E1-E2 ATPase (E1-E2_ATPase)	E1-E2 ATPase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Potassium-transporting ATPase potassium-binding subunit	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 potassium ion transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity P-type potassium transmembrane 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 potassium ion transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity P-type potassium transmembrane transporter activity ATP-dependent activity P-type ion transporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity	localization transport monoatomic ion transport potassium ion transport monoatomic cation transport establishment of localization metal ion transport monoatomic ion transmembrane transport potassium ion transmembrane transport inorganic ion transmembrane transport inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport cellular process	cell periphery cellular anatomical structure plasma membrane membrane potassium:proton antiporter complex protein-containing complex transmembrane transporter complex membrane protein complex transporter complex ATPase dependent transmembrane transport complex cation-transporting ATPase complex potassium ion-transporting ATPase complex
B [auth C]	Potassium-transporting ATPase KdpC subunit	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 P-type transmembrane transporter activity potassium ion transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity P-type potassium transmembrane transporter activity ATP-dependent activity P-type ion transporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity	localization transport monoatomic ion transport potassium ion transport monoatomic cation transport establishment of localization metal ion transport monoatomic ion transmembrane transport potassium ion transmembrane transport inorganic ion transmembrane transport inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport cellular process	cell periphery cellular anatomical structure plasma membrane membrane potassium:proton antiporter complex protein-containing complex transmembrane transporter complex membrane protein complex transporter complex ATPase dependent transmembrane transport complex cation-transporting ATPase complex potassium ion-transporting ATPase complex
C [auth D]	Potassium-transporting ATPase KdpF subunit	monoatomic cation transmembrane transporter activity P-type transmembrane transporter activity potassium ion transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity P-type potassium transmembrane transporter activity ATP-dependent activity P-type ion transporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity monoatomic cation transmembrane transporter activity P-type transmembrane transporter activity potassium ion transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity P-type potassium transmembrane transporter activity ATP-dependent activity P-type ion transporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity	localization transport monoatomic ion transport potassium ion transport monoatomic cation transport establishment of localization metal ion transport monoatomic ion transmembrane transport potassium ion transmembrane transport inorganic ion transmembrane transport inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport cellular process	cell periphery cellular anatomical structure plasma membrane membrane potassium:proton antiporter complex protein-containing complex transmembrane transporter complex membrane protein complex transporter complex ATPase dependent transmembrane transport complex cation-transporting ATPase complex potassium ion-transporting ATPase complex
D [auth B]	Potassium-transporting ATPase ATP-binding subunit	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule 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 monoatomic cation transmembrane transporter activity P-type transmembrane transporter activity potassium ion transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity P-type potassium transmembrane transporter activity ATP-dependent activity P-type ion transporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity 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	localization transport monoatomic ion transport potassium ion transport monoatomic cation transport establishment of localization metal ion transport monoatomic ion transmembrane transport potassium ion transmembrane transport inorganic ion transmembrane transport inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport cellular process	potassium:proton antiporter complex protein-containing complex cellular anatomical structure transmembrane transporter complex membrane membrane protein complex transporter complex cell periphery plasma membrane ATPase dependent transmembrane transport complex cation-transporting ATPase complex potassium ion-transporting ATPase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR004623	Potassium-transporting ATPase A chain	Family
B [auth C]	IPR003820	Potassium-transporting ATPase C chain	Family
C [auth D]	IPR011726	K+ transporting P-type ATPase, F subunit	Family
D [auth B]	IPR023214	HAD superfamily	Homologous Superfamily
D [auth B]	IPR008250	P-type ATPase, A domain superfamily	Homologous Superfamily
D [auth B]	IPR001757	P-type ATPase	Family
D [auth B]	IPR044492	P-type ATPase, haloacid dehalogenase domain	Domain
D [auth B]	IPR018303	P-type ATPase, phosphorylation site	PTM
D [auth B]	IPR036412	HAD-like superfamily	Homologous Superfamily
D [auth B]	IPR006391	P-type ATPase, B chain, subfamily IA	Family
D [auth B]	IPR023298	P-type ATPase, transmembrane domain superfamily	Homologous Superfamily
D [auth B]	IPR023299	P-type ATPase, cytoplasmic domain N	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B [auth C], C [auth D], D [auth B]	OPM	Transmembrane	Alpha-helical polytopic	P-type ATPase (P-ATPase)	KdpA ATPase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B [auth C], C [auth D], D [auth B]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Superfamily of K⁺ Transporters (SKT proteins)	Potassium-importing KdpFABC membrane complex in the E1-ATP early state under turnover conditions

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D [auth B]	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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.