3J09 | pdb_00003j09

High resolution helical reconstruction of the bacterial p-type ATPase copper transporter CopA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	HAD-like	8037720	3001890	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8037720	3001890	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metal cation-transporting ATPase, ATP-binding domain N	8037721	3000981	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HAD-like	8037720	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HAD-like	8037720	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metal cation-transporting ATPase, ATP-binding domain N	8037721	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)
B	YonK	e3j09B4	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: YonK	ECOD (v294.1)
B	MR_MLE_N	e3j09B6	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: MR_MLE_N	ECOD (v294.1)
B	YkuD	e3j09B8	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.1)
A	Polysacc_synt_2,Polysacc_syn_2C	e3j09A1	A: a/b three-layered sandwiches	X: jelly-roll	H: Galactose-binding domain-like	T: Galactose-binding domain-like	F: Polysacc_synt_2,Polysacc_syn_2C	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00403	Heavy-metal-associated domain (HMA)	Heavy-metal-associated domain		Domain
A, 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
A, B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	copper-exporting P-type ATPase 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 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 ATP-dependent activity cation binding transition metal ion binding copper ion binding metal ion binding monoatomic cation transmembrane transporter activity P-type transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity copper ion transmembrane transporter activity ATPase-coupled monoatomic cation 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 transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity transmembrane transporter activity P-type divalent copper transporter activity identical protein binding protein binding P-type monovalent copper transporter activity	inorganic ion homeostasis chemical homeostasis homeostatic process monoatomic ion homeostasis copper ion homeostasis monoatomic cation homeostasis	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017969	Heavy-metal-associated, conserved site	Conserved Site
A, B	IPR023214	HAD superfamily	Homologous Superfamily
A, B	IPR006121	Heavy metal-associated domain, HMA	Domain
A, B	IPR008250	P-type ATPase, A domain superfamily	Homologous Superfamily
A, B	IPR001757	P-type ATPase	Family
A, B	IPR044492	P-type ATPase, haloacid dehalogenase domain	Domain
A, B	IPR027256	P-type ATPase, subfamily IB	Family
A, B	IPR018303	P-type ATPase, phosphorylation site	PTM
A, B	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B	IPR059000	P-type ATPase, A domain	Domain
A, B	IPR023298	P-type ATPase, transmembrane domain superfamily	Homologous Superfamily
A, B	IPR006122	Heavy metal-associated domain, copper ion-binding	Domain
A, B	IPR036163	Heavy metal-associated domain superfamily	Homologous Superfamily
A, 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	OPM	Transmembrane	Alpha-helical polytopic	P-type ATPase (P-ATPase)	Copper-transporting P-type ATPase

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

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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