1KVJ | pdb_00001kvj

Solution Structure of the Cu(I) bound form of the first heavy metal binding motif of the Menkes protein

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1kvja_	Alpha and beta proteins (a+b)	Ferredoxin-like	HMA, heavy metal-associated domain	HMA, heavy metal-associated domain	Menkes copper-transporting ATPase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ABM	e1kvjA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: ABM	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Copper-transporting ATPase 1	monoatomic cation transmembrane transporter activity copper ion transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity transmembrane transporter activity cation binding cuprous ion binding transition metal ion binding copper ion binding ion binding binding metal ion binding monoatomic cation transmembrane transporter activity copper ion transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity transmembrane transporter activity cation binding cuprous ion binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding protein binding copper-dependent protein 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 superoxide dismutase copper chaperone activity metallochaperone activity molecular carrier activity copper chaperone activity P-type transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity ATP-dependent activity P-type ion transporter activity P-type monovalent copper transporter activity active monoatomic ion transmembrane transporter activity active 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 P-type divalent copper transporter activity	developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development cellular developmental process central nervous system neuron development cell development nervous system development developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development cellular developmental process central nervous system neuron development cell development nervous system development generation of neurons central nervous system neuron differentiation neurogenesis central nervous system development neuron differentiation cell differentiation neuron development cellular process T-helper cell differentiation hemopoiesis cell activation mononuclear cell differentiation lymphocyte activation lymphocyte differentiation CD4-positive, alpha-beta T cell differentiation leukocyte activation alpha-beta T cell differentiation T cell activation immune system process CD4-positive, alpha-beta T cell activation alpha-beta T cell activation T cell differentiation leukocyte differentiation inorganic ion homeostasis homeostatic process intracellular copper ion homeostasis copper ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization copper ion transmembrane transport transport monoatomic ion transmembrane transport establishment of localization metal ion transport monoatomic cation transmembrane transport transmembrane transport localization copper ion transport transition metal ion transport monoatomic ion transport copper ion export monoatomic cation transport norepinephrine biosynthetic process catechol-containing compound metabolic process norepinephrine metabolic process amine metabolic process biogenic amine biosynthetic process catecholamine metabolic process amine biosynthetic process phenol-containing compound metabolic process catecholamine biosynthetic process phenol-containing compound biosynthetic process catechol-containing compound biosynthetic process biogenic amine metabolic process epithelium development epidermis development molting cycle process hair cycle epidermis morphogenesis morphogenesis of an epithelium tissue morphogenesis anatomical structure morphogenesis skin development skin epidermis development hair follicle development molting cycle hair cycle process hair follicle morphogenesis collagen fibril organization dopamine metabolic process carbohydrate derivative biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process protein metabolic process aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds regulation of generation of precursor metabolites and energy generation of precursor metabolites and energy regulation of cellular respiration regulation of aerobic respiration regulation of oxidative phosphorylation detoxification of inorganic compound response to copper ion detoxification of copper ion response to stimulus detoxification stress response to copper ion response to toxic substance response to metal ion response to chemical response to stress stress response to metal ion aromatic amino acid metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process small molecule metabolic process tyrosine metabolic process pigmentation vasculature development blood vessel development circulatory system development elastic fiber assembly cellular component biogenesis cellular component assembly supramolecular fiber organization extracellular matrix assembly cerebellar cortex morphogenesis hindbrain morphogenesis cerebellar Purkinje cell layer formation cerebellar Purkinje cell layer development cerebellar Purkinje cell differentiation metencephalon development cerebellar Purkinje cell layer morphogenesis cerebellar cortex formation cerebellum morphogenesis head development brain development cerebellar cortex development cerebellum development anatomical structure formation involved in morphogenesis hindbrain development cell differentiation in hindbrain neuron cellular homeostasis behavior locomotory behavior nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process ATP 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 nucleoside triphosphate metabolic process purine ribonucleotide metabolic process phosphorus metabolic process pyramidal neuron development forebrain development forebrain generation of neurons forebrain neuron development forebrain neuron differentiation pyramidal neuron differentiation cellular response to stimulus cellular response to oxidative stress reactive oxygen species metabolic process cellular response to chemical stress response to superoxide cellular oxidant detoxification cellular response to oxygen radical cellular response to reactive oxygen species cellular response to stress cellular detoxification response to oxygen-containing compound cellular response to oxygen-containing compound response to reactive oxygen species removal of superoxide radicals superoxide metabolic process response to oxidative stress cellular response to chemical stimulus cellular response to superoxide cellular response to toxic substance response to oxygen radical epinephrine metabolic process pigment metabolic process regulation of melanin biosynthetic process positive regulation of biological process pigment biosynthetic process melanin metabolic process secondary metabolic process positive regulation of secondary metabolite biosynthetic process positive regulation of metabolic process secondary metabolite biosynthetic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of melanin biosynthetic process regulation of secondary metabolite biosynthetic process regulation of secondary metabolic process melanin biosynthetic process indole-containing compound metabolic process L-tryptophan metabolic process cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cell projection morphogenesis neuron projection morphogenesis dendrite development plasma membrane bounded cell projection organization dendrite morphogenesis cell morphogenesis involved in neuron differentiation neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process serotonin metabolic process cellular localization establishment of localization in cell copper ion import blood vessel remodeling tissue remodeling organelle organization mitochondrion organization signaling apoptotic mitochondrial changes cell communication apoptotic signaling pathway release of cytochrome c from mitochondria signal transduction tube development respiratory tube development lung development respiratory system development lung alveolus development	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol cell periphery basal part of cell plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane somatodendritic compartment cell projection dendrite cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol cell periphery basal part of cell plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle intracellular organelle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane vesicle organelle membrane endocytic vesicle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system trans-Golgi network perinuclear region of cytoplasm cell body neuronal cell body axon pigment granule chitosome melanosome melanosome membrane pigment granule membrane transport vesicle trans-Golgi network transport vesicle clathrin-coated vesicle coated vesicle Golgi-associated vesicle endosome membrane early endosome endosome early endosome membrane postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization synapse cell junction asymmetric synapse trans-Golgi network membrane late endosome endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001757	P-type ATPase	Family
A	IPR027256	P-type ATPase, subfamily IB	Family
A	IPR018303	P-type ATPase, phosphorylation site	PTM
A	IPR023298	P-type ATPase, transmembrane domain superfamily	Homologous Superfamily
A	IPR017969	Heavy-metal-associated, conserved site	Conserved Site
A	IPR036412	HAD-like superfamily	Homologous Superfamily
A	IPR006122	Heavy metal-associated domain, copper ion-binding	Domain
A	IPR023299	P-type ATPase, cytoplasmic domain N	Homologous Superfamily
A	IPR006121	Heavy metal-associated domain, HMA	Domain
A	IPR044492	P-type ATPase, haloacid dehalogenase domain	Domain
A	IPR059000	P-type ATPase, A domain	Domain
A	IPR023214	HAD superfamily	Homologous Superfamily
A	IPR008250	P-type ATPase, A domain superfamily	Homologous Superfamily
A	IPR036163	Heavy metal-associated domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q04656	Menkes disease occipital horn syndrome X-linked distal spinal muscular atrophy type 3 Liver Neoplasms, Experimental visual epilepsy pulmonary hypertension anemia cutis laxa malignant colon neoplasm aortic aneurysm Charcot-Marie-Tooth disease palsy Pick disease tuberculosis pituitary cancer Menkes disease occipital horn syndrome X-linked distal spinal muscular atrophy type 3 Liver Neoplasms, Experimental visual epilepsy pulmonary hypertension anemia cutis laxa malignant colon neoplasm aortic aneurysm Charcot-Marie-Tooth disease palsy Pick disease tuberculosis pituitary cancer psoriasis Ehlers-Danlos syndrome acute myeloid leukemia glioblastoma breast cancer osteosarcoma transitional cell carcinoma inborn errors of metabolism pancreatic intraductal papillary-mucinous carcinoma colonic neoplasm interstitial cystitis lung cancer Wilson disease medulloblastoma neurodegenerative disease atypical teratoid rhabdoid tumor cerebrovascular disorder ovarian cancer intellectual disability pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia leukodystrophy pilocytic astrocytoma primitive neuroectodermal tumor genetic endocrine growth disease benign colon neoplasm subependymal giant cell astrocytoma hepatitis

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.