2KMX

Solution structure of the nucleotide binding domain of the human Menkes protein in the ATP-bound form

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	P-type_ATPase_Cu-like	e2kmxA1	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: P-type_ATPase_Cu-like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	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

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 inorganic molecular entity transmembrane transporter activity copper ion transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity transmembrane transporter activity protein binding binding copper-dependent protein binding protein-folding chaperone binding adenyl ribonucleotide binding monoatomic cation transmembrane transporter activity inorganic molecular entity transmembrane transporter activity copper ion transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity transmembrane transporter activity protein binding binding copper-dependent protein binding protein-folding chaperone binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding superoxide dismutase copper chaperone activity metallochaperone activity molecular carrier activity copper chaperone 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 ATP-dependent activity small GTPase binding enzyme binding GTPase binding cation binding cuprous ion binding transition metal ion binding copper ion binding metal ion binding P-type transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ATPase-coupled monoatomic cation transmembrane transporter activity P-type ion transporter activity P-type monovalent copper transporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter 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 response to stimulus cellular response to inorganic substance cellular response to metal ion response to stimulus 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 response to stimulus cellular response to inorganic substance cellular response to metal ion response to stimulus response to inorganic substance cellular response to iron ion cellular response to chemical stimulus response to metal ion response to chemical response to iron ion cellular process cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization cellular response to cobalt ion response to cobalt ion 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 organonitrogen compound metabolic process cellular metabolic process organic hydroxy compound metabolic process dopamine metabolic process catechol-containing compound metabolic process organic cyclic compound metabolic process amine metabolic process organic substance metabolic process catecholamine metabolic process phenol-containing compound metabolic process nitrogen compound metabolic process metabolic process cellular aromatic compound metabolic process biogenic amine metabolic process aerobic respiration cellular respiration oxidative phosphorylation regulation of biological process regulation of cellular process energy derivation by oxidation of organic compounds biological regulation regulation of generation of precursor metabolites and energy regulation of cellular metabolic process generation of precursor metabolites and energy regulation of cellular respiration regulation of aerobic respiration regulation of oxidative phosphorylation regulation of metabolic process response to zinc ion cellular response to antibiotic response to antibiotic peptidyl-lysine modification primary metabolic process macromolecule modification peptidyl-amino acid modification protein metabolic process macromolecule metabolic process protein modification process regulation of body fluid levels secretion transport mammary gland development gland development establishment of localization body fluid secretion localization lactation regulation of biological quality vasculature development blood vessel development circulatory system development elastic fiber assembly cellular component biogenesis cellular component assembly supramolecular fiber organization extracellular matrix assembly regulation of catalytic activity positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity regulation of molecular function positive regulation of molecular function regulation of monooxygenase activity positive regulation of monooxygenase activity regulation of tyrosinase activity positive regulation of tyrosinase activity response to manganese ion cellular response to oxidative stress detoxification 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 response to stress cellular detoxification response to oxygen-containing compound cellular response to oxygen-containing compound response to reactive oxygen species response to toxic substance removal of superoxide radicals superoxide metabolic process response to oxidative stress cellular response to superoxide cellular response to toxic substance response to oxygen radical epinephrine metabolic process inorganic ion homeostasis chemical homeostasis homeostatic process monoatomic ion homeostasis copper ion homeostasis monoatomic cation homeostasis norepinephrine metabolic process positive regulation of cell size regulation of cellular component size regulation of cell size regulation of anatomical structure size response to lead ion cellular response to lead ion regulation of cellular component organization positive regulation of cellular component organization cell projection organization positive regulation of biological process plasma membrane bounded cell projection assembly regulation of lamellipodium assembly regulation of lamellipodium organization positive regulation of cell projection organization positive regulation of cellular process lamellipodium assembly plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly positive regulation of lamellipodium assembly regulation of cellular component biogenesis positive regulation of lamellipodium organization regulation of plasma membrane bounded cell projection assembly lamellipodium organization cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly tube development respiratory tube development lung development respiratory system development lung alveolus 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 mononuclear cell differentiation lymphocyte activation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation CD4-positive, alpha-beta T cell differentiation involved in immune response alpha-beta T cell differentiation involved in immune response leukocyte activation alpha-beta T cell differentiation T cell activation involved in immune response alpha-beta T cell activation involved in immune response T cell activation CD4-positive, alpha-beta T cell activation leukocyte activation involved in immune response alpha-beta T cell activation T cell differentiation lymphocyte activation involved in immune response T-helper cell differentiation immune response hemopoiesis cell activation T cell differentiation involved in immune response immune effector process immune system process leukocyte differentiation intracellular copper ion homeostasis cellular homeostasis intracellular monoatomic cation homeostasis intracellular chemical homeostasis intracellular monoatomic ion homeostasis response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus copper ion transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport metal ion transport inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport copper ion transport transition metal ion transport monoatomic ion transport copper ion export monoatomic cation transport collagen fibril organization embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development detoxification of inorganic compound response to copper ion detoxification of copper ion stress response to copper ion stress response to metal ion cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to organic substance response to amino acid pigmentation response to cadmium ion cellular response to cadmium ion regulation of localization negative regulation of monoatomic ion transport negative regulation of biological process negative regulation of iron ion transmembrane transport negative regulation of transport regulation of monoatomic ion transmembrane transport negative regulation of transmembrane transport regulation of iron ion transmembrane transport negative regulation of monoatomic ion transmembrane transport negative regulation of cellular process negative regulation of cation transmembrane transport regulation of metal ion transport negative regulation of iron ion transport regulation of transport regulation of monoatomic ion transport regulation of iron ion transport iron ion transport iron ion transmembrane transport regulation of transmembrane transport regulation of monoatomic cation transmembrane transport positive regulation of response to wounding regulation of response to wounding positive regulation of response to stimulus regulation of response to stimulus regulation of response to stress response to wounding oxoacid metabolic process indole-containing compound metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process heterocycle metabolic process indolalkylamine metabolic process small molecule metabolic process aromatic amino acid metabolic process carboxylic acid metabolic process cellular nitrogen compound metabolic process tryptophan metabolic process 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 hepaticobiliary system development liver development behavior locomotory behavior pyramidal neuron development forebrain development forebrain generation of neurons forebrain neuron development forebrain neuron differentiation pyramidal neuron differentiation cellular response to endogenous stimulus cellular response to growth factor stimulus cellular response to platelet-derived growth factor stimulus response to endogenous stimulus response to growth factor response to platelet-derived growth factor multi-multicellular organism process reproductive process female pregnancy multi-organism reproductive process carbohydrate derivative biosynthetic process cellular biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process glycoprotein biosynthetic process glycoprotein metabolic process macromolecule biosynthetic process elastin metabolic process biosynthetic process organic substance biosynthetic process elastin biosynthetic process pigment metabolic process regulation of melanin biosynthetic process pigment biosynthetic process positive regulation of cellular metabolic 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 regulation of biosynthetic process positive regulation of melanin biosynthetic process regulation of secondary metabolite biosynthetic process regulation of cellular biosynthetic process regulation of secondary metabolic process aromatic compound biosynthetic process organic hydroxy compound biosynthetic process organic cyclic compound biosynthetic process phenol-containing compound biosynthetic process melanin biosynthetic process positive regulation of cellular biosynthetic process cell population proliferation positive regulation of cell population proliferation positive regulation of epithelial cell proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation response to iron(III) ion plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cell projection morphogenesis neuron projection morphogenesis serotonin metabolic process primary amino compound metabolic process ammonium ion metabolic process regulation of vascular associated smooth muscle cell migration positive regulation of locomotion vascular associated smooth muscle cell migration regulation of cell motility regulation of smooth muscle cell migration positive regulation of smooth muscle cell migration positive regulation of cell migration smooth muscle cell migration muscle cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of vascular associated smooth muscle cell migration cellular response to copper ion copper ion import blood vessel remodeling tissue remodeling organelle organization mitochondrion organization	somatodendritic compartment cell body perikaryon neuronal cell body cellular anatomical entity intracellular anatomical structure cytoplasm cytosol cell leading edge membrane-bounded organelle pigment granule membrane intracellular vesicle intracellular membrane-bounded organelle somatodendritic compartment cell body perikaryon neuronal cell body cellular anatomical entity intracellular anatomical structure cytoplasm cytosol cell leading edge membrane-bounded organelle pigment granule membrane intracellular vesicle intracellular membrane-bounded organelle chitosome intracellular organelle melanosome cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle melanosome membrane vesicle organelle membrane pigment granule membrane cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network membrane endomembrane system trans-Golgi network brush border membrane cluster of actin-based cell projections plasma membrane bounded cell projection brush border cell projection cell projection membrane endosome late endosome basal part of cell basal plasma membrane basolateral plasma membrane secretory granule secretory vesicle dendrite dendritic tree neuron projection phagocytic vesicle phagocytic vesicle membrane endocytic vesicle membrane endocytic vesicle actin-based cell projection microvillus perinuclear region of cytoplasm axon transport vesicle trans-Golgi network transport vesicle clathrin-coated vesicle coated vesicle Golgi-associated vesicle endosome membrane early endosome early endosome membrane postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization synapse cell junction asymmetric synapse endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001757	P-type ATPase	Family
A	IPR023298	P-type ATPase, transmembrane domain superfamily	Homologous Superfamily
A	IPR036412	HAD-like superfamily	Homologous Superfamily
A	IPR006121	Heavy metal-associated domain, HMA	Domain
A	IPR044492	P-type ATPase, haloacid dehalogenase domain	Domain
A	IPR027256	P-type ATPase, subfamily IB	Family
A	IPR018303	P-type ATPase, phosphorylation site	PTM
A	IPR017969	Heavy-metal-associated, conserved site	Conserved Site
A	IPR006122	Heavy metal-associated domain, copper ion-binding	Domain
A	IPR023299	P-type ATPase, cytoplasmic domain N	Homologous Superfamily
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 visual epilepsy Liver Neoplasms, Experimental 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 visual epilepsy Liver Neoplasms, Experimental 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 Wilson disease lung cancer 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 National Science Foundation (DBI-1832184), 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 R01GM133198.