5UVG | pdb_00005uvg

Crystal structure of the human neutral sphingomyelinase 2 (nSMase2) catalytic domain with insertion deleted and calcium bound

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	AMP-binding	e5uvgA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: RelE-like	T: RelE-like	F: AMP-binding	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03372	Endonuclease/Exonuclease/phosphatase family (Exo_endo_phos)	Endonuclease/Exonuclease/phosphatase family	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3. ...	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3.1.21.1 e.g. Swiss:P24855, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56 Swiss:O43426, Sphingomyelinase EC:3.1.4.12 Swiss:P11889 and Nocturnin Swiss:O35710.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Sphingomyelin phosphodiesterase 3,Sphingomyelin phosphodiesterase 3	sphingomyelin phosphodiesterase activity phosphoric ester hydrolase activity phospholipase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity sphingophospholipase activity hydrolase activity catalytic activity lipase activity cation binding ion binding binding metal ion binding small molecule binding sphingomyelin phosphodiesterase activity phosphoric ester hydrolase activity phospholipase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity sphingophospholipase activity hydrolase activity catalytic activity lipase activity cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding modified amino acid binding anion binding phospholipid binding lipid binding phosphatidylserine binding phosphatidic acid binding neutral sphingomyelin phosphodiesterase activity	developmental process multicellular organismal process ossification bone mineralization animal organ development anatomical structure development biomineral tissue development tissue development response to stimulus response to redox state cellular response to redox state cellular response to stimulus cellular response to low-density lipoprotein particle stimulus cellular response to oxidised low-density lipoprotein particle stimulus developmental process multicellular organismal process ossification bone mineralization animal organ development anatomical structure development biomineral tissue development tissue development response to stimulus response to redox state cellular response to redox state cellular response to stimulus cellular response to low-density lipoprotein particle stimulus cellular response to oxidised low-density lipoprotein particle stimulus response to endogenous stimulus response to chemical response to lipoprotein particle cellular process cellular response to lipoprotein particle stimulus cell cycle G1 to G0 transition cell cycle process endochondral ossification replacement ossification endochondral bone morphogenesis multicellular organism development anatomical structure morphogenesis skeletal system development skeletal system morphogenesis animal organ morphogenesis bone morphogenesis bone development system development positive regulation of organelle organization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of biological process regulation of mitotic nuclear division positive regulation of mitotic nuclear division mitotic cell cycle cellular component organization regulation of mitotic cell cycle positive regulation of cell cycle process cellular component organization or biogenesis regulation of cell cycle positive regulation of cellular process regulation of biological process mitotic nuclear division regulation of cell cycle process organelle fission biological regulation positive regulation of nuclear division regulation of organelle organization positive regulation of cell cycle organelle organization nuclear division mitotic cell cycle process regulation of nuclear division cell surface receptor signaling pathway signaling platelet-derived growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction enzyme-linked receptor protein signaling pathway primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process DNA biosynthetic process response to peptide cellular response to chemical stimulus cellular response to peptide connective tissue development cellular developmental process cell development chondrocyte differentiation involved in endochondral bone morphogenesis cell differentiation chondrocyte development involved in endochondral bone morphogenesis chondrocyte differentiation cartilage development involved in endochondral bone morphogenesis chondrocyte development cartilage development regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction cell population proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation cellular component biogenesis cellular component assembly extracellular matrix organization extracellular matrix assembly extracellular structure organization external encapsulating structure organization localization polysaccharide localization transport macromolecule localization carbohydrate transport polysaccharide transport establishment of localization ceramide metabolic process sphingolipid metabolic process lipid metabolic process multicellular organism growth developmental growth growth regulation of cell motility regulation of leukocyte migration leukocyte migration immune system process regulation of locomotion regulation of cell migration cell migration regulation of immune system process cell motility locomotion sphingolipid mediated signaling pathway cellular response to BMP stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus cellular response to endogenous stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor BMP signaling pathway regulation of cartilage development regulation of multicellular organismal development regulation of developmental process regulation of multicellular organismal process organ growth bone growth nitrogen compound transport secretion regulation of hormone levels cell-cell signaling export from cell hormone secretion peptide transport peptide secretion secretion by cell peptide hormone secretion signal release hormone transport regulation of biological quality cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to stress response to stress cellular response to tumor necrosis factor response to cytokine cellular response to cytokine stimulus response to tumor necrosis factor sphingolipid catabolic process lipid catabolic process catabolic process sphingomyelin catabolic process phospholipid catabolic process organophosphate catabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process sphingomyelin metabolic process odontogenesis of dentin-containing tooth dentinogenesis anatomical structure formation involved in morphogenesis odontogenesis cellular response to metal ion response to metal ion response to magnesium ion cellular response to magnesium ion collagen metabolic process exosomal secretion establishment of organelle localization regulation of localization cellular localization positive regulation of secretion by cell positive regulation of exosomal secretion vesicle-mediated transport positive regulation of exocytosis regulation of secretion by cell positive regulation of secretion organelle localization establishment of localization in cell vesicle localization positive regulation of cellular component biogenesis regulation of transport regulation of exosomal secretion establishment of vesicle localization regulation of cellular component biogenesis regulation of vesicle-mediated transport extracellular exosome biogenesis regulation of secretion exocytosis positive regulation of transport extracellular vesicle biogenesis regulation of exocytosis hemopoiesis hematopoietic progenitor cell differentiation glycosaminoglycan metabolic process regulation of hyaluronan biosynthetic process carbohydrate derivative metabolic process regulation of polysaccharide metabolic process regulation of primary metabolic process negative regulation of hyaluronan biosynthetic process hyaluronan metabolic process polysaccharide metabolic process glycosaminoglycan biosynthetic process regulation of carbohydrate metabolic process negative regulation of carbohydrate metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process negative regulation of metabolic process carbohydrate biosynthetic process regulation of macromolecule metabolic process hyaluronan biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of polysaccharide biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process regulation of macromolecule biosynthetic process regulation of carbohydrate biosynthetic process regulation of metabolic process tube development respiratory tube development lung development respiratory system development lung alveolus development	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle Golgi membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle organelle membrane cell periphery cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle Golgi membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle organelle membrane cell periphery plasma membrane Golgi apparatus subcompartment organelle subcompartment Golgi cisterna Golgi cis cisterna Golgi stack extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017766	Sphingomyelinase C/phospholipase C	Family
A	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	Homologous Superfamily
A	IPR005135	Endonuclease/exonuclease/phosphatase	Domain
A	IPR038772	Sphingomyelinase C/Sphingomyelin phosphodiesterase 2-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NY59	myelodysplastic syndrome leukemia atypical teratoid rhabdoid tumor malignant ependymoma osteosarcoma pilocytic astrocytoma glioblastoma lung carcinoma malignant glioma ovarian cancer psoriasis Hematopoetic Myelodysplasia malignant colon neoplasm pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia systemic lupus erythematosus

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Monotopic/peripheral	Alpha + Beta monotopic/peripheral	DNase I-like	Endonuclease/exonuclease/phosphatase family

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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