2YS0 | pdb_00002ys0

Solution structure of the Somatomedin B domain of human Ectonucleotide pyrophosphatase/phosphodiesterase family member

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	TGF_beta	e2ys0A1	A: alpha bundles	X: Profilin-like	H: sensor domains	T: sensor domains	F: TGF_beta	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	4.10.410.20	Few Secondary Structures	Irregular	Factor Xa Inhibitor		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01033	Somatomedin B domain (Somatomedin_B)	Somatomedin B domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ectonucleotide pyrophosphatase/phosphodiesterase family member 1	binding nucleic acid binding pyrophosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity GTP diphosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity protein binding signaling receptor binding insulin receptor binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds binding nucleic acid binding pyrophosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity GTP diphosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity protein binding signaling receptor binding insulin receptor binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity cargo receptor activity scavenger receptor activity phosphoric diester hydrolase activity 3',5'-cyclic-nucleotide phosphodiesterase activity 3',5'-cyclic-AMP phosphodiesterase activity cyclic-nucleotide phosphodiesterase activity nuclease activity phosphodiesterase I activity catalytic activity, acting on a nucleic acid exonuclease activity 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 ATP diphosphatase activity UTP diphosphatase activity polysaccharide binding carbohydrate binding cation binding calcium ion binding metal ion binding 3'-phosphoadenosine 5'-phosphosulfate binding sulfur compound binding dinucleotide phosphatase activity identical protein binding protein homodimerization activity protein dimerization activity transition metal ion binding zinc ion binding cyclic-GMP-AMP hydrolase activity	developmental process multicellular organismal process ossification bone mineralization animal organ development anatomical structure development biomineral tissue development tissue development phosphate ion homeostasis inorganic ion homeostasis chemical homeostasis homeostatic process regulation of biological process regulation of growth developmental process multicellular organismal process ossification bone mineralization animal organ development anatomical structure development biomineral tissue development tissue development phosphate ion homeostasis inorganic ion homeostasis chemical homeostasis homeostatic process regulation of biological process regulation of growth regulation of cellular component organization regulation of cellular process negative regulation of biological process biological regulation growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth negative regulation of cellular process cellular process cellular component organization or biogenesis cellular response to stimulus cellular response to nitrogen compound response to stimulus negative regulation of signaling signaling response to peptide hormone regulation of signal transduction insulin receptor signaling pathway regulation of cellular response to insulin stimulus negative regulation of cell communication cell surface receptor protein tyrosine kinase signaling pathway cell communication cellular response to endogenous stimulus response to hormone signal transduction enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus response to endogenous stimulus regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound negative regulation of signal transduction cellular response to oxygen-containing compound cellular response to chemical stimulus negative regulation of cellular response to insulin stimulus regulation of response to stimulus negative regulation of insulin receptor signaling pathway response to chemical response to insulin regulation of cell communication cellular response to insulin stimulus regulation of multicellular organismal development regulation of developmental process regulation of biomineral tissue development regulation of bone mineralization multicellular organism development regulation of multicellular organismal process regulation of ossification regulation of glycogen biosynthetic process negative regulation of glycogen biosynthetic process glucan biosynthetic process energy derivation by oxidation of organic compounds regulation of glucan biosynthetic process regulation of generation of precursor metabolites and energy regulation of polysaccharide metabolic process regulation of primary metabolic process polysaccharide metabolic process glucan metabolic process regulation of carbohydrate metabolic process negative regulation of carbohydrate metabolic process negative regulation of glycogen metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process glycogen metabolic process negative regulation of metabolic process primary metabolic process generation of precursor metabolites and energy regulation of macromolecule metabolic process glycogen biosynthetic process macromolecule biosynthetic process biosynthetic process negative regulation of biosynthetic process regulation of polysaccharide biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process energy reserve metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of carbohydrate biosynthetic process regulation of glycogen metabolic process regulation of metabolic process regulation of localization import into cell hexose transmembrane transport regulation of D-glucose import across plasma membrane transport carbohydrate import across plasma membrane carbohydrate transport negative regulation of transport negative regulation of D-glucose import across plasma membrane negative regulation of transmembrane transport hexose import across plasma membrane localization regulation of transport import across plasma membrane negative regulation of D-glucose transmembrane transport establishment of localization transmembrane transport regulation of transmembrane transport D-glucose import across plasma membrane D-glucose transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport nucleoside phosphate metabolic process catabolic process nucleoside triphosphate catabolic process organophosphate catabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process nucleoside triphosphate metabolic process phosphorus metabolic process intracellular phosphate ion homeostasis cellular homeostasis intracellular chemical homeostasis inorganic diphosphate transport inorganic anion transport fat cell differentiation cellular developmental process negative regulation of developmental process regulation of cell differentiation negative regulation of fat cell differentiation cell differentiation negative regulation of cell differentiation regulation of fat cell differentiation ribose phosphate metabolic process purine nucleoside triphosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process nucleotide metabolic process purine-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process purine ribonucleoside triphosphate metabolic process purine ribonucleotide metabolic process immune response immune system process pigment cell differentiation pigmentation developmental pigmentation melanocyte differentiation nucleic acid metabolic process gene expression response to organophosphorus response to ATP response to purine-containing compound nucleoside bisphosphate metabolic process purine nucleoside bisphosphate metabolic process ribonucleoside bisphosphate metabolic process oxoacid metabolic process organic acid metabolic process purine ribonucleoside bisphosphate metabolic process sulfur compound metabolic process 3'-phosphoadenosine 5'-phosphosulfate metabolic process negative regulation of biomineral tissue development negative regulation of bone mineralization negative regulation of ossification negative regulation of multicellular organismal process	cellular anatomical structure membrane cell periphery basal part of cell plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane vacuolar membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle cellular anatomical structure membrane cell periphery basal part of cell plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane vacuolar membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm organelle membrane lysosome extracellular region extracellular space cell surface

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR020821	ENPP1-3/EXOG-like, endonuclease/phosphodiesterase domain	Domain
A	IPR017850	Alkaline-phosphatase-like, core domain superfamily	Homologous Superfamily
A	IPR020436	Somatomedin B domain, chordata	Domain
A	IPR036024	Somatomedin B-like domain superfamily	Homologous Superfamily
A	IPR044929	DNA/RNA non-specific endonuclease superfamily	Homologous Superfamily
A	IPR001212	Somatomedin B domain	Domain
A	IPR002591	Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase	Family
A	IPR044925	His-Me finger superfamily	Homologous Superfamily
A	IPR001604	DNA/RNA non-specific endonuclease/pyrophosphatase/phosphodiesterase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P22413	type 2 diabetes mellitus hypophosphatemic rickets, autosomal recessive, 2 arterial calcification of infancy autosomal recessive inherited pseudoxanthoma elasticum hypopigmentation-punctate palmoplantar keratoderma syndrome obesity disorder ossification of the posterior longitudinal ligament of the spine arterial calcification, generalized, of infancy, 1 endometriosis lung cancer maturity-onset diabetes of the young ovarian cancer pancreatic intraductal papillary-mucinous carcinoma acquired metabolic disease pituitary cancer type 2 diabetes mellitus hypophosphatemic rickets, autosomal recessive, 2 arterial calcification of infancy autosomal recessive inherited pseudoxanthoma elasticum hypopigmentation-punctate palmoplantar keratoderma syndrome obesity disorder ossification of the posterior longitudinal ligament of the spine arterial calcification, generalized, of infancy, 1 endometriosis lung cancer maturity-onset diabetes of the young ovarian cancer pancreatic intraductal papillary-mucinous carcinoma acquired metabolic disease pituitary cancer Crohn disease Diabetes Mellitus, Non-Insulin-Dependent erythrokeratoderma intellectual disability lung carcinoma monogenic obesity osteogenesis imperfecta palmoplantar keratosis pancreatic intraductal papillary-mucinous neoplasm rickets breast cancer ulcerative colitis cystic fibrosis hypophosphatemia invasive ductal breast carcinoma malignant colon neoplasm osteosarcoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia subependymal giant cell astrocytoma diabetes mellitus hypophosphatemic rickets, autosomal recessive, 1

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.