2JQ8

Solution structure of the Somatomedin B domain from vitronectin produced in Pichia pastoris

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2jq8a_	Small proteins	Somatomedin B domain	Somatomedin B domain	Somatomedin B domain	Vitronectin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Somatomedin B domain	8033943	3001699	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)
A	Somatomedin_B	e2jq8A1	A: few secondary structure elements	X: Somatomedin B domain (From Topology)	H: Somatomedin B domain (From Topology)	T: Somatomedin B domain	F: Somatomedin_B	ECOD (1.6)

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	Vitronectin	cargo receptor activity scavenger receptor activity binding polysaccharide binding carbohydrate binding identical protein binding protein binding extracellular matrix binding collagen binding protein-containing complex binding cell adhesion molecule binding integrin binding signaling receptor binding structural molecule activity cargo receptor activity scavenger receptor activity binding polysaccharide binding carbohydrate binding identical protein binding protein binding extracellular matrix binding collagen binding protein-containing complex binding cell adhesion molecule binding integrin binding signaling receptor binding structural molecule activity extracellular matrix structural constituent heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation cellular process positive regulation of response to wounding wound healing response to stimulus positive regulation of biological process regulation of response to wounding positive regulation of response to stimulus positive regulation of wound healing regulation of response to stimulus regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation cellular process positive regulation of response to wounding wound healing response to stimulus positive regulation of biological process regulation of response to wounding positive regulation of response to stimulus positive regulation of wound healing regulation of response to stimulus response to stress regulation of response to stress regulation of wound healing response to wounding regulation of cell-substrate adhesion positive regulation of cell adhesion cell-substrate adhesion positive regulation of cell-substrate adhesion positive regulation of cellular process cellular response to stimulus positive regulation of cell communication cellular response to growth factor stimulus positive regulation of signal transduction signaling regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway cell communication regulation of vascular endothelial growth factor receptor signaling pathway cellular response to endogenous stimulus signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus vascular endothelial growth factor receptor signaling pathway positive regulation of vascular endothelial growth factor receptor signaling pathway regulation of cell communication response to growth factor positive regulation of signaling cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization multicellular organismal process regulation of body fluid levels regulation of response to external stimulus negative regulation of biological process regulation of coagulation coagulation regulation of multicellular organismal process regulation of biological quality regulation of hemostasis negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation hemostasis response to external stimulus negative regulation of response to wounding blood coagulation negative regulation of hemostasis negative regulation of coagulation negative regulation of response to external stimulus negative regulation of multicellular organismal process positive regulation of locomotion regulation of cell motility positive regulation of smooth muscle cell migration 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 regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport vesicle-mediated transport localization positive regulation of endocytosis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of transport endocytosis receptor-mediated endocytosis regulation of protein binding positive regulation of molecular function regulation of molecular function positive regulation of protein binding regulation of binding positive regulation of binding cell-matrix adhesion cellular component biogenesis protein polymerization cellular component assembly protein-containing complex organization protein-containing complex assembly developmental process cellular developmental process nervous system development multicellular organism development neurogenesis central nervous system development gliogenesis oligodendrocyte differentiation glial cell differentiation cell differentiation anatomical structure development system development immune response immune system process formation of primary germ layer embryonic morphogenesis tissue development embryo development gastrulation anatomical structure morphogenesis endoderm development anatomical structure formation involved in morphogenesis endoderm formation endodermal cell differentiation gland development animal organ development animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration cell adhesion mediated by integrin smooth muscle cell-matrix adhesion negative regulation of hydrolase activity negative regulation of proteolysis regulation of catalytic activity negative regulation of catalytic activity negative regulation of endopeptidase activity regulation of primary metabolic process negative regulation of peptidase activity organic substance metabolic process regulation of proteolysis proteolysis regulation of endopeptidase activity protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process organonitrogen compound metabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of peptidase activity negative regulation of molecular function primary metabolic process regulation of macromolecule metabolic process regulation of hydrolase activity metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of coagulation positive regulation of blood coagulation positive regulation of response to external stimulus positive regulation of hemostasis fibrinolysis regulation of fibrinolysis positive regulation of multicellular organismal process negative regulation of fibrinolysis regulation of protein modification process positive regulation of phosphorylation regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process peptidyl-tyrosine modification positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of peptidyl-tyrosine phosphorylation regulation of cellular metabolic process macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process peptidyl-tyrosine phosphorylation	basement membrane cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle basement membrane cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen rough endoplasmic reticulum intracellular organelle rough endoplasmic reticulum lumen organelle lumen endoplasmic reticulum cytoplasm protein-containing complex peptidase inhibitor complex protein complex involved in cell-matrix adhesion protein complex involved in cell adhesion plasma membrane protein complex membrane plasma membrane membrane protein complex alphav-beta3 integrin-vitronectin complex Golgi apparatus Golgi lumen blood microparticle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR020436	Somatomedin B domain, chordata	Domain
A	IPR036024	Somatomedin B-like domain superfamily	Homologous Superfamily
A	IPR018486	Hemopexin, conserved site	Conserved Site
A	IPR036375	Hemopexin-like domain superfamily	Homologous Superfamily
A	IPR001212	Somatomedin B domain	Domain
A	IPR018487	Hemopexin-like repeats	Repeat
A	IPR000585	Hemopexin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P04004	Crohn disease cirrhosis of liver age-related macular degeneration Crohn's disease of the ileum ileocolitis wet macular degeneration amyotrophic lateral sclerosis Crohn's colitis lung carcinoma hypertensive disorder

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.