7YYK | pdb_00007yyk

Crystal structure of the O-fucosylated form of TSRs1-3 from the human thrombospondin 1

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	TSP-1 type 1 repeat	8043102	3000814	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TSP-1 type 1 repeat	8043103	3000814	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	PhnJ	e7yykA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PhnJ	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00090	Thrombospondin type 1 domain (TSP_1)	Thrombospondin type 1 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Thrombospondin-1	protein-containing complex binding fibrinogen binding binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein binding enzyme binding protease binding transforming growth factor beta binding growth factor binding cytokine binding protein-containing complex binding fibrinogen binding binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein binding enzyme binding protease binding transforming growth factor beta binding growth factor binding cytokine binding structural molecule activity extracellular matrix structural constituent identical protein binding protein homodimerization activity protein dimerization activity lipoprotein particle binding protein-lipid complex binding low-density lipoprotein particle binding proteoglycan binding carbohydrate derivative binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity extracellular matrix binding laminin binding fibroblast growth factor binding fibronectin binding modified amino acid binding anion binding phospholipid binding lipid binding phosphatidylserine binding collagen binding collagen V binding cell adhesion molecule binding integrin binding signaling receptor binding heparin binding glycosaminoglycan binding sulfur compound binding	response to stimulus response to chemical response to xenobiotic stimulus multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process negative regulation of biological process negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process response to stimulus response to chemical response to xenobiotic stimulus multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process negative regulation of biological process negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation tumor necrosis factor superfamily cytokine production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production regulation of gene expression negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process response to ketone response to lipid response to oxygen-containing compound response to testosterone response to topologically incorrect protein response to stress response to unfolded protein cellular response to stimulus cellular response to heat cellular response to stress response to heat response to abiotic stimulus response to temperature stimulus chemotaxis positive regulation of locomotion regulation of response to external stimulus positive regulation of biological process response to external stimulus regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to stimulus positive regulation of response to external stimulus taxis regulation of response to stimulus regulation of locomotion locomotion apoptotic process cell death programmed cell death negative regulation of signaling signaling regulation of signal transduction negative regulation of receptor guanylyl cyclase signaling pathway negative regulation of cell communication cell communication receptor guanylyl cyclase signaling pathway signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of cell communication behavior multicellular organismal response to stress response to pain behavioral response to pain regulation of cell motility macrophage migration positive regulation of cell migration cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of macrophage migration positive regulation of leukocyte chemotaxis granulocyte migration leukocyte migration macrophage chemotaxis regulation of granulocyte chemotaxis regulation of macrophage migration positive regulation of cell motility regulation of cell migration myeloid leukocyte migration positive regulation of mononuclear cell migration cell motility positive regulation of cellular process cell chemotaxis regulation of macrophage chemotaxis positive regulation of leukocyte migration cellular response to chemical stimulus immune system process granulocyte chemotaxis mononuclear cell migration positive regulation of macrophage chemotaxis leukocyte chemotaxis nitric oxide mediated signal transduction negative regulation of intracellular signal transduction intracellular signal transduction nitric oxide-cGMP-mediated signaling regulation of intracellular signal transduction intracellular signaling cassette negative regulation of nitric oxide-cGMP mediated signal transduction regulation of nitric oxide mediated signal transduction regulation of nitric oxide-cGMP mediated signal transduction negative regulation of nitric oxide mediated 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 negative regulation of locomotion cell migration involved in sprouting angiogenesis regulation of blood vessel endothelial cell migration endothelial cell migration angiogenesis negative regulation of endothelial cell migration negative regulation of blood vessel endothelial cell migration multicellular organism development tube morphogenesis anatomical structure development regulation of endothelial cell migration blood vessel endothelial cell migration negative regulation of cell migration blood vessel development system development developmental process blood vessel morphogenesis tube development regulation of cell migration involved in sprouting angiogenesis sprouting angiogenesis vasculature development circulatory system development anatomical structure morphogenesis anatomical structure formation involved in morphogenesis negative regulation of cell motility negative regulation of cell migration involved in sprouting angiogenesis regulation of programmed cell death extrinsic apoptotic signaling pathway negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of programmed cell death regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of apoptotic signaling pathway response to endoplasmic reticulum stress response to fibroblast growth factor cellular response to growth factor stimulus negative regulation of cellular response to growth factor stimulus cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus negative regulation of fibroblast growth factor receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus fibroblast growth factor receptor signaling pathway response to growth factor cellular response to fibroblast growth factor stimulus regulation of fibroblast growth factor receptor signaling pathway regulation of macrophage activation positive regulation of macrophage activation regulation of leukocyte activation cell activation regulation of cell activation myeloid leukocyte activation leukocyte activation macrophage activation positive regulation of cell activation positive regulation of leukocyte activation positive regulation of multicellular organismal process chronic inflammatory response defense response inflammatory response regulation of sprouting angiogenesis regulation of developmental process regulation of vasculature development regulation of anatomical structure morphogenesis regulation of multicellular organismal development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis negative regulation of vasculature development regulation of angiogenesis negative regulation of sprouting angiogenesis immune response regulation of body fluid levels wound healing protein activation cascade hemostasis primary metabolic process blood coagulation protein maturation blood coagulation, fibrin clot formation coagulation protein metabolic process regulation of biological quality response to wounding response to hexose response to monosaccharide response to carbohydrate response to glucose reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process positive regulation of metabolic process regulation of reactive oxygen species metabolic process response to peptide cellular response to tumor necrosis factor response to cytokine cellular response to cytokine stimulus response to tumor necrosis factor positive regulation of blood vessel endothelial cell migration positive regulation of endothelial cell migration regulation of cell-substrate adhesion regulation of cell adhesion cell-substrate adhesion negative regulation of cell-matrix adhesion negative regulation of cell adhesion cell adhesion cell-matrix adhesion regulation of cell-matrix adhesion negative regulation of cell-substrate adhesion positive regulation of endothelial cell apoptotic process positive regulation of programmed cell death positive regulation of apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process import into cell regulation of localization carboxylic acid transmembrane transport transport fatty acid transmembrane transport regulation of lipid transport negative regulation of transport negative regulation of lipid localization negative regulation of transmembrane transport localization long-chain fatty acid import across plasma membrane regulation of long-chain fatty acid import across plasma membrane monocarboxylic acid transport fatty acid transport lipid import into cell long-chain fatty acid import into cell long-chain fatty acid transport organic anion transport negative regulation of lipid transport carboxylic acid transport regulation of transport negative regulation of fatty acid transport import across plasma membrane negative regulation of long-chain fatty acid import across plasma membrane regulation of long-chain fatty acid import into cell lipid localization lipid transport establishment of localization regulation of fatty acid transport organic acid transport transmembrane transport regulation of transmembrane transport negative regulation of long-chain fatty acid import into cell regulation of lipid localization negative regulation of organic acid transport macromolecule localization regulation of organic acid transport positive regulation of phosphorylation positive regulation of phosphorus metabolic process phosphorylation positive regulation of phosphate metabolic process phosphate-containing compound metabolic process regulation of phosphorus metabolic process regulation of phosphorylation phosphorus metabolic process positive regulation of macromolecule biosynthetic process positive regulation of tumor necrosis factor superfamily cytokine production positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of tumor necrosis factor production positive regulation of gene expression positive regulation of cytokine production negative regulation of cell population proliferation endothelial cell proliferation negative regulation of endothelial cell proliferation regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation response to metal ion response to calcium ion response to hormone response to steroid hormone response to progesterone regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis blood vessel endothelial cell proliferation involved in sprouting angiogenesis regulation of dendritic cell antigen processing and presentation negative regulation of dendritic cell antigen processing and presentation antigen processing and presentation regulation of antigen processing and presentation negative regulation of immune system process negative regulation of antigen processing and presentation dendritic cell antigen processing and presentation response to decreased oxygen levels response to hypoxia response to oxygen levels negative regulation of chemotaxis endothelial cell chemotaxis regulation of endothelial cell chemotaxis negative regulation of response to external stimulus negative regulation of endothelial cell chemotaxis regulation of cellular component organization cell-substrate junction assembly negative regulation of cell-substrate junction organization cellular component organization cellular component biogenesis cellular component assembly negative regulation of cell junction assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly negative regulation of cellular component organization regulation of cellular component biogenesis negative regulation of focal adhesion assembly regulation of cell junction assembly cell junction organization cell-substrate junction organization regulation of focal adhesion assembly regulation of cell-substrate junction assembly positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway positive regulation of signal transduction cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of transforming growth factor beta receptor signaling pathway regulation of cellular response to transforming growth factor beta stimulus positive regulation of transforming growth factor beta receptor signaling pathway positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of cellular response to transforming growth factor beta stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor superfamily signaling pathway positive regulation of signaling regulation of transforming growth factor beta production transforming growth factor beta1 production regulation of transforming growth factor beta1 production positive regulation of transforming growth factor beta1 production transforming growth factor beta production positive regulation of transforming growth factor beta production regulation of fibroblast migration positive regulation of fibroblast migration fibroblast migration ameboidal-type cell migration regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of interleukin-10 production interleukin-10 production regulation of interleukin-10 production extrinsic apoptotic signaling pathway via death domain receptors positive regulation of apoptotic signaling pathway positive regulation of extrinsic apoptotic signaling pathway via death domain receptors positive regulation of extrinsic apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway via death domain receptors positive regulation of protein metabolic process positive regulation of translation protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of protein metabolic process translation regulation of translation positive regulation of coagulation positive regulation of blood coagulation regulation of response to wounding regulation of coagulation regulation of response to stress positive regulation of hemostasis regulation of hemostasis positive regulation of response to wounding regulation of blood coagulation negative regulation of wound healing negative regulation of blood coagulation negative regulation of response to wounding negative regulation of hemostasis positive regulation of wound healing fibrinolysis regulation of fibrinolysis negative regulation of coagulation regulation of wound healing negative regulation of fibrinolysis positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade response to mechanical stimulus positive regulation of developmental process positive regulation of angiogenesis positive regulation of vasculature development regulation of protein maturation negative regulation of plasminogen activation negative regulation of proteolysis negative regulation of protein maturation regulation of proteolysis proteolysis regulation of plasminogen activation plasminogen activation negative regulation of protein metabolic process zymogen activation regulation of protein processing protein processing negative regulation of protein processing regulation of interleukin-12 production negative regulation of interleukin-12 production interleukin-12 production negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II membrane organization vesicle-mediated transport engulfment of apoptotic cell phagocytosis, engulfment membrane invagination phagocytosis apoptotic cell clearance endocytosis plasma membrane invagination response to magnesium ion	membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm sarcoplasm membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm sarcoplasm sarcoplasmic reticulum cell surface extracellular matrix external encapsulating structure extracellular region cell periphery membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome extracellular vesicle extracellular organelle vesicle extracellular membrane-bounded organelle intracellular vesicle cytoplasmic vesicle secretory granule secretory vesicle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen platelet alpha granule platelet alpha granule lumen protein-containing complex extracellular protein-containing complex fibrinogen complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000884	Thrombospondin type-1 (TSP1) repeat	Repeat
A	IPR003367	Thrombospondin, type 3-like repeat	Repeat
A	IPR036383	Thrombospondin type-1 repeat superfamily	Homologous Superfamily
A	IPR001881	EGF-like calcium-binding domain	Domain
A	IPR028974	TSP type-3 repeat	Homologous Superfamily
A	IPR000742	EGF-like domain	Domain
A	IPR017897	Thrombospondin, type 3 repeat	Repeat
A	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A	IPR048287	Thrombospondin-like, N-terminal domain	Domain
A	IPR008859	Thrombospondin, C-terminal	Domain
A	IPR001007	VWFC domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P07996	diabetic retinopathy cirrhosis of liver interstitial nephritis breast cancer diabetic peripheral angiopathy schizophrenia juvenile idiopathic arthritis breast carcinoma Fibrosis psoriasis glioblastoma tuberculosis interstitial cystitis ischemia reperfusion injury lung cancer diabetic retinopathy cirrhosis of liver interstitial nephritis breast cancer diabetic peripheral angiopathy schizophrenia juvenile idiopathic arthritis breast carcinoma Fibrosis psoriasis glioblastoma tuberculosis interstitial cystitis ischemia reperfusion injury lung cancer adrenal cortex adenoma malignant mesothelioma atypical teratoid rhabdoid tumor MALT lymphoma cancer medulloblastoma osteosarcoma cystic fibrosis pancreatic intraductal papillary-mucinous carcinoma Emery-Dreifuss muscular dystrophy pituitary cancer head and neck cancer ulcerative colitis lung carcinoma adrenal cortex carcinoma chronic obstructive pulmonary disease congestive heart failure ovarian cancer pancreatic intraductal papillary-mucinous neoplasm esophageal adenocarcinoma polycystic ovary syndrome gastric carcinoma hepatocellular carcinoma invasive ductal breast carcinoma large cell medulloblastoma malignant colon neoplasm adrenoleukodystrophy malignant pancreatic neoplasm nasopharyngeal carcinoma Crohn disease pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.