3FBY | pdb_00003fby

The crystal structure of the signature domain of cartilage oligomeric matrix protein.

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)
B	NUDIX	e3fbyB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: NUDIX	ECOD (develop294)
B	Peptidase_M49	e3fbyB4	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
B	Internalin_N	e3fbyB3	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Internalin_N	ECOD (develop294)
C	ABC_tran	e3fbyC2	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: ABC_tran	ECOD (develop294)
C	Internalin_N	e3fbyC4	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Internalin_N	ECOD (develop294)
A	Ribosomal_L10	e3fbyA1	A: alpha bundles	X: Ribonuclease H-like	H: Immunoglobulin-related	T: Defensin-related	F: Ribosomal_L10	ECOD (develop294)
A	FXa_inhibition	e3fbyA6	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: PreATP-grasp domain	F: FXa_inhibition	ECOD (develop294)
A	Ribosomal_L24e	e3fbyA3	A: alpha bundles	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: Ribosomal_L24e	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.10.25.10	Mainly Beta	Ribbon	Laminin	Laminin	CATH (4.3.0)
B	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.10.25.10	Mainly Beta	Ribbon	Laminin	Laminin	CATH (4.3.0)
C	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
A	2.10.25.10	Mainly Beta	Ribbon	Laminin	Laminin	CATH (4.3.0)
A	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF02412	Thrombospondin type 3 repeat (TSP_3)	Thrombospondin type 3 repeat	The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats [1]. The repeat lacks defined secondary structure [2].	Domain
A, B, C	PF05735	Thrombospondin C-terminal region (TSP_C)	Thrombospondin C-terminal region	This region is found at the C-terminus of thrombospondin and related proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Cartilage oligomeric matrix protein	BMP binding protein binding binding cytokine binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding cation binding ion binding calcium ion binding metal ion binding small molecule binding enzyme binding protease binding BMP binding protein binding binding cytokine binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding cation binding ion binding calcium ion binding metal ion binding small molecule binding enzyme binding protease 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 sulfur compound binding	multicellular organismal process connective tissue development developmental growth endochondral bone morphogenesis organ growth multicellular organism development skeletal system development growth plate cartilage development anatomical structure development endochondral bone growth animal organ morphogenesis bone development system development developmental process multicellular organismal process connective tissue development developmental growth endochondral bone morphogenesis organ growth multicellular organism development skeletal system development growth plate cartilage development anatomical structure development endochondral bone growth animal organ morphogenesis bone development system development developmental process growth animal organ development tissue development anatomical structure morphogenesis bone growth skeletal system morphogenesis cartilage development involved in endochondral bone morphogenesis bone morphogenesis cartilage development negative regulation of hemostasis regulation of body fluid levels regulation of biological process biological regulation hemostasis negative regulation of biological process regulation of biological quality regulation of hemostasis ossification bone mineralization biomineral tissue development cellular developmental process cell development cell differentiation chondrocyte differentiation cellular process chondrocyte development response to stimulus response to topologically incorrect protein response to stress response to unfolded protein regulation of biosynthetic process regulation of cellular process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process apoptotic process cell death programmed cell death wound healing homotypic cell-cell adhesion cell activation platelet aggregation blood coagulation cell adhesion cell-cell adhesion coagulation response to wounding platelet activation blood vessel morphogenesis tube development artery development vasculature development circulatory system development tube morphogenesis artery morphogenesis blood vessel development cellular response to stimulus cellular response to stress cellular senescence cellular component organization collagen fibril organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization regulation of multicellular organismal development regulation of developmental process regulation of biomineral tissue development regulation of bone mineralization regulation of multicellular organismal process regulation of ossification cell population proliferation chondrocyte proliferation positive regulation of cell population proliferation positive regulation of biological process positive regulation of chondrocyte proliferation regulation of cell population proliferation positive regulation of cellular process limb development appendage development establishment of protein localization transport secretion establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region localization secretion by cell protein transport macromolecule localization intracellular protein localization multicellular organism growth tendon development cellular response to BMP stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus cell surface receptor signaling pathway signaling response to endogenous stimulus cell communication cellular response to endogenous stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway signal transduction response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway skin development negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process smooth muscle cell differentiation muscle cell differentiation muscle structure development vascular associated smooth muscle cell differentiation muscle cell development vascular associated smooth muscle cell development primary metabolic process protein maturation proteolysis protein processing protein metabolic process multicellular organismal movement musculoskeletal movement system process nervous system process neuromuscular process regulation of tube diameter vascular associated smooth muscle contraction regulation of tube size muscle contraction muscle system process circulatory system process smooth muscle contraction vascular process in circulatory system blood vessel diameter maintenance vasoconstriction blood circulation regulation of anatomical structure size multicellular organismal-level homeostasis homeostatic process cartilage homeostasis anatomical structure homeostasis tissue homeostasis cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR017897	Thrombospondin, type 3 repeat	Repeat
A, B, C	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A, B, C	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B, C	IPR024665	Thrombospondin/cartilage oligomeric matrix protein, coiled-coil domain	Domain
A, B, C	IPR003367	Thrombospondin, type 3-like repeat	Repeat
A, B, C	IPR001881	EGF-like calcium-binding domain	Domain
A, B, C	IPR049883	NOTCH1, EGF-like calcium-binding domain	Domain
A, B, C	IPR008859	Thrombospondin, C-terminal	Domain
A, B, C	IPR046970	TSP/COMP, coiled-coil domain superfamily	Homologous Superfamily
A, B, C	IPR028974	TSP type-3 repeat	Homologous Superfamily
A, B, C	IPR000742	EGF-like domain	Domain
A, B, C	IPR039081	Thrombospondin-5, coiled coil domain	Domain
A, B, C	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P49747	pseudoachondroplasia multiple epiphyseal dysplasia type 1 multiple epiphyseal dysplasia osteoarthritis osteochondrodysplasia Joint Instability osteoarthritis susceptibility 1 ovarian cancer pancreatic intraductal papillary-mucinous neoplasm atrial fibrillation psoriasis breast carcinoma gastroesophageal reflux disease interstitial lung disease mucopolysaccharidosis type 4 pseudoachondroplasia multiple epiphyseal dysplasia type 1 multiple epiphyseal dysplasia osteoarthritis osteochondrodysplasia Joint Instability osteoarthritis susceptibility 1 ovarian cancer pancreatic intraductal papillary-mucinous neoplasm atrial fibrillation psoriasis breast carcinoma gastroesophageal reflux disease interstitial lung disease mucopolysaccharidosis type 4 non-small cell lung carcinoma osteoarthritis susceptibility 5 pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Barrett esophagus breast fibroadenoma esophageal adenocarcinoma intellectual disability invasive ductal breast carcinoma lung adenocarcinoma osteoarthritis, hip osteogenesis imperfecta pancreatic intraductal papillary-mucinous carcinoma breast cancer ductal breast carcinoma in situ Fairbank disease interstitial cystitis malignant pancreatic neoplasm

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.