6SF6 | pdb_00006sf6

Crystal structure of the mAb 15A in complex with COMP-epitope P6

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth B]	C1-set_4	e6sf6B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth B]	V-set	e6sf6B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
B [auth L]	C1-set_4	e6sf6L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B [auth L]	V-set	e6sf6L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
C [auth A]	V-set_8	e6sf6A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth A]	C1-set_1	e6sf6A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
A [auth H]	V-set_8	e6sf6H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
A [auth H]	C1-set_1	e6sf6H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L], D [auth B]	Light Chain	IGKV1	Kappa	p6 epitope of cartilage oligomeric matrix protein (comp)	SAbDab (2025-12-19)
A [auth H], C [auth A]	Heavy Chain	IGHV1	-	p6 epitope of cartilage oligomeric matrix protein (comp)	SAbDab (2025-12-19)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth C], F [auth D]	P6 epitope of cartilage oligomeric matrix protein (COMP)	vitamin binding binding vitamin D binding steroid binding lipid binding small molecule binding BMP binding protein binding cytokine binding fibronectin binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding cation binding vitamin binding binding vitamin D binding steroid binding lipid binding small molecule binding BMP binding protein binding cytokine binding fibronectin binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding cation binding ion binding calcium ion binding metal ion 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	developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development developmental growth endochondral bone morphogenesis organ growth growth plate cartilage development developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development developmental growth endochondral bone morphogenesis organ growth growth plate cartilage development endochondral bone growth animal organ morphogenesis bone development growth anatomical structure morphogenesis bone growth skeletal system morphogenesis cartilage development involved in endochondral bone morphogenesis bone morphogenesis regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding negative regulation of hemostasis regulation of biological process negative regulation of biological process regulation of hemostasis ossification bone mineralization biomineral tissue development cellular developmental process cell development cell differentiation chondrocyte differentiation cellular process chondrocyte development response to topologically incorrect protein 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 homotypic cell-cell adhesion cell activation platelet aggregation cell adhesion cell-cell adhesion 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 system process nervous system process neuromuscular process 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 nitrogen compound transport 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 muscle structure development muscle cell development muscle cell differentiation 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 vascular associated smooth muscle cell differentiation vascular associated smooth muscle cell development primary metabolic process protein maturation proteolysis protein processing protein metabolic process multicellular organismal movement musculoskeletal movement 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	cellular anatomical structure extracellular region extracellular space cell periphery extracellular matrix external encapsulating structure protein-containing complex
B [auth L], D [auth B]	COMP-reactive monoclonal antibody 15A Fab fragment, light chain	-	-	-
A [auth H], C [auth A]	COMP-reactive monoclonal antibody 15A Fab fragment, heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth C], F [auth D]	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

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.