2ADF

Crystal Structure and Paratope Determination of 82D6A3, an Antithrombotic Antibody Directed Against the von Willebrand factor A3-Domain

External Resource: Annotation

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2adfa_	Alpha and beta proteins (a/b)	vWA-like	vWA-like	Integrin A (or I) domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d2adfh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d2adfl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d2adfl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	vWA-like	8032262	3000832	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	PF00092	e2adfA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: PF00092	ECOD (1.6)
B [auth H]	PF07654	e2adfH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B [auth H]	PF07686	e2adfH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth L]	PF07654	e2adfL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth L]	PF07686	e2adfL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B [auth H]	82D6A3 IGG	VH-CH1	Mus musculus (house mouse)	IGHV9-302, IGHJ401, IGHG2A01, IGHG2A02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202416-0)
C [auth L]	82D6A3 IGG	L-KAPPA	Mus musculus (house mouse)	IGKV19-9301, IGKV19-9302, IGKJ101, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV9	-	von willebrand factor	SAbDab (2024-04-26)
C [auth L]	Light Chain	IGKV19	Kappa	von willebrand factor	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00092	von Willebrand factor type A domain (VWA)	von Willebrand factor type A domain	-	Domain
B [auth H]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
B [auth H]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Von Willebrand factor	protein binding binding enzyme binding protease binding collagen binding protein-containing complex binding protein-folding chaperone binding cell adhesion molecule binding integrin binding signaling receptor binding immunoglobulin binding identical protein binding	multicellular organismal process 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 cell activation cellular process platelet activation multicellular organismal process 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 cell activation cellular process platelet activation cellular response to stimulus positive regulation of cell communication regulation of biological process regulation of signaling regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process positive regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication signal transduction positive regulation of cellular process positive regulation of signaling cell adhesion cell-substrate adhesion	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle Weibel-Palade body secretory granule clathrin-coated vesicle secretory vesicle coated vesicle cytoplasm platelet alpha granule vesicle lumen membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular organelle lumen organelle lumen platelet alpha granule lumen endoplasmic reticulum
B [auth H]	82D6A3 IgG	binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process	protein-containing complex immunoglobulin complex extracellular region cellular anatomical entity
C [auth L]	82D6A3 IgG	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002919	Trypsin Inhibitor-like, cysteine rich domain	Domain
A	IPR001007	VWFC domain	Domain
A	IPR037578	Von Willebrand factor	Family
A	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A	IPR001846	von Willebrand factor, type D domain	Domain
A	IPR014853	VWF/SSPO/Zonadhesin-like, cysteine-rich domain	Domain
A	IPR032361	von Willebrand factor, VWA N-terminal domain	Domain
A	IPR036084	Serine protease inhibitor-like superfamily	Homologous Superfamily
A	IPR002035	von Willebrand factor, type A	Domain
A	IPR006207	Cystine knot, C-terminal	Domain
B [auth H]	IPR003597	Immunoglobulin C1-set	Domain
B [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth H]	IPR003599	Immunoglobulin subtype	Domain
B [auth H]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth H]	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P04275	von Willebrand disease 1 von Willebrand disease 2 von Willebrand disease 3 atrial fibrillation hypertensive disorder hereditary von Willebrand disease thrombotic disease intracranial thrombosis cardiovascular disease Liver Cirrhosis, Experimental congestive heart failure Down syndrome ovarian cancer drug-induced liver injury pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia von Willebrand disease 1 von Willebrand disease 2 von Willebrand disease 3 atrial fibrillation hypertensive disorder hereditary von Willebrand disease thrombotic disease intracranial thrombosis cardiovascular disease Liver Cirrhosis, Experimental congestive heart failure Down syndrome ovarian cancer drug-induced liver injury pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia gastric carcinoma peripheral neuropathy heart failure thrombocytopenia acquired von willebrand syndrome herpes zoster transitional cell carcinoma interstitial cystitis kidney disease von Willebrand disease type 2A lung adenocarcinoma von Willebrand disease type 2N coronary artery disease non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma ductal breast carcinoma in situ thrombophilia thrombotic thrombocytopenic purpura adrenal cortex carcinoma ulcerative colitis angiodysplasia Bernard-Soulier syndrome breast carcinoma von Willebrand disease type 2B lung cancer medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm familial atrial fibrillation peripheral nervous system disease heart disease pulmonary embolism hemophilia A inborn carbohydrate metabolic disorder vascular disease atherosclerosis invasive ductal breast carcinoma von Willebrand disease type 2M cerebrovascular disorder lung carcinoma

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.