1OAK

CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR (VWF) A1 DOMAIN IN COMPLEX WITH THE FUNCTION BLOCKING NMC-4 FAB

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 [auth L]	d1oakl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d1oakl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d1oakh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d1oakh2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth A]	d1oaka_	Alpha and beta proteins (a/b)	vWA-like	vWA-like	Integrin A (or I) domain	von Willebrand factor A1 domain, vWA1	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)
C [auth A]	SCOP2B Superfamily	vWA-like	8032264	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 [auth L]	C1-set_4	e1oakL2	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)
A [auth L]	V-set	e1oakL1	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 H]	V-set_8	e1oakH1	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)
B [auth H]	C1-set_1	e1oakH2	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)
C [auth A]	UNK_F_TYPE	e1oakA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth A]	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	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
A [auth L]	Nmc-4	L-KAPPA	Mus musculus (house mouse)	IGKV10-9401, IGKJ101, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
B [auth H]	Nmc-4	VH-CH1	Mus musculus (house mouse)	IGHV2-6-701, IGHV2-6-702, IGHJ401, IGHG102	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L]	Light Chain	IGKV10	Kappa	von willebrand factor	SAbDab (2024-04-19)
B [auth H]	Heavy Chain	IGHV2	-	von willebrand factor	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth H]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
C [auth A]	PF00092	von Willebrand factor type A domain (VWA)	von Willebrand factor type A domain	-	Domain
C [auth A]	PF16164	VWA N-terminal (VWA_N2)	VWA N-terminal	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L]	NMC-4 IGG1	-	-	-
B [auth H]	NMC-4 IGG1	protein-containing complex binding protein binding binding signaling receptor binding immunoglobulin receptor binding Fc-gamma receptor I complex binding antigen binding	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process membrane organization import into cell transport establishment of localization vesicle-mediated transport cellular component organization localization phagocytosis, engulfment membrane invagination cellular process phagocytosis cellular component organization or biogenesis endocytosis plasma membrane invagination positive regulation of acute inflammatory response to antigenic stimulus regulation of immune effector process regulation of acute inflammatory response to antigenic stimulus positive regulation of leukocyte mediated immunity inflammatory response to antigenic stimulus positive regulation of hypersensitivity positive regulation of inflammatory response positive regulation of adaptive immune response positive regulation of immunoglobulin mediated immune response hypersensitivity regulation of adaptive immune response response to external stimulus regulation of inflammatory response regulation of B cell mediated immunity regulation of leukocyte mediated immunity positive regulation of defense response regulation of acute inflammatory response inflammatory response positive regulation of type I hypersensitivity regulation of type I hypersensitivity regulation of defense response regulation of response to external stimulus positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of acute inflammatory response positive regulation of B cell mediated immunity type I hypersensitivity positive regulation of response to external stimulus regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains response to stress regulation of response to stress regulation of immunoglobulin mediated immune response positive regulation of immune effector process acute inflammatory response regulation of hypersensitivity defense response regulation of inflammatory response to antigenic stimulus acute inflammatory response to antigenic stimulus positive regulation of inflammatory response to antigenic stimulus regulation of lymphocyte mediated immunity myeloid leukocyte mediated immunity antibody-dependent cellular cytotoxicity leukocyte mediated cytotoxicity type II hypersensitivity type IIa hypersensitivity cell killing developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation anatomical structure development leukocyte differentiation humoral immune response complement activation humoral immune response mediated by circulating immunoglobulin complement activation, classical pathway activation of immune response biological process involved in interspecies interaction between organisms response to other organism antibacterial humoral response defense response to symbiont antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to bacterium response to external biotic stimulus regulation of localization positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization positive regulation of endocytosis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis positive regulation of transport regulation of myeloid leukocyte mediated immunity regulation of type IIa hypersensitivity regulation of type II hypersensitivity positive regulation of myeloid leukocyte mediated immunity positive regulation of type IIa hypersensitivity positive regulation of type II hypersensitivity phagocytosis, recognition cell recognition	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm IgG immunoglobulin complex protein-containing complex immunoglobulin complex extracellular region extracellular space cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm IgG immunoglobulin complex protein-containing complex immunoglobulin complex extracellular region extracellular space immunoglobulin complex, circulating
C [auth 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

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

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