Annotations: 9MOV

Cryo-EM structure of factor Va bound to activated protein C

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Trypsin-like serine proteases	8042258	3000114	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GLA-domain	8041437	3001028	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EGF/Laminin-like	8038297	3000412	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EGF/Laminin-like	8038301	3000412	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	galactose-binding domain-like	8041135	3000087	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)
D	Myb_DNA-binding	e9movD1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Myb_DNA-binding	ECOD (v295.2)
C	EF-hand_1, EF-hand_6, EF-hand_7	e9movC1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (v295.2)
B	Beta-Casp	e9movB1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Beta-Casp	ECOD (v295.2)
A	Beta-Casp	e9movA1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Beta-Casp	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF00089	Trypsin (Trypsin)	Trypsin		Domain
C	PF14670	Coagulation Factor Xa inhibitory site (FXa_inhibition)	Coagulation Factor Xa inhibitory site	This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442 [1].	Domain
C	PF00594	Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain (Gla)	Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain	This domain is responsible for the high-affinity binding of calcium ions. This domain contains post-translational modifications of many glutamate residues by Vitamin K-dependent carboxylation to form gamma-carboxyglutamate (Gla).	Domain
B	PF00754	F5/8 type C domain (F5_F8_type_C)	F5/8 type C domain	This domain is also known as the discoidin (DS) domain family [1].	Domain
B	PF07732	Multicopper oxidase (Cu-oxidase_3)	Multicopper oxidase	This entry contains many divergent copper oxidase-like domains that are not recognised by the Pfam:PF00394 model.	Domain
A	PF07732	Multicopper oxidase (Cu-oxidase_3)	Multicopper oxidase	This entry contains many divergent copper oxidase-like domains that are not recognised by the Pfam:PF00394 model.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	Vitamin K-dependent protein C heavy chain	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity	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 regulation of biological process regulation of cellular process negative regulation of programmed cell death 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 regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response regulation of response to wounding regulation of coagulation regulation of multicellular organismal process regulation of hemostasis negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation negative regulation of response to wounding negative regulation of hemostasis negative regulation of coagulation regulation of wound healing negative regulation of multicellular organismal process regulation of establishment of endothelial barrier cellular developmental process regulation of developmental process positive regulation of endothelial cell development endothelium development positive regulation of biological process cell development regulation of cell differentiation epithelial cell differentiation regulation of cell development regulation of epithelial cell differentiation endothelial cell development positive regulation of developmental process multicellular organism development positive regulation of cell differentiation cell differentiation regulation of endothelial cell development anatomical structure development positive regulation of cellular process developmental process epithelium development regulation of multicellular organismal development endothelial cell differentiation regulation of endothelial cell differentiation positive regulation of cell development positive regulation of establishment of endothelial barrier tissue development epithelial cell development establishment of endothelial barrier animal gross anatomical part developmental process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm endoplasmic reticulum lumen membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm endoplasmic reticulum lumen endoplasmic reticulum extracellular region
C	Vitamin K-dependent protein C	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity	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 regulation of biological process regulation of cellular process negative regulation of programmed cell death 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 regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response regulation of response to wounding regulation of coagulation regulation of multicellular organismal process regulation of hemostasis negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation negative regulation of response to wounding negative regulation of hemostasis negative regulation of coagulation regulation of wound healing negative regulation of multicellular organismal process regulation of establishment of endothelial barrier cellular developmental process regulation of developmental process positive regulation of endothelial cell development endothelium development positive regulation of biological process cell development regulation of cell differentiation epithelial cell differentiation regulation of cell development regulation of epithelial cell differentiation endothelial cell development positive regulation of developmental process multicellular organism development positive regulation of cell differentiation cell differentiation regulation of endothelial cell development anatomical structure development positive regulation of cellular process developmental process epithelium development regulation of multicellular organismal development endothelial cell differentiation regulation of endothelial cell differentiation positive regulation of cell development positive regulation of establishment of endothelial barrier tissue development epithelial cell development establishment of endothelial barrier animal gross anatomical part developmental process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm endoplasmic reticulum lumen membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm endoplasmic reticulum lumen endoplasmic reticulum extracellular region
B	Coagulation factor Va light chain	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule 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 response to nutrient levels response to ketone response to chemical 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 response to nutrient levels response to ketone response to chemical response to nutrient response to oxygen-containing compound response to vitamin K response to vitamin system process circulatory system process blood circulation	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region intracellular vesicle cytoplasmic vesicle secretory granule secretory vesicle platelet alpha granule vesicle bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment organelle membrane extracellular vesicle extracellular organelle extracellular membrane-bounded organelle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen platelet alpha granule lumen cell periphery plasma membrane COPII-coated ER to Golgi transport vesicle coated vesicle
A	Coagulation factor Va heavy chain	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule 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 response to nutrient levels response to ketone response to chemical 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 response to nutrient levels response to ketone response to chemical response to nutrient response to oxygen-containing compound response to vitamin K response to vitamin system process circulatory system process blood circulation	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region intracellular vesicle cytoplasmic vesicle secretory granule secretory vesicle platelet alpha granule vesicle bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment organelle membrane extracellular vesicle extracellular organelle extracellular membrane-bounded organelle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen platelet alpha granule lumen cell periphery plasma membrane COPII-coated ER to Golgi transport vesicle coated vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
D	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
D	IPR018114	Serine protease-like, trypsin family, histidine active site	Active Site
D	IPR000742	EGF-like domain	Domain
D	IPR050442	Peptidase S1 family, coagulation factors	Family
D	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
D	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
D	IPR001314	Peptidase S1A, chymotrypsin family	Family
D	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
D	IPR001254	Serine proteases, trypsin domain	Domain
D	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
D	IPR001881	EGF-like calcium-binding domain	Domain
D	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
D	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family
C	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
C	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
C	IPR018114	Serine protease-like, trypsin family, histidine active site	Active Site
C	IPR000742	EGF-like domain	Domain
C	IPR050442	Peptidase S1 family, coagulation factors	Family
C	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
C	IPR001314	Peptidase S1A, chymotrypsin family	Family
C	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
C	IPR001254	Serine proteases, trypsin domain	Domain
C	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
C	IPR001881	EGF-like calcium-binding domain	Domain
C	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
C	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family
B	IPR033138	Multicopper oxidases, conserved site	Conserved Site
B	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
B	IPR011707	Multicopper oxidase-like, N-terminal	Domain
B	IPR024715	Coagulation factor 5/8-like	Family
B	IPR000421	Coagulation factor 5/8, C-terminal domain	Domain
B	IPR008972	Cupredoxin	Homologous Superfamily
B	IPR050633	Neuropilin/Multicopper Oxidase/Coagulation Factor	Family
A	IPR033138	Multicopper oxidases, conserved site	Conserved Site
A	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A	IPR011707	Multicopper oxidase-like, N-terminal	Domain
A	IPR024715	Coagulation factor 5/8-like	Family
A	IPR000421	Coagulation factor 5/8, C-terminal domain	Domain
A	IPR008972	Cupredoxin	Homologous Superfamily
A	IPR050633	Neuropilin/Multicopper Oxidase/Coagulation Factor	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D	: P04070	thrombophilia due to protein C deficiency, autosomal recessive purpura fulminans Venous Thrombosis disseminated intravascular coagulation hereditary thrombophilia due to congenital protein C deficiency thrombophilia due to protein C deficiency, autosomal dominant venous thromboembolism arteritis hypertensive disorder thrombophilia pancreatic intraductal papillary-mucinous carcinoma thrombotic disease chronic kidney disease lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia thrombophilia due to protein C deficiency, autosomal recessive purpura fulminans Venous Thrombosis disseminated intravascular coagulation hereditary thrombophilia due to congenital protein C deficiency thrombophilia due to protein C deficiency, autosomal dominant venous thromboembolism arteritis hypertensive disorder thrombophilia pancreatic intraductal papillary-mucinous carcinoma thrombotic disease chronic kidney disease lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ovarian cancer
C	: P04070	thrombophilia due to protein C deficiency, autosomal recessive purpura fulminans Venous Thrombosis disseminated intravascular coagulation hereditary thrombophilia due to congenital protein C deficiency thrombophilia due to protein C deficiency, autosomal dominant venous thromboembolism arteritis hypertensive disorder thrombophilia pancreatic intraductal papillary-mucinous carcinoma thrombotic disease chronic kidney disease lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia thrombophilia due to protein C deficiency, autosomal recessive purpura fulminans Venous Thrombosis disseminated intravascular coagulation hereditary thrombophilia due to congenital protein C deficiency thrombophilia due to protein C deficiency, autosomal dominant venous thromboembolism arteritis hypertensive disorder thrombophilia pancreatic intraductal papillary-mucinous carcinoma thrombotic disease chronic kidney disease lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ovarian cancer
B	: P12259	congenital factor V deficiency retinal vein occlusion thrombophilia due to activated protein C resistance pregnancy loss, recurrent, susceptibility to, 1 hepatic vein thrombosis sagittal sinus thrombosis Budd-Chiari syndrome Venous Thrombosis myocardial infarction cirrhosis of liver thrombophilia brain ischemia classic familial adenomatous polyposis malignant colon neoplasm thrombotic disease congenital factor V deficiency retinal vein occlusion thrombophilia due to activated protein C resistance pregnancy loss, recurrent, susceptibility to, 1 hepatic vein thrombosis sagittal sinus thrombosis Budd-Chiari syndrome Venous Thrombosis myocardial infarction cirrhosis of liver thrombophilia brain ischemia classic familial adenomatous polyposis malignant colon neoplasm thrombotic disease cerebral infarction venous thromboembolism pancreatic intraductal papillary-mucinous carcinoma peripheral arterial disease East Texas bleeding disorder factor V deficiency acne astrocytic tumor MALT lymphoma blood coagulation disease tuberculosis cerebrovascular disorder ovarian cancer colonic neoplasm pancreatic intraductal papillary-mucinous neoplasm cystic fibrosis Pick disease esophageal adenocarcinoma rheumatoid arthritis inflammatory bowel disease lung cancer malignant ependymoma Barrett esophagus ulcerative colitis oligodendroglioma pancreatic ductal adenocarcinoma colorectal cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pituitary cancer exocrine pancreatic carcinoma genetic intestinal polyposis intellectual disability sinusitis lung carcinoma malignant pancreatic neoplasm benign colon neoplasm osteosarcoma
A	: P12259	congenital factor V deficiency retinal vein occlusion thrombophilia due to activated protein C resistance pregnancy loss, recurrent, susceptibility to, 1 hepatic vein thrombosis sagittal sinus thrombosis Budd-Chiari syndrome Venous Thrombosis myocardial infarction cirrhosis of liver thrombophilia brain ischemia classic familial adenomatous polyposis malignant colon neoplasm thrombotic disease congenital factor V deficiency retinal vein occlusion thrombophilia due to activated protein C resistance pregnancy loss, recurrent, susceptibility to, 1 hepatic vein thrombosis sagittal sinus thrombosis Budd-Chiari syndrome Venous Thrombosis myocardial infarction cirrhosis of liver thrombophilia brain ischemia classic familial adenomatous polyposis malignant colon neoplasm thrombotic disease cerebral infarction venous thromboembolism pancreatic intraductal papillary-mucinous carcinoma peripheral arterial disease East Texas bleeding disorder factor V deficiency acne astrocytic tumor MALT lymphoma blood coagulation disease tuberculosis cerebrovascular disorder ovarian cancer colonic neoplasm pancreatic intraductal papillary-mucinous neoplasm cystic fibrosis Pick disease esophageal adenocarcinoma rheumatoid arthritis inflammatory bowel disease lung cancer malignant ependymoma Barrett esophagus ulcerative colitis oligodendroglioma pancreatic ductal adenocarcinoma colorectal cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pituitary cancer exocrine pancreatic carcinoma genetic intestinal polyposis intellectual disability sinusitis lung carcinoma malignant pancreatic neoplasm benign colon neoplasm osteosarcoma