7TPQ

Cryo-em structure of human prothrombinase on a nanodisc at 5.3 Angstrom resolution

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	GLA-domain	8038060	3001028	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EGF/Laminin-like	8035338	3000412	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	galactose-binding domain-like	8041135	3000087	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Trypsin-like serine proteases	8035341	3000114	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	PF00008	e7tpqA2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: PF00008	ECOD (1.6)
A	PF14670	e7tpqA1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: PF14670	ECOD (1.6)
A	PF00594	e7tpqA3	A: few secondary structure elements	X: GLA-domain (From Topology)	H: GLA-domain (From Topology)	T: GLA-domain	F: PF00594	ECOD (1.6)
B [auth C]	F_UNCLASSIFIED	e7tpqC1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
B [auth C]	PF00394	e7tpqC4	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: PF00394	ECOD (1.6)
B [auth C]	PF07732	e7tpqC2	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: PF07732	ECOD (1.6)
C [auth D]	PF00754	e7tpqD1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF00754	ECOD (1.6)
C [auth D]	PF07731	e7tpqD2	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: PF07731	ECOD (1.6)
C [auth D]	PF07732	e7tpqD3	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: PF07732	ECOD (1.6)
D [auth B]	PF00089	e7tpqB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: PF00089	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00008	EGF-like domain (EGF)	EGF-like domain	There is no clear separation between noise and signal. Pfam:PF00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is t ...	There is no clear separation between noise and signal. Pfam:PF00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.	Domain
A	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
A	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 [auth C]	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
C [auth D]	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
C [auth D]	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
D [auth B]	PF00089	Trypsin (Trypsin)	Trypsin	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Factor X light 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 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 phospholipid binding lipid 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 cellular response to stimulus positive regulation of cell communication regulation of cellular process 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 cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction positive regulation of cellular process TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication cellular process positive regulation of signaling positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen organelle cytoplasm endoplasmic reticulum lumen endoplasmic reticulum extracellular region extracellular space
B [auth C]	Coagulation factor Va	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 organic substance 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 organic substance 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	membrane cellular anatomical entity 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 membrane cellular anatomical entity 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 extracellular space
C [auth D]	Coagulation factor Va	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 organic substance 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 organic substance 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	membrane cellular anatomical entity 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 membrane cellular anatomical entity 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 extracellular space
D [auth B]	Activated factor Xa 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 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 phospholipid binding lipid 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 cellular response to stimulus positive regulation of cell communication regulation of cellular process 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 cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction positive regulation of cellular process TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication cellular process positive regulation of signaling positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen organelle cytoplasm endoplasmic reticulum lumen endoplasmic reticulum extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
A	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A	IPR000742	EGF-like domain	Domain
A	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
A	IPR001314	Peptidase S1A, chymotrypsin family	Family
A	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A	IPR001254	Serine proteases, trypsin domain	Domain
A	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
A	IPR001881	EGF-like calcium-binding domain	Domain
A	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
A	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family
B [auth C]	IPR033138	Multicopper oxidases, conserved site	Conserved Site
B [auth C]	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
B [auth C]	IPR011707	Multicopper oxidase-like, N-terminal	Domain
B [auth C]	IPR024715	Coagulation factor 5/8-like	Family
B [auth C]	IPR008972	Cupredoxin	Homologous Superfamily
B [auth C]	IPR000421	Coagulation factor 5/8 C-terminal domain	Domain
C [auth D]	IPR033138	Multicopper oxidases, conserved site	Conserved Site
C [auth D]	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
C [auth D]	IPR011707	Multicopper oxidase-like, N-terminal	Domain
C [auth D]	IPR024715	Coagulation factor 5/8-like	Family
C [auth D]	IPR008972	Cupredoxin	Homologous Superfamily
C [auth D]	IPR000421	Coagulation factor 5/8 C-terminal domain	Domain
D [auth B]	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
D [auth B]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
D [auth B]	IPR000742	EGF-like domain	Domain
D [auth B]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
D [auth B]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
D [auth B]	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
D [auth B]	IPR001314	Peptidase S1A, chymotrypsin family	Family
D [auth B]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
D [auth B]	IPR001254	Serine proteases, trypsin domain	Domain
D [auth B]	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
D [auth B]	IPR001881	EGF-like calcium-binding domain	Domain
D [auth B]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
D [auth B]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
D [auth B]	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P00742	congenital factor X deficiency atrial fibrillation factor X deficiency thrombotic disease Prevention of deep vein thrombosis pulmonary embolism blood coagulation disease pancreatic ductal adenocarcinoma lung adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm psoriasis breast fibroadenoma ductal breast carcinoma in situ invasive ductal breast carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia
B [auth C]	Pharos: 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 ovarian cancer cerebrovascular disorder pancreatic intraductal papillary-mucinous neoplasm colonic neoplasm Pick disease cystic fibrosis esophageal adenocarcinoma rheumatoid arthritis inflammatory bowel disease lung cancer malignant ependymoma Barrett esophagus ulcerative colitis oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia colorectal cancer pituitary cancer exocrine pancreatic carcinoma genetic intestinal polyposis intellectual disability sinusitis lung carcinoma malignant pancreatic neoplasm benign colon neoplasm osteosarcoma
C [auth D]	Pharos: 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 ovarian cancer cerebrovascular disorder pancreatic intraductal papillary-mucinous neoplasm colonic neoplasm Pick disease cystic fibrosis esophageal adenocarcinoma rheumatoid arthritis inflammatory bowel disease lung cancer malignant ependymoma Barrett esophagus ulcerative colitis oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia colorectal cancer pituitary cancer exocrine pancreatic carcinoma genetic intestinal polyposis intellectual disability sinusitis lung carcinoma malignant pancreatic neoplasm benign colon neoplasm osteosarcoma
D [auth B]	Pharos: P00742	congenital factor X deficiency atrial fibrillation factor X deficiency thrombotic disease Prevention of deep vein thrombosis pulmonary embolism blood coagulation disease pancreatic ductal adenocarcinoma lung adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm psoriasis breast fibroadenoma ductal breast carcinoma in situ invasive ductal breast carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia