Annotations: 12BN

Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryoEM

External Resource: Annotation

Domain Annotation: SCOP2 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)
F [auth D]	SCOP2B Superfamily	Trypsin-like serine proteases	8044201	3000114	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Trypsin-like serine proteases	8044201	3000114	SCOP2B (2022-06-29)
B [auth F]	SCOP2B Superfamily	GLA-domain	8069549	3001028	SCOP2B (2022-06-29)
A [auth E]	SCOP2B Superfamily	EGF/Laminin-like	8038255	3000412	SCOP2B (2022-06-29)
A [auth E]	SCOP2B Superfamily	Trypsin-like serine proteases	8042263	3000114	SCOP2B (2022-06-29)
A [auth E]	SCOP2B Superfamily	GLA-domain	8069549	3001028	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth B], F [auth D]	PF00089	Trypsin (Trypsin)	Trypsin		Domain
C [auth A], E [auth C]	PF00024	PAN domain (PAN_1)	PAN domain	The PAN domain [1] contains a conserved core of three disulphide bridges. In some members of the family there is an additional fourth disulphide bridge the links the N and C termini of the domain. The domain is found in diverse proteins, in some the ...	The PAN domain [1] contains a conserved core of three disulphide bridges. In some members of the family there is an additional fourth disulphide bridge the links the N and C termini of the domain. The domain is found in diverse proteins, in some they mediate protein-protein interactions, in others they mediate protein-carbohydrate interactions.	Domain
A [auth E], B [auth F]	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 [auth E], B [auth F]	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 [auth E], B [auth F]	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
A [auth E], B [auth F]	PF00089	Trypsin (Trypsin)	Trypsin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth B], F [auth D]	Coagulation factor XIa light chain	serine-type exopeptidase activity peptidase activity serine-type aminopeptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity aminopeptidase activity hydrolase activity exopeptidase activity catalytic activity serine-type endopeptidase activity endopeptidase activity identical protein binding protein binding serine-type exopeptidase activity peptidase activity serine-type aminopeptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity aminopeptidase activity hydrolase activity exopeptidase activity catalytic activity serine-type endopeptidase activity endopeptidase activity identical protein binding protein binding 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 regulation of response to external stimulus negative regulation of biological process positive regulation of biological 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 regulation of response to external stimulus negative regulation of biological process positive regulation of biological process regulation of response to wounding regulation of coagulation regulation of response to stress regulation of multicellular organismal process regulation of hemostasis regulation of biological process negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation response to external stimulus negative regulation of response to wounding positive regulation of fibrinolysis negative regulation of hemostasis fibrinolysis negative regulation of coagulation regulation of fibrinolysis regulation of response to stimulus negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process zymogen activation primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process plasminogen activation	cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane
C [auth A], E [auth C]	Coagulation factor XIa heavy chain	serine-type exopeptidase activity peptidase activity serine-type aminopeptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity aminopeptidase activity hydrolase activity exopeptidase activity catalytic activity serine-type endopeptidase activity endopeptidase activity identical protein binding protein binding serine-type exopeptidase activity peptidase activity serine-type aminopeptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity aminopeptidase activity hydrolase activity exopeptidase activity catalytic activity serine-type endopeptidase activity endopeptidase activity identical protein binding protein binding 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 regulation of response to external stimulus negative regulation of biological process positive regulation of biological 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 regulation of response to external stimulus negative regulation of biological process positive regulation of biological process regulation of response to wounding regulation of coagulation regulation of response to stress regulation of multicellular organismal process regulation of hemostasis regulation of biological process negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation response to external stimulus negative regulation of response to wounding positive regulation of fibrinolysis negative regulation of hemostasis fibrinolysis negative regulation of coagulation regulation of fibrinolysis regulation of response to stimulus negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process zymogen activation primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process plasminogen activation	cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane
A [auth E], B [auth F]	Coagulation factor IX	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 proteolysis metabolic process 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 proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process zymogen activation gene expression macromolecule biosynthetic process protein maturation biosynthetic process protein processing	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane extracellular matrix external encapsulating structure extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane extracellular matrix external encapsulating structure intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen cytoplasm endoplasmic reticulum lumen endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth B], F [auth D]	IPR000177	Apple domain	Domain
D [auth B], F [auth D]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
D [auth B], F [auth D]	IPR001314	Peptidase S1A, chymotrypsin family	Family
D [auth B], F [auth D]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
D [auth B], F [auth D]	IPR001254	Serine proteases, trypsin domain	Domain
D [auth B], F [auth D]	IPR018114	Serine protease-like, trypsin family, histidine active site	Active Site
D [auth B], F [auth D]	IPR003609	PAN/Apple domain	Domain
C [auth A], E [auth C]	IPR000177	Apple domain	Domain
C [auth A], E [auth C]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C [auth A], E [auth C]	IPR001314	Peptidase S1A, chymotrypsin family	Family
C [auth A], E [auth C]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
C [auth A], E [auth C]	IPR001254	Serine proteases, trypsin domain	Domain
C [auth A], E [auth C]	IPR018114	Serine protease-like, trypsin family, histidine active site	Active Site
C [auth A], E [auth C]	IPR003609	PAN/Apple domain	Domain
A [auth E], B [auth F]	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
A [auth E], B [auth F]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A [auth E], B [auth F]	IPR018114	Serine protease-like, trypsin family, histidine active site	Active Site
A [auth E], B [auth F]	IPR000742	EGF-like domain	Domain
A [auth E], B [auth F]	IPR050442	Peptidase S1 family, coagulation factors	Family
A [auth E], B [auth F]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth E], B [auth F]	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
A [auth E], B [auth F]	IPR001314	Peptidase S1A, chymotrypsin family	Family
A [auth E], B [auth F]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A [auth E], B [auth F]	IPR001254	Serine proteases, trypsin domain	Domain
A [auth E], B [auth F]	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
A [auth E], B [auth F]	IPR001881	EGF-like calcium-binding domain	Domain
A [auth E], B [auth F]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
A [auth E], B [auth F]	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth B], F [auth D]	: P03951	congenital factor XI deficiency hypertensive disorder cerebrovascular disorder lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia lung adenocarcinoma malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous carcinoma thrombotic disease factor XI deficiency lung cancer non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm vascular disease
C [auth A], E [auth C]	: P03951	congenital factor XI deficiency hypertensive disorder cerebrovascular disorder lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia lung adenocarcinoma malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous carcinoma thrombotic disease factor XI deficiency lung cancer non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm vascular disease
A [auth E], B [auth F]	: P00740	hemophilia B hemophilia A thrombophilia, X-linked, due to factor 9 defect coumarin resistance malignant mesothelioma thrombophilia thrombotic disease Autosomal Hemophilia A hemophilia bipolar disorder psoriasis vascular disease congenital factor XI deficiency