Annotations: 1YCP

THE CRYSTAL STRUCTURE OF FIBRINOGEN-AA PEPTIDE 1-23 (F8Y) BOUND TO BOVINE THROMBIN EXPLAINS WHY THE MUTATION OF PHE-8 TO TYROSINE STRONGLY INHIBITS NORMAL CLEAVAGE AT ARGININE-16

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
F [auth M]	d1ycp.2	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Thrombin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
E [auth K]	d1ycp.2	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Thrombin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B [auth H]	d1ycp.1	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Thrombin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
D [auth J]	d1ycp.2	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Thrombin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A [auth L]	d1ycp.1	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Thrombin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth M]		e1ycpM01	A: alpha arrays	X: Colicin-A N-terminal domain	H: Colicin-A N-terminal domain	T: Colicin-A N-terminal domain	F:	ECOD (v295.2)
E [auth K]		e1ycpK01	A: alpha arrays	X: Colicin-A N-terminal domain	H: Colicin-A N-terminal domain	T: Colicin-A N-terminal domain	F:	ECOD (v295.2)
B [auth H]	Flu_M2	e1ycpH1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Flu_M2	ECOD (v295.2)
A [auth L]	Flu_M2	e1ycpL1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Flu_M2	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth M]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
E [auth K]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B [auth H]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth K]	PF00089	Trypsin (Trypsin)	Trypsin		Domain
B [auth H]	PF00089	Trypsin (Trypsin)	Trypsin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth M]	EPSILON THROMBIN	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein-containing complex binding fibrinogen binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein-containing complex binding fibrinogen 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 cell activation hemostasis biological regulation blood coagulation response to stress coagulation cellular process regulation of biological quality response to wounding platelet activation multicellular organismal process regulation of body fluid levels wound healing response to stimulus cell activation hemostasis biological regulation blood coagulation response to stress coagulation cellular process regulation of biological quality response to wounding platelet activation cellular component organization cellular component biogenesis protein polymerization cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis positive regulation of coagulation regulation of response to external stimulus positive regulation of biological process positive regulation of blood coagulation regulation of response to wounding regulation of coagulation positive regulation of response to stimulus regulation of response to stress regulation of multicellular organismal process positive regulation of hemostasis regulation of hemostasis positive regulation of response to wounding regulation of biological process regulation of blood coagulation response to external stimulus positive regulation of wound healing regulation of response to stimulus regulation of wound healing positive regulation of multicellular organismal process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular matrix cellular anatomical structure external encapsulating structure extracellular region
E [auth K]	EPSILON THROMBIN	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein-containing complex binding fibrinogen binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein-containing complex binding fibrinogen 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 cell activation hemostasis biological regulation blood coagulation response to stress coagulation cellular process regulation of biological quality response to wounding platelet activation multicellular organismal process regulation of body fluid levels wound healing response to stimulus cell activation hemostasis biological regulation blood coagulation response to stress coagulation cellular process regulation of biological quality response to wounding platelet activation cellular component organization cellular component biogenesis protein polymerization cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis positive regulation of coagulation regulation of response to external stimulus positive regulation of biological process positive regulation of blood coagulation regulation of response to wounding regulation of coagulation positive regulation of response to stimulus regulation of response to stress regulation of multicellular organismal process positive regulation of hemostasis regulation of hemostasis positive regulation of response to wounding regulation of biological process regulation of blood coagulation response to external stimulus positive regulation of wound healing regulation of response to stimulus regulation of wound healing positive regulation of multicellular organismal process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular matrix cellular anatomical structure external encapsulating structure extracellular region
C [auth F], G [auth N]	FIBRINOPEPTIDE A-ALPHA	protein binding binding signaling receptor binding protein-macromolecule adaptor activity molecular adaptor activity structural molecule activity extracellular matrix structural constituent	cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis protein polymerization cellular response to stimulus positive regulation of cell communication regulation of cellular process cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis protein polymerization cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of MAPK cascade biological regulation positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling regulation of tube diameter multicellular organismal process system process regulation of tube size regulation of system process positive regulation of vasoconstriction circulatory system process regulation of blood circulation vascular process in circulatory system regulation of vasoconstriction positive regulation of multicellular organismal process regulation of multicellular organismal process blood vessel diameter maintenance regulation of biological quality vasoconstriction blood circulation regulation of anatomical structure size response to metal ion response to chemical response to calcium ion regulation of body fluid levels blood coagulation, common pathway protein maturation response to stress blood coagulation, fibrin clot formation coagulation protein metabolic process response to wounding wound healing protein activation cascade hemostasis primary metabolic process gene expression macromolecule biosynthetic process blood coagulation biosynthetic process metabolic process macromolecule metabolic process extrinsic apoptotic signaling pathway via death domain receptors negative regulation of signaling negative regulation of biological process regulation of programmed cell death extrinsic apoptotic signaling pathway negative regulation of cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process negative regulation of extrinsic apoptotic signaling pathway via death domain receptors cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway via death domain receptors apoptotic process programmed cell death regulation of apoptotic signaling pathway regulation of localization transport positive regulation of secretion by cell positive regulation of exocytosis vesicle-mediated transport localization regulation of secretion by cell secretion by cell positive regulation of secretion regulation of transport secretion export from cell regulation of vesicle-mediated transport establishment of localization regulation of secretion positive regulation of transport exocytosis regulation of exocytosis regulation of response to external stimulus regulation of response to wounding regulation of coagulation regulation of response to stress regulation of hemostasis negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation response to external stimulus negative regulation of response to wounding negative regulation of hemostasis fibrinolysis negative regulation of coagulation negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process homotypic cell-cell adhesion cell activation platelet aggregation cell-cell adhesion platelet activation zymogen activation proteolysis protein processing plasminogen activation positive regulation of substrate adhesion-dependent cell spreading regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion positive regulation of cell-substrate adhesion substrate adhesion-dependent cell spreading establishment of protein localization regulation of protein localization positive regulation of establishment of protein localization protein localization to extracellular region positive regulation of protein transport intracellular protein localization regulation of establishment of protein localization establishment of protein localization to extracellular region regulation of protein transport protein secretion positive regulation of protein secretion regulation of protein secretion protein transport macromolecule localization positive regulation of protein localization positive regulation of cell-cell adhesion heterotypic cell-cell adhesion positive regulation of heterotypic cell-cell adhesion regulation of cell-cell adhesion regulation of heterotypic cell-cell adhesion humoral immune response biological process involved in interspecies interaction between organisms response to other organism defense response immune response antibacterial humoral response defense response to symbiont antimicrobial humoral response response to biotic stimulus defense response to bacterium induction of bacterial agglutination defense response to other organism immune system process response to bacterium response to external biotic stimulus negative regulation of endothelial cell apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process nitrogen compound transport regulation of hormone secretion regulation of peptide secretion hormone secretion peptide secretion positive regulation of hormone secretion signal release regulation of peptide hormone secretion positive regulation of peptide secretion regulation of hormone levels positive regulation of peptide hormone secretion regulation of peptide transport cell-cell signaling peptide transport peptide hormone secretion hormone transport	protein-containing complex cellular anatomical structure extracellular region extracellular protein-containing complex fibrinogen complex cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle protein-containing complex cellular anatomical structure extracellular region extracellular protein-containing complex fibrinogen complex cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle extracellular matrix external encapsulating structure blood microparticle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen endoplasmic reticulum cytoplasm intracellular vesicle cytoplasmic vesicle secretory granule secretory vesicle platelet alpha granule basement membrane non-collagenous component of basement membrane solid phase of basement membrane vesicle lumen cytoplasmic vesicle lumen secretory granule lumen platelet alpha granule lumen
B [auth H]	ALPHA THROMBIN	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein-containing complex binding fibrinogen binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein-containing complex binding fibrinogen 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 cell activation hemostasis biological regulation blood coagulation response to stress coagulation cellular process regulation of biological quality response to wounding platelet activation multicellular organismal process regulation of body fluid levels wound healing response to stimulus cell activation hemostasis biological regulation blood coagulation response to stress coagulation cellular process regulation of biological quality response to wounding platelet activation cellular component organization cellular component biogenesis protein polymerization cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis positive regulation of coagulation regulation of response to external stimulus positive regulation of biological process positive regulation of blood coagulation regulation of response to wounding regulation of coagulation positive regulation of response to stimulus regulation of response to stress regulation of multicellular organismal process positive regulation of hemostasis regulation of hemostasis positive regulation of response to wounding regulation of biological process regulation of blood coagulation response to external stimulus positive regulation of wound healing regulation of response to stimulus regulation of wound healing positive regulation of multicellular organismal process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular matrix cellular anatomical structure external encapsulating structure extracellular region
A [auth L], D [auth J]	EPSILON THROMBIN	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein-containing complex binding fibrinogen binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein-containing complex binding fibrinogen 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 cell activation hemostasis biological regulation blood coagulation response to stress coagulation cellular process regulation of biological quality response to wounding platelet activation multicellular organismal process regulation of body fluid levels wound healing response to stimulus cell activation hemostasis biological regulation blood coagulation response to stress coagulation cellular process regulation of biological quality response to wounding platelet activation cellular component organization cellular component biogenesis protein polymerization cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis positive regulation of coagulation regulation of response to external stimulus positive regulation of biological process positive regulation of blood coagulation regulation of response to wounding regulation of coagulation positive regulation of response to stimulus regulation of response to stress regulation of multicellular organismal process positive regulation of hemostasis regulation of hemostasis positive regulation of response to wounding regulation of biological process regulation of blood coagulation response to external stimulus positive regulation of wound healing regulation of response to stimulus regulation of wound healing positive regulation of multicellular organismal process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular matrix cellular anatomical structure external encapsulating structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth M]	IPR013806	Kringle-like fold	Homologous Superfamily
F [auth M]	IPR038178	Kringle superfamily	Homologous Superfamily
F [auth M]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
F [auth M]	IPR018992	Thrombin light chain	Domain
F [auth M]	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
F [auth M]	IPR037111	Thrombin light chain domain superfamily	Homologous Superfamily
F [auth M]	IPR001314	Peptidase S1A, chymotrypsin family	Family
F [auth M]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
F [auth M]	IPR051659	Serine Protease S1 Domain-Containing Protein	Family
F [auth M]	IPR003966	Prothrombin/thrombin	Family
F [auth M]	IPR001254	Serine proteases, trypsin domain	Domain
F [auth M]	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
F [auth M]	IPR018056	Kringle, conserved site	Conserved Site
F [auth M]	IPR018114	Serine protease-like, trypsin family, histidine active site	Active Site
F [auth M]	IPR000001	Kringle	Domain
E [auth K]	IPR013806	Kringle-like fold	Homologous Superfamily
E [auth K]	IPR038178	Kringle superfamily	Homologous Superfamily
E [auth K]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
E [auth K]	IPR018992	Thrombin light chain	Domain
E [auth K]	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
E [auth K]	IPR037111	Thrombin light chain domain superfamily	Homologous Superfamily
E [auth K]	IPR001314	Peptidase S1A, chymotrypsin family	Family
E [auth K]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
E [auth K]	IPR051659	Serine Protease S1 Domain-Containing Protein	Family
E [auth K]	IPR003966	Prothrombin/thrombin	Family
E [auth K]	IPR001254	Serine proteases, trypsin domain	Domain
E [auth K]	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
E [auth K]	IPR018056	Kringle, conserved site	Conserved Site
E [auth K]	IPR018114	Serine protease-like, trypsin family, histidine active site	Active Site
E [auth K]	IPR000001	Kringle	Domain
C [auth F], G [auth N]	IPR037579	Fibrinogen/angiopoietin-like	Family
C [auth F], G [auth N]	IPR012290	Fibrinogen, alpha/beta/gamma chain, coiled coil domain	Domain
C [auth F], G [auth N]	IPR020837	Fibrinogen, conserved site	Conserved Site
C [auth F], G [auth N]	IPR021996	Fibrinogen alpha C domain	Domain
C [auth F], G [auth N]	IPR014716	Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1	Homologous Superfamily
C [auth F], G [auth N]	IPR002181	Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain	Domain
C [auth F], G [auth N]	IPR036056	Fibrinogen-like, C-terminal	Homologous Superfamily
B [auth H]	IPR013806	Kringle-like fold	Homologous Superfamily
B [auth H]	IPR038178	Kringle superfamily	Homologous Superfamily
B [auth H]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B [auth H]	IPR018992	Thrombin light chain	Domain
B [auth H]	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
B [auth H]	IPR037111	Thrombin light chain domain superfamily	Homologous Superfamily
B [auth H]	IPR001314	Peptidase S1A, chymotrypsin family	Family
B [auth H]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
B [auth H]	IPR051659	Serine Protease S1 Domain-Containing Protein	Family
B [auth H]	IPR003966	Prothrombin/thrombin	Family
B [auth H]	IPR001254	Serine proteases, trypsin domain	Domain
B [auth H]	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
B [auth H]	IPR018056	Kringle, conserved site	Conserved Site
B [auth H]	IPR018114	Serine protease-like, trypsin family, histidine active site	Active Site
B [auth H]	IPR000001	Kringle	Domain
A [auth L], D [auth J]	IPR013806	Kringle-like fold	Homologous Superfamily
A [auth L], D [auth J]	IPR038178	Kringle superfamily	Homologous Superfamily
A [auth L], D [auth J]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth L], D [auth J]	IPR018992	Thrombin light chain	Domain
A [auth L], D [auth J]	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
A [auth L], D [auth J]	IPR037111	Thrombin light chain domain superfamily	Homologous Superfamily
A [auth L], D [auth J]	IPR001314	Peptidase S1A, chymotrypsin family	Family
A [auth L], D [auth J]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A [auth L], D [auth J]	IPR051659	Serine Protease S1 Domain-Containing Protein	Family
A [auth L], D [auth J]	IPR003966	Prothrombin/thrombin	Family
A [auth L], D [auth J]	IPR001254	Serine proteases, trypsin domain	Domain
A [auth L], D [auth J]	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
A [auth L], D [auth J]	IPR018056	Kringle, conserved site	Conserved Site
A [auth L], D [auth J]	IPR018114	Serine protease-like, trypsin family, histidine active site	Active Site
A [auth L], D [auth J]	IPR000001	Kringle	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth F], G [auth N]	: P02671	congenital afibrinogenemia familial visceral amyloidosis thrombophilia pulmonary embolism familial dysfibrinogenemia kidney disease osteoporosis venous thromboembolism amyloidosis cholestasis Dysfibrinogenemia, Congenital hereditary amyloidosis acquired metabolic disease osteosarcoma periodic fever syndrome congenital afibrinogenemia familial visceral amyloidosis thrombophilia pulmonary embolism familial dysfibrinogenemia kidney disease osteoporosis venous thromboembolism amyloidosis cholestasis Dysfibrinogenemia, Congenital hereditary amyloidosis acquired metabolic disease osteosarcoma periodic fever syndrome thrombotic disease drug-induced hepatitis familial hypofibrinogenemia lung adenocarcinoma ovarian cancer cerebrovascular disorder lung cancer oral cavity neoplasm pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia vascular disease drug-induced liver injury