5EDM

Crystal structure of prothrombin deletion mutant residues 154-167 ( Form I )

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
Membrane Protein Annotation: OPM
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Kringle-like	8038667	3000761	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8042154	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	Thrombin_light,Trypsin	e5edmA4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Thrombin_light,Trypsin	ECOD (1.6)
A	Kringle	e5edmA1	A: few secondary structure elements	X: Kringle-like (From Topology)	H: Kringle-like (From Topology)	T: Kringle-like	F: Kringle	ECOD (1.6)
A	Gla_like,Gla	e5edmA2	A: few secondary structure elements	X: GLA-domain (From Topology)	H: GLA-domain (From Topology)	T: GLA-domain	F: Gla_like,Gla	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00051	Kringle domain (Kringle)	Kringle domain	Kringle domains have been found in plasminogen, hepatocyte growth factors, prothrombin, and apolipoprotein A. Structure is disulfide-rich, nearly all-beta.	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
A	PF00089	Trypsin (Trypsin)	Trypsin	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Prothrombin	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity 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 calcium ion binding metal ion binding small molecule binding lipid binding lipopolysaccharide binding carbohydrate derivative binding molecular transducer activity signaling receptor activity thrombospondin receptor activity heparin binding glycosaminoglycan binding sulfur compound 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 biological process involved in interspecies interaction between organisms response to other organism defense response 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 biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus disruption of cell in another organism response to biotic stimulus biological process involved in symbiotic interaction killing by host of symbiont cells cytolysis by host of symbiont cells defense response to other organism cellular process response to external biotic stimulus disruption of anatomical structure in another organism biological process involved in interaction with symbiont killing of cells of another organism cell killing neutrophil-mediated killing of symbiont cell defense response to Gram-negative bacterium myeloid leukocyte mediated immunity defense response to bacterium neutrophil mediated immunity response to bacterium leukocyte mediated immunity neutrophil-mediated killing of bacterium neutrophil mediated cytotoxicity leukocyte mediated cytotoxicity immune effector process neutrophil-mediated killing of gram-negative bacterium immune system process regulation of response to external stimulus negative 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 negative regulation of response to wounding negative regulation of hemostasis fibrinolysis negative regulation of coagulation regulation of response to stimulus negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis regulation of cytosolic calcium ion concentration cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis cell activation platelet activation acute-phase response inflammatory response acute inflammatory response positive regulation of coagulation positive regulation of biological process positive regulation of blood coagulation positive regulation of response to stimulus positive regulation of hemostasis positive regulation of response to wounding positive regulation of wound healing positive regulation of multicellular organismal process regulation of cellular process positive regulation of phosphorylation regulation of catalytic activity regulation of lipid metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function regulation of lipid kinase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of lipid metabolic process phosphorus metabolic process positive regulation of cellular process positive regulation of lipid kinase activity positive regulation of transferase activity positive regulation of phosphorus metabolic process phosphorylation positive regulation of catalytic activity primary metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of phosphorylation regulation of phosphorus metabolic process metabolic process regulation of metabolic process lipid metabolic process regulation of biosynthetic process collagen biosynthetic process regulation of collagen biosynthetic process regulation of collagen metabolic process positive regulation of collagen metabolic process biosynthetic process positive regulation of biosynthetic process positive regulation of collagen biosynthetic process collagen metabolic process regulation of cell activation negative regulation of platelet activation negative regulation of cellular process negative regulation of cell activation regulation of platelet activation regulation of growth regulation of cellular component organization growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular component organization or biogenesis cellular developmental process regulation of developmental process astrocyte differentiation cell development regulation of cell differentiation regulation of neurogenesis regulation of astrocyte differentiation regulation of gliogenesis regulation of cell development regulation of nervous system development multicellular organism development neurogenesis negative regulation of neurogenesis gliogenesis cell differentiation anatomical structure development negative regulation of nervous system development negative regulation of cell differentiation system development developmental process regulation of multicellular organismal development negative regulation of developmental process regulation of glial cell differentiation nervous system development negative regulation of astrocyte differentiation negative regulation of gliogenesis negative regulation of cell development negative regulation of glial cell differentiation central nervous system development glial cell differentiation protein localization regulation of localization cellular localization regulation of protein localization positive regulation of protein localization to nucleus regulation of protein localization to nucleus protein localization to nucleus localization regulation of cellular localization cellular macromolecule localization macromolecule localization protein localization to organelle positive regulation of protein localization negative regulation of proteolysis regulation of protein metabolic process negative regulation of metabolic process regulation of macromolecule metabolic process regulation of proteolysis proteolysis protein metabolic process macromolecule metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process cellular response to stimulus positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis regulation of anatomical structure morphogenesis cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation phospholipase C-activating G protein-coupled receptor signaling pathway regulation of G protein-coupled receptor signaling pathway positive regulation of G protein-coupled receptor signaling pathway positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway regulation of phospholipase C-activating G protein-coupled receptor signaling pathway positive regulation of response to external stimulus regulation of fibrinolysis negative regulation of fibrinolysis cell surface receptor signaling pathway humoral immune response immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide cell surface receptor signaling pathway via STAT positive regulation of receptor signaling pathway via STAT positive regulation of receptor signaling pathway via JAK-STAT regulation of receptor signaling pathway via JAK-STAT regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT regulation of calcium ion transport positive regulation of cation transmembrane transport positive regulation of calcium ion transport calcium ion transport positive regulation of monoatomic ion transport positive regulation of monoatomic ion transmembrane transport monoatomic cation transport regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol regulation of transmembrane transport transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport negative regulation of sequestering of calcium ion metal ion transport maintenance of location in cell regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of release of sequestered calcium ion into cytosol regulation of metal ion transport regulation of sequestering of calcium ion calcium ion transmembrane import into cytosol regulation of transport sequestering of calcium ion positive regulation of transport regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process positive regulation of protein phosphorylation protein modification process protein phosphorylation macromolecule modification establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization positive regulation of insulin secretion regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion regulation of protein secretion regulation of secretion regulation of hormone secretion regulation of peptide secretion positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion secretion by cell regulation of secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of peptide secretion secretion regulation of peptide transport regulation of establishment of protein localization cell-cell signaling export from cell regulation of protein transport positive regulation of protein secretion peptide transport protein transport regulation of insulin secretion peptide hormone secretion hormone transport insulin secretion ligand-gated ion channel signaling pathway regulation of cytokine production involved in inflammatory response cytokine production regulation of cytokine production negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response negative regulation of cytokine production cytokine production involved in inflammatory response gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix 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 plasma membrane membrane Golgi apparatus Golgi lumen blood microparticle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR018992	Thrombin light chain	Domain
A	IPR037111	Thrombin light chain domain superfamily	Homologous Superfamily
A	IPR003966	Prothrombin/thrombin	Family
A	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
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	IPR000001	Kringle	Domain
A	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
A	IPR051659	Serine Protease S1 Domain-Containing Protein	Family
A	IPR018056	Kringle, conserved site	Conserved Site
A	IPR013806	Kringle-like fold	Homologous Superfamily
A	IPR038178	Kringle superfamily	Homologous Superfamily
A	IPR001314	Peptidase S1A, chymotrypsin family	Family
A	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P00734	congenital prothrombin deficiency thrombophilia pregnancy loss, recurrent, susceptibility to, 2 liver failure cirrhosis of liver Venous Thrombosis intracranial sinus thrombosis brain ischemia myocardial infarction disseminated intravascular coagulation Alzheimer disease rheumatoid arthritis thrombotic disease hepatocellular carcinoma schizophrenia congenital prothrombin deficiency thrombophilia pregnancy loss, recurrent, susceptibility to, 2 liver failure cirrhosis of liver Venous Thrombosis intracranial sinus thrombosis brain ischemia myocardial infarction disseminated intravascular coagulation Alzheimer disease rheumatoid arthritis thrombotic disease hepatocellular carcinoma schizophrenia non-alcoholic fatty liver disease obesity disorder paratuberculosis skin vascular disease cerebrovascular disorder thrombophilia due to thrombin defect nephrosis venous thromboembolism cerebral infarction COVID-19 varicose disease osteoarthritis anemia pulmonary embolism autoimmune disease esophageal varices vascular disease vitamin K deficiency hemorrhagic disease heart disease alcohol abuse hepatic encephalopathy inborn carbohydrate metabolic disorder respiratory failure blood coagulation disease cancer liver disease thrombocytopenia coronary artery disease fatty liver disease hemochromatosis type 1 pneumonia hepatitis B virus infection hypertensive disorder autism spectrum disorder kidney disease

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM				GLA-domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	CGU	Parent Component: GLU RESID: AA0032 PSI-MOD : L-gamma-carboxyglutamic acid MOD:00041

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.