3PB1 | pdb_00003pb1

Crystal Structure of a Michaelis Complex between Plasminogen Activator Inhibitor-1 and Urokinase-type Plasminogen Activator

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
B [auth E]	d3pb1e_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth I]	d3pb1i_	Multi-domain proteins (alpha and beta)	Serpins	Serpins	Serpins	Plasminogen activator inhibitor-1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth E]	SCOP2B Superfamily	Trypsin-like serine proteases	8042216	3000114	SCOP2B (2022-06-29)
A [auth I]	SCOP2B Superfamily	Serpins	8041305	3001563	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)
B [auth E]	Gal-bind_lectin	e3pb1E1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Gal-bind_lectin	ECOD (develop294)
A [auth I]	COX1	e3pb1I1	A: alpha bundles	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: Macro domain-like	T: Macro domain-like	F: COX1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth E]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
A [auth I]	3.30.497.10	Alpha Beta	2-Layer Sandwich	Antithrombin	Chain I, domain 2	CATH (4.3.0)
A [auth I]	2.30.39.10	Mainly Beta	Roll	Alpha-1-antitrypsin	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth E]	PF00089	Trypsin (Trypsin)	Trypsin		Domain
A [auth I]	PF00079	Serpin (serine protease inhibitor) (Serpin)	Serpin (serine protease inhibitor)	Structure is a multi-domain fold containing a bundle of helices and a beta sandwich.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth E]	Plasminogen activator, urokinase	molecular function activator activity molecular function regulator activity signaling receptor regulator 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	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 cell adhesion 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 regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion cellular process muscle cell migration cell migration cell motility smooth muscle cell migration cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin 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 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 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 zymogen activation primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process protein metabolic process macromolecule metabolic process plasminogen activation cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway cell communication positive regulation of response to stimulus positive regulation of ERBB signaling pathway regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process positive regulation of epidermal growth factor receptor signaling pathway regulation of ERBB signaling pathway regulation of signaling cell surface receptor signaling pathway ERBB signaling pathway regulation of cell communication positive regulation of signaling regulation of cell motility regulation of smooth muscle cell migration regulation of locomotion regulation of cell migration locomotion regulation of protein maturation regulation of primary metabolic process regulation of proteolysis regulation of plasminogen activation regulation of biosynthetic process regulation of protein metabolic process regulation of macromolecule metabolic process regulation of gene expression regulation of protein processing regulation of macromolecule biosynthetic process regulation of metabolic process chemotaxis taxis response to chemical positive regulation of coagulation positive regulation of blood coagulation positive regulation of response to external stimulus positive regulation of hemostasis positive regulation of response to wounding positive regulation of wound healing regulation of fibrinolysis positive regulation of multicellular organismal process negative regulation of fibrinolysis negative regulation of plasminogen activation negative regulation of proteolysis negative regulation of protein maturation negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of protein processing positive regulation of locomotion positive regulation of cell migration positive regulation of cell motility response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus cell population proliferation regulation of cell population proliferation regulation of cell-substrate adhesion cell-substrate adhesion regulation of smooth muscle cell-matrix adhesion smooth muscle cell-matrix adhesion cell-matrix adhesion regulation of cell-matrix adhesion regulation of integrin-mediated signaling pathway integrin-mediated signaling pathway urokinase plasminogen activator signaling pathway	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane anchoring junction cell junction focal adhesion cell-substrate junction specific granule membrane specific granule cell periphery cell surface plasma membrane external side of plasma membrane side of membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle protein-containing complex serine protease inhibitor complex protease inhibitor complex peptidase inhibitor complex catalytic complex peptidase complex endopeptidase complex serine-type endopeptidase complex serine-type peptidase complex protein complex involved in cell-matrix adhesion protein complex involved in cell adhesion
A [auth I]	Plasminogen activator inhibitor 1	protein binding binding signaling receptor binding enzyme binding protease binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity serine-type endopeptidase inhibitor activity	positive regulation of coagulation multicellular organismal process regulation of biological process biological regulation positive regulation of biological process coagulation positive regulation of multicellular organismal process regulation of multicellular organismal process regulation of coagulation negative regulation of locomotion regulation of cell motility regulation of cellular process regulation of smooth muscle cell migration negative regulation of biological process positive regulation of coagulation multicellular organismal process regulation of biological process biological regulation positive regulation of biological process coagulation positive regulation of multicellular organismal process regulation of multicellular organismal process regulation of coagulation negative regulation of locomotion regulation of cell motility regulation of cellular process regulation of smooth muscle cell migration negative regulation of biological process smooth muscle cell migration muscle cell migration negative regulation of smooth muscle cell migration regulation of locomotion regulation of cell migration negative regulation of cellular process negative regulation of cell motility cell migration cellular process cell motility locomotion negative regulation of cell migration regulation of defense response response to stimulus regulation of response to external stimulus defense response response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress positive regulation of defense response inflammatory response developmental process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development cellular response to stimulus regulation of integrin-mediated signaling pathway signaling negative regulation of signaling regulation of signal transduction negative regulation of cell communication cell communication negative regulation of integrin-mediated signaling pathway signal transduction regulation of signaling integrin-mediated signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of cell communication extrinsic apoptotic signaling pathway via death domain receptors regulation of programmed cell death extrinsic apoptotic signaling pathway negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of programmed cell death regulation of apoptotic process negative regulation of extrinsic apoptotic signaling pathway via death domain receptors cell death 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 body fluid levels regulation of response to wounding regulation of biological quality response to wounding regulation of hemostasis wound healing negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation hemostasis negative regulation of response to wounding blood coagulation 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 negative regulation of cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of cell adhesion negative regulation of cell adhesion cell adhesion cell adhesion mediated by integrin replicative senescence cell cycle cell cycle process biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin negative regulation of thrombin-activated receptor signaling pathway negative regulation of G protein-coupled receptor signaling pathway thrombin-activated receptor signaling pathway regulation of G protein-coupled receptor signaling pathway regulation of thrombin-activated receptor signaling pathway G protein-coupled receptor signaling pathway negative regulation of proteolysis regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process regulation of proteolysis proteolysis metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process positive regulation of interleukin-8 production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process interleukin-8 production gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of interleukin-8 production odontogenesis of dentin-containing tooth dentinogenesis odontogenesis animal organ development animal organ morphogenesis positive regulation of blood coagulation positive regulation of hemostasis positive regulation of response to wounding positive regulation of wound healing regulation of fibrinolysis negative regulation of fibrinolysis regulation of developmental process regulation of vasculature development vascular wound healing regulation of anatomical structure morphogenesis regulation of multicellular organismal development negative regulation of blood vessel morphogenesis negative regulation of developmental process angiogenesis involved in wound healing negative regulation of angiogenesis negative regulation of vasculature development regulation of angiogenesis negative regulation of vascular wound healing regulation of vascular wound healing positive regulation of odontoblast differentiation cellular developmental process regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation positive regulation of developmental process positive regulation of cell differentiation cell differentiation neuroepithelial cell differentiation odontoblast differentiation epithelium development regulation of odontoblast differentiation tissue development positive regulation of epithelial cell differentiation columnar/cuboidal epithelial cell differentiation positive regulation of neuroepithelial cell differentiation regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport vesicle-mediated transport cellular component organization localization positive regulation of endocytosis cellular component organization or biogenesis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of transport endocytosis receptor-mediated endocytosis positive regulation of angiogenesis positive regulation of vasculature development positive regulation of monocyte chemotaxis positive regulation of locomotion positive regulation of chemotaxis positive regulation of cell migration regulation of monocyte chemotaxis taxis positive regulation of cell motility myeloid leukocyte migration positive regulation of mononuclear cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process cell chemotaxis chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte migration positive regulation of leukocyte chemotaxis regulation of chemotaxis monocyte chemotaxis leukocyte migration immune system process mononuclear cell migration leukocyte chemotaxis regulation of protein maturation negative regulation of plasminogen activation negative regulation of protein maturation protein maturation regulation of plasminogen activation plasminogen activation zymogen activation negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of protein processing protein processing negative regulation of protein processing defense response to Gram-negative bacterium defense response to bacterium negative regulation of endothelial cell apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process regulation of cell-substrate adhesion cell-substrate adhesion negative regulation of smooth muscle cell-matrix adhesion negative regulation of cell-matrix adhesion regulation of smooth muscle cell-matrix adhesion smooth muscle cell-matrix adhesion cell-matrix adhesion regulation of cell-matrix adhesion negative regulation of cell-substrate adhesion arachidonate metabolite production involved in inflammatory response regulation of leukotriene production involved in inflammatory response production of molecular mediator involved in inflammatory response positive regulation of leukotriene production involved in inflammatory response leukotriene production involved in inflammatory response	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane 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 plasma membrane membrane extracellular matrix external encapsulating structure protein-containing complex peptidase inhibitor complex serine protease inhibitor complex protease inhibitor complex vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen secretory granule secretory vesicle cytoplasm platelet alpha granule platelet alpha granule lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth E]	IPR018056	Kringle, conserved site	Conserved Site
B [auth E]	IPR000742	EGF-like domain	Domain
B [auth E]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
B [auth E]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
B [auth E]	IPR013806	Kringle-like fold	Homologous Superfamily
B [auth E]	IPR038178	Kringle superfamily	Homologous Superfamily
B [auth E]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B [auth E]	IPR001314	Peptidase S1A, chymotrypsin family	Family
B [auth E]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
B [auth E]	IPR001254	Serine proteases, trypsin domain	Domain
B [auth E]	IPR050127	Serine Proteases (Peptidase S1 Family)	Family
B [auth E]	IPR000001	Kringle	Domain
A [auth I]	IPR023795	Serpin, conserved site	Conserved Site
A [auth I]	IPR000215	Serpin family	Family
A [auth I]	IPR036186	Serpin superfamily	Homologous Superfamily
A [auth I]	IPR023796	Serpin domain	Domain
A [auth I]	IPR042178	Serpin superfamily, domain 1	Homologous Superfamily
A [auth I]	IPR042185	Serpin superfamily, domain 2	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth E]	Pharos: P00749	Quebec platelet disorder Alzheimer disease idiopathic pulmonary fibrosis transitional cell carcinoma Henoch-Schoenlein purpura IgA glomerulonephritis Venous Thrombosis malignant pancreatic neoplasm adenocarcinoma cerebrovascular disorder cholesterol embolism tubular adenocarcinoma ventricular fibrillation psoriasis granular cell carcinoma Quebec platelet disorder Alzheimer disease idiopathic pulmonary fibrosis transitional cell carcinoma Henoch-Schoenlein purpura IgA glomerulonephritis Venous Thrombosis malignant pancreatic neoplasm adenocarcinoma cerebrovascular disorder cholesterol embolism tubular adenocarcinoma ventricular fibrillation psoriasis granular cell carcinoma cerebral infarction myocardial infarction intermediate coronary syndrome cirrhosis of liver anuria nephritis brain edema prostate cancer brain ischemia pulmonary embolism carotid artery disease middle cerebral artery infarction sagittal sinus thrombosis asthma ischemia reperfusion injury bone cancer pilocytic astrocytoma gastric carcinoma breast cancer malignant glioma hereditary diffuse gastric adenocarcinoma idiopathic interstitial pneumonia multiple sclerosis inflammatory bowel disease nasopharyngeal carcinoma coronary artery disease interstitial cystitis cribriform carcinoma of breast osteosarcoma invasive ductal breast carcinoma atopic eczema pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ischemic disease primitive neuroectodermal tumor gastric neoplasm malignant colon neoplasm cancer Alzheimer disease type 1 thrombotic disease interstitial lung disease Crohn disease ulcerative colitis intracranial hemorrhage ovarian cancer atypical teratoid rhabdoid tumor pancreatic neoplasm large cell medulloblastoma gastric cancer lung adenocarcinoma glioblastoma malignant ependymoma acute interstitial pneumonia hypotensive disorder congestive heart failure cribriform carcinoma tuberculosis intracerebral hemorrhage non-small cell lung carcinoma cystic fibrosis pancreatic ductal adenocarcinoma
A [auth I]	Pharos: P05121	atherosclerosis congestive heart failure nephrotic syndrome obesity disorder hypertensive disorder chronic kidney disease congenital plasminogen activator inhibitor type 1 deficiency Diabetes Mellitus, Experimental focal segmental glomerulosclerosis prostate cancer Behcet disease cholestasis nervous system disorder preeclampsia liver cancer atherosclerosis congestive heart failure nephrotic syndrome obesity disorder hypertensive disorder chronic kidney disease congenital plasminogen activator inhibitor type 1 deficiency Diabetes Mellitus, Experimental focal segmental glomerulosclerosis prostate cancer Behcet disease cholestasis nervous system disorder preeclampsia liver cancer thrombotic disease major depressive disorder type 2 diabetes mellitus malignant mesothelioma ureteral obstruction gastric neoplasm ovarian cancer heart failure pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor inborn carbohydrate metabolic disorder kidney disease liver disease thrombophilia cystic fibrosis lung carcinoma diabetic kidney disease malignant ependymoma ulcerative colitis fatty liver disease gastric cancer glioblastoma pancreatic ductal adenocarcinoma arteriosclerosis disorder pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia atopic eczema autism interstitial cystitis cancer coronary artery disease liver neoplasm lung disease tuberculosis malignant glioma esophageal adenocarcinoma malignant pancreatic neoplasm gastric carcinoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma hereditary diffuse gastric adenocarcinoma pilocytic astrocytoma attention deficit hyperactivity disorder, inattentive type IgA glomerulonephritis invasive ductal breast carcinoma psoriasis cerebrovascular disorder cutaneous lupus erythematosus lung cancer

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.