3U73

Crystal structure of stabilized human uPAR mutant in complex with ATF

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)
A [auth U]	d3u73u1	Small proteins	Snake toxin-like	Snake toxin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth A]	d3u73a1	Small proteins	Knottins (small inhibitors, toxins, lectins)	EGF/Laminin	EGF-type module	Plasminogen activator (urokinase-type)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth A]	d3u73a2	Small proteins	Kringle-like	Kringle-like	Kringle modules	Urokinase-type plasminogen activator	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)
A [auth U]	SCOP2B Superfamily	Snake toxin-like	8032874	3000545	SCOP2B (2022-06-29)
A [auth U]	SCOP2B Superfamily	Snake toxin-like	8032872	3000545	SCOP2B (2022-06-29)
A [auth U]	SCOP2B Superfamily	Snake toxin-like	8032873	3000545	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Kringle-like	8042599	3000761	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	EGF/Laminin-like	8042597	3000412	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 [auth U]	UPAR_LY6	e3u73U7	A: few secondary structure elements	X: Snake toxin-like (From Topology)	H: Snake toxin-like (From Topology)	T: Snake toxin-like	F: UPAR_LY6	ECOD (1.6)
A [auth U]	UPAR_LY6_1	e3u73U8	A: few secondary structure elements	X: Snake toxin-like (From Topology)	H: Snake toxin-like (From Topology)	T: Snake toxin-like	F: UPAR_LY6_1	ECOD (1.6)
B [auth A]	Kringle	e3u73A4	A: few secondary structure elements	X: Kringle-like (From Topology)	H: Kringle-like (From Topology)	T: Kringle-like	F: Kringle	ECOD (1.6)
B [auth A]	EGF	e3u73A3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: EGF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth U]	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
B [auth A]	2.10.25.10	Mainly Beta	Ribbon	Laminin	Laminin	CATH (4.3.0)
B [auth A]	2.40.20.10	Mainly Beta	Beta Barrel	Plasminogen Kringle 4	Plasminogen Kringle 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth U]	PF00021	u-PAR/Ly-6 domain (UPAR_LY6)	u-PAR/Ly-6 domain	This extracellular disulphide bond rich domain is related to Pfam:PF00087.	Domain
B [auth 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth U]	Urokinase plasminogen activator surface receptor	protein binding binding protein domain specific binding molecular transducer activity signaling receptor activity signaling receptor binding urokinase plasminogen activator receptor activity enzyme 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 molecular function positive regulation of molecular function regulation of DNA 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 molecular function positive regulation of molecular function regulation of DNA binding regulation of binding positive regulation of binding positive regulation of DNA binding regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion cellular process cellular response to stimulus positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization signaling apoptotic mitochondrial changes positive regulation of biological process regulation of release of cytochrome c from mitochondria cell communication cellular component organization positive regulation of release of cytochrome c from mitochondria cellular component organization or biogenesis signal transduction positive regulation of cellular process mitochondrion organization cell death regulation of organelle organization apoptotic signaling pathway release of cytochrome c from mitochondria organelle organization regulation of mitochondrion organization apoptotic process programmed cell death negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process organonitrogen compound metabolic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process organic substance metabolic process regulation of proteolysis proteolysis metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway 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 enzyme-linked receptor protein signaling pathway positive regulation of epidermal growth factor receptor signaling pathway regulation of ERBB signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of response to stimulus ERBB signaling pathway regulation of cell communication positive regulation of signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of intrinsic apoptotic signaling pathway intracellular signal transduction negative regulation of cell communication regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of intrinsic apoptotic signaling pathway regulation of apoptotic signaling pathway regulation of protein maturation cellular biosynthetic process protein maturation organic substance biosynthetic process regulation of plasminogen activation plasminogen activation zymogen activation regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of protein processing protein processing regulation of macromolecule biosynthetic process chemotaxis taxis response to chemical response to external stimulus locomotion regulation of response to external stimulus regulation of coagulation regulation of response to wounding regulation of response to stress regulation of multicellular organismal process regulation of hemostasis regulation of blood coagulation negative regulation of wound healing negative regulation of blood coagulation negative regulation of response to wounding negative regulation of hemostasis fibrinolysis regulation of fibrinolysis negative regulation of coagulation negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process regulation of homotypic cell-cell adhesion positive regulation of cell adhesion homotypic cell-cell adhesion positive regulation of cell-cell adhesion cell-cell adhesion positive regulation of homotypic cell-cell adhesion regulation of cell-cell adhesion positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation negative regulation of proteolysis regulation of catalytic activity negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway negative regulation of catalytic activity negative regulation of peptidase activity negative regulation of cysteine-type endopeptidase activity involved in apoptotic process negative regulation of protein metabolic process regulation of cysteine-type endopeptidase activity negative regulation of metabolic process regulation of peptidase activity regulation of hydrolase activity negative regulation of cysteine-type endopeptidase activity regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway negative regulation of hydrolase activity negative regulation of endopeptidase activity regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of endopeptidase activity negative regulation of macromolecule metabolic process negative regulation of molecular function urokinase plasminogen activator signaling pathway	anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule cell periphery cell surface plasma membrane external side of plasma membrane side of membrane extrinsic component of membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen extracellular region protein-containing 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 cell projection
B [auth A]	Urokinase-type plasminogen activator	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 organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process biosynthetic process proteolysis organic substance biosynthetic process protein processing metabolic process protein metabolic process macromolecule metabolic process plasminogen activation regulation of cell motility regulation of smooth muscle cell migration regulation of locomotion regulation of cell migration locomotion cellular response to stimulus signaling signal transduction cell communication 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 cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic 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 biological process positive regulation of blood coagulation positive regulation of response to stimulus 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 cellular metabolic process negative regulation of protein metabolic process negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process negative regulation of protein maturation negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process negative regulation of protein processing positive regulation of locomotion positive regulation of cell migration positive regulation of cell motility positive regulation of cellular process 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 signaling regulation of signaling receptor activity regulation of signal transduction regulation of molecular function regulation of cell communication 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 cell surface receptor signaling pathway urokinase plasminogen activator signaling pathway	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth U]	IPR045860	Snake toxin-like superfamily	Homologous Superfamily
A [auth U]	IPR016054	Ly-6 antigen/uPA receptor-like	Domain
A [auth U]	IPR018363	CD59 antigen, conserved site	Conserved Site
B [auth A]	IPR018056	Kringle, conserved site	Conserved Site
B [auth A]	IPR000742	EGF-like domain	Domain
B [auth A]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
B [auth A]	IPR013806	Kringle-like fold	Homologous Superfamily
B [auth A]	IPR038178	Kringle superfamily	Homologous Superfamily
B [auth A]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B [auth A]	IPR001314	Peptidase S1A, chymotrypsin family	Family
B [auth A]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
B [auth A]	IPR001254	Serine proteases, trypsin domain	Domain
B [auth A]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B [auth A]	IPR000001	Kringle	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth U]	Pharos: Q03405	cancer carcinoma sarcomatoid carcinoma Inflammation prostate cancer juvenile idiopathic arthritis invasive ductal breast carcinoma lung carcinoma malignant glioma MALT lymphoma acute myeloid leukemia autism pancreatic ductal adenocarcinoma benign neoplasm peripheral neuropathy cancer carcinoma sarcomatoid carcinoma Inflammation prostate cancer juvenile idiopathic arthritis invasive ductal breast carcinoma lung carcinoma malignant glioma MALT lymphoma acute myeloid leukemia autism pancreatic ductal adenocarcinoma benign neoplasm peripheral neuropathy ductal breast carcinoma in situ undifferentiated carcinoma gastric carcinoma malignant colon neoplasm malignant mesothelioma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm breast cancer tuberculosis esophageal adenocarcinoma glioblastoma interstitial cystitis lung cancer malignant ependymoma malignant pancreatic neoplasm atypical teratoid rhabdoid tumor ovarian cancer Barrett esophagus peripheral nervous system disease cystic fibrosis ulcerative colitis gastric cancer hepatocellular carcinoma
B [auth A]	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 cirrhosis of liver intermediate coronary syndrome anuria nephritis brain edema brain ischemia prostate cancer carotid artery disease pulmonary embolism middle cerebral artery infarction sagittal sinus thrombosis asthma ischemia reperfusion injury bone cancer pilocytic astrocytoma breast cancer gastric carcinoma malignant glioma hereditary diffuse gastric adenocarcinoma multiple sclerosis idiopathic interstitial pneumonia nasopharyngeal carcinoma inflammatory bowel disease coronary artery disease interstitial cystitis osteosarcoma cribriform carcinoma of breast invasive ductal breast carcinoma atopic eczema pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ischemic disease primitive neuroectodermal tumor malignant colon neoplasm cancer gastric neoplasm Alzheimer disease type 1 thrombotic disease interstitial lung disease ovarian cancer Crohn disease ulcerative colitis intracranial hemorrhage atypical teratoid rhabdoid tumor pancreatic neoplasm large cell medulloblastoma lung adenocarcinoma gastric cancer malignant ependymoma glioblastoma acute interstitial pneumonia hypotensive disorder congestive heart failure non-small cell lung carcinoma cribriform carcinoma tuberculosis intracerebral hemorrhage pancreatic ductal adenocarcinoma cystic fibrosis

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.