1YWH | pdb_00001ywh

crystal structure of urokinase plasminogen activator receptor

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
O	d1ywho1	Small proteins	Snake toxin-like	Snake toxin-like	Extracellular domain of cell surface receptors	Urokinase plasminogen activator surface receptor uPAR	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
M	d1ywhm1	Small proteins	Snake toxin-like	Snake toxin-like	Extracellular domain of cell surface receptors	Urokinase plasminogen activator surface receptor uPAR	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d1ywhk1	Small proteins	Snake toxin-like	Snake toxin-like	Extracellular domain of cell surface receptors	Urokinase plasminogen activator surface receptor uPAR	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d1ywhi1	Small proteins	Snake toxin-like	Snake toxin-like	Extracellular domain of cell surface receptors	Urokinase plasminogen activator surface receptor uPAR	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d1ywhg1	Small proteins	Snake toxin-like	Snake toxin-like	Extracellular domain of cell surface receptors	Urokinase plasminogen activator surface receptor uPAR	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1ywhe1	Small proteins	Snake toxin-like	Snake toxin-like	Extracellular domain of cell surface receptors	Urokinase plasminogen activator surface receptor uPAR	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1ywhc1	Small proteins	Snake toxin-like	Snake toxin-like	Extracellular domain of cell surface receptors	Urokinase plasminogen activator surface receptor uPAR	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1ywha1	Small proteins	Snake toxin-like	Snake toxin-like	Extracellular domain of cell surface receptors	Urokinase plasminogen activator surface receptor uPAR	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)
O	SCOP2B Superfamily	Snake toxin-like	8032874	3000545	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Snake toxin-like	8032873	3000545	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Snake toxin-like	8032872	3000545	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Snake toxin-like	8032874	3000545	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Snake toxin-like	8032872	3000545	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Snake toxin-like	8032873	3000545	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Snake toxin-like	8032872	3000545	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Snake toxin-like	8032873	3000545	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Snake toxin-like	8032874	3000545	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Snake toxin-like	8032873	3000545	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Snake toxin-like	8032872	3000545	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Snake toxin-like	8032874	3000545	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Snake toxin-like	8032872	3000545	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Snake toxin-like	8032873	3000545	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Snake toxin-like	8032874	3000545	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Snake toxin-like	8032874	3000545	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Snake toxin-like	8032873	3000545	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Snake toxin-like	8032872	3000545	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Snake toxin-like	8032872	3000545	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Snake toxin-like	8032873	3000545	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Snake toxin-like	8032874	3000545	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Snake toxin-like	8032874	3000545	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Snake toxin-like	8032872	3000545	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Snake toxin-like	8032873	3000545	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)
O	UPAR_LY6	e1ywhO1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: UPAR_LY6	ECOD (v294.1)
O	Kunitz_BPTI	e1ywhO3	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Kunitz_BPTI	ECOD (v294.1)
M	UPAR_LY6	e1ywhM1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: UPAR_LY6	ECOD (v294.1)
M	Kunitz_BPTI	e1ywhM3	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Kunitz_BPTI	ECOD (v294.1)
K	UPAR_LY6	e1ywhK1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: UPAR_LY6	ECOD (v294.1)
K	Kunitz_BPTI	e1ywhK3	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Kunitz_BPTI	ECOD (v294.1)
I	UPAR_LY6	e1ywhI1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: UPAR_LY6	ECOD (v294.1)
I	Kunitz_BPTI	e1ywhI3	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Kunitz_BPTI	ECOD (v294.1)
G	UPAR_LY6	e1ywhG1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: UPAR_LY6	ECOD (v294.1)
G	Kunitz_BPTI	e1ywhG3	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Kunitz_BPTI	ECOD (v294.1)
E	UPAR_LY6	e1ywhE1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: UPAR_LY6	ECOD (v294.1)
E	Kunitz_BPTI	e1ywhE3	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Kunitz_BPTI	ECOD (v294.1)
C	UPAR_LY6	e1ywhC1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: UPAR_LY6	ECOD (v294.1)
C	Kunitz_BPTI	e1ywhC3	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Kunitz_BPTI	ECOD (v294.1)
A	UPAR_LY6	e1ywhA1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: UPAR_LY6	ECOD (v294.1)
A	Kunitz_BPTI	e1ywhA3	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Kunitz_BPTI	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
O	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
M	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
K	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
I	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
G	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
E	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
C	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
A	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K, M, O	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L, N, P	antagonist peptide	-	-	-
A, C, E, G, I A, C, E, G, I, K, M, O	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 regulation of protein 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 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 protein maturation regulation of plasminogen activation plasminogen activation zymogen activation regulation of biosynthetic process gene expression macromolecule 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 phosphate metabolic process positive regulation of metabolic process positive regulation of protein modification 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 urokinase plasminogen activator signaling pathway	cellular anatomical structure anchoring junction cell junction 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 cellular anatomical structure anchoring junction cell junction 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O	IPR045860	Snake toxin-like superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR016054	Ly-6 antigen/uPA receptor-like	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR018363	CD59 antigen, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I A, C, E, G, I, K, M, O	Pharos: Q03405	cancer carcinoma sarcomatoid carcinoma Inflammation prostate cancer juvenile idiopathic arthritis invasive ductal breast carcinoma lung carcinoma malignant glioma acute myeloid leukemia MALT lymphoma autism benign neoplasm pancreatic ductal adenocarcinoma peripheral neuropathy cancer carcinoma sarcomatoid carcinoma Inflammation prostate cancer juvenile idiopathic arthritis invasive ductal breast carcinoma lung carcinoma malignant glioma acute myeloid leukemia MALT lymphoma autism benign neoplasm pancreatic ductal adenocarcinoma peripheral neuropathy ductal breast carcinoma in situ gastric carcinoma undifferentiated carcinoma malignant colon neoplasm malignant mesothelioma oligodendroglioma breast cancer pancreatic intraductal papillary-mucinous neoplasm esophageal adenocarcinoma tuberculosis glioblastoma interstitial cystitis lung cancer malignant ependymoma malignant pancreatic neoplasm atypical teratoid rhabdoid tumor Barrett esophagus ovarian cancer peripheral nervous system disease cystic fibrosis gastric cancer ulcerative colitis hepatocellular carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D, F, H, J B, D, F, H, J, L, N, P	ALC	Parent Component: ALA
B, D, F, H, J B, D, F, H, J, L, N, P	DLY
B, D, F, H, J B, D, F, H, J, L, N, P	DSN	RESID: AA0195 , AA0624 PSI-MOD : D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987