4DW2

The crystal structure of uPA in complex with the Fab fragment of mAb-112

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody 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]	d4dw2u_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Urokinase-type plasminogen activator (LMW U-PA), catalytic domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d4dw2h_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d4dw2l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d4dw2l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	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	Trypsin-like serine proteases	8042216	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 [auth U]	Trypsin_1	e4dw2U1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin_1	ECOD (1.6)
B [auth H]	V-set_8	e4dw2H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B [auth H]	C1-set_1	e4dw2H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C [auth L]	C1-set_4	e4dw2L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
C [auth L]	V-set	e4dw2L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth U]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B [auth H]	FAB FRAGMENT OF PRO-UPA ANTIBODY MAB-112	VH-CH1	Mus musculus (house mouse)	IGHV5-9-101, IGHV5-9-301, IGHJ401, IGHG102	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202442-0)
C [auth L]	FAB FRAGMENT OF PRO-UPA ANTIBODY MAB-112	L-KAPPA	Mus musculus (house mouse)	IGKV4-57-101, IGKJ101, IGKJ102, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202442-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV5	-	urokinase-type plasminogen activator	SAbDab (2024-10-25)
C [auth L]	Light Chain	IGKV4	Kappa	urokinase-type plasminogen activator	SAbDab (2024-10-25)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth U]	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 cellular biosynthetic process cellular metabolic process 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 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 protein maturation negative regulation of cellular metabolic process 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 cellular biosynthetic 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 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
B [auth H]	Fab fragment of pro-uPA antibody mAb-112	-	-	-
C [auth L]	Fab fragment of pro-uPA antibody mAb-112	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth U]	IPR018056	Kringle, conserved site	Conserved Site
A [auth U]	IPR000742	EGF-like domain	Domain
A [auth U]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A [auth U]	IPR013806	Kringle-like fold	Homologous Superfamily
A [auth U]	IPR038178	Kringle superfamily	Homologous Superfamily
A [auth U]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth U]	IPR001314	Peptidase S1A, chymotrypsin family	Family
A [auth U]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A [auth U]	IPR001254	Serine proteases, trypsin domain	Domain
A [auth U]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A [auth U]	IPR050127	Serine Proteases (Peptidase S1 Family)	Family
A [auth U]	IPR000001	Kringle	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth U]	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 nephritis anuria brain edema prostate cancer brain ischemia pulmonary embolism carotid artery disease middle cerebral artery infarction sagittal sinus thrombosis asthma pilocytic astrocytoma ischemia reperfusion injury bone cancer 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 osteosarcoma cribriform carcinoma of breast pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia invasive ductal breast carcinoma atopic eczema ischemic disease primitive neuroectodermal tumor gastric neoplasm malignant colon neoplasm cancer Alzheimer disease type 1 thrombotic disease interstitial lung disease ovarian cancer Crohn disease ulcerative colitis intracranial hemorrhage pancreatic neoplasm atypical teratoid rhabdoid tumor large cell medulloblastoma gastric cancer lung adenocarcinoma glioblastoma malignant ependymoma 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 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.