5LHP

The p-aminobenzamidine active site inhibited catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory nanobody Nb7

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5lhpa_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Urokinase-type plasminogen activator (LMW U-PA), catalytic domain	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d5lhpb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
B	d5lhpb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Trypsin_1	e5lhpA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin_1	ECOD (1.6)
B	V-set_8	e5lhpB1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B	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	VHH Camelid Nb22	VH	Vicugna pacos (alpaca)	IGHV3S101, IGHJ101	V-DOMAIN VH	IG	VH	IMGT (202442-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV1	-	urokinase-type plasminogen activator	SAbDab (2024-10-25)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00089	Trypsin (Trypsin)	Trypsin	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Urokinase-type plasminogen activator	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity endopeptidase activity	regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation 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 developmental process multicellular organismal process regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation 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 developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis blood vessel development system development regulation of hepatocyte proliferation gland development liver development gland morphogenesis animal organ morphogenesis epithelial cell proliferation liver morphogenesis cell population proliferation animal organ development epithelial cell proliferation involved in liver morphogenesis hepatocyte proliferation regulation of cell population proliferation hepaticobiliary system development regulation of epithelial cell proliferation regulation of body fluid levels response to stimulus regulation of response to external stimulus negative regulation of biological process regulation of response to wounding regulation of coagulation response to stress regulation of response to stress coagulation regulation of multicellular organismal process regulation of biological quality response to wounding regulation of hemostasis wound healing negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation hemostasis response to external stimulus negative regulation of response to wounding blood coagulation 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 positive regulation of locomotion regulation of cell motility positive regulation of smooth muscle cell migration regulation of smooth muscle cell migration positive regulation of biological process positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration locomotion positive regulation of cellular process reactive oxygen species metabolic process regulation of cellular metabolic process positive regulation of cellular metabolic process positive regulation of reactive oxygen species metabolic process positive regulation of metabolic process regulation of metabolic process regulation of reactive oxygen species metabolic process 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 cellular biosynthetic process regulation of gene expression regulation of protein processing regulation of macromolecule biosynthetic process positive regulation of cell population proliferation positive regulation of coagulation 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 response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus tissue regeneration skeletal muscle tissue regeneration developmental growth growth regeneration 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 cellular response to stimulus cell surface receptor signaling pathway signaling cell communication urokinase plasminogen activator signaling pathway signal transduction	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane protein-containing complex serine protease inhibitor complex protease inhibitor complex peptidase inhibitor complex catalytic complex peptidase complex endopeptidase complex cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane 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 extracellular region extracellular space
B	Camelid-Derived Antibody Fragment	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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.