Annotations: 4D3Z

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Legumain-like	8049301	4006439	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Caspase-like	8104075	3001096	SCOP2 (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	KOG1348	e4d3zA1	A: alpha arrays	X: Legumain prodomain (From Topology)	H: Legumain prodomain (From Topology)	T: Legumain prodomain	F: KOG1348	ECOD (1.6)
A	Peptidase_C13	e4d3zA2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C13	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	1.10.132.130	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01650	Peptidase C13 family (Peptidase_C13)	Peptidase C13 family	-	Family
A	PF20985	Legumain, prodomain (Legum_prodom)	Legumain, prodomain	This domain is found in the proenzyme form of Vacuolar-processing enzyme (VPE), known as legumain. VPE is an asparagine-specific endopeptidase that plays important roles in many physiological processes, including the maturation of toll-like receptors ...	This domain is found in the proenzyme form of Vacuolar-processing enzyme (VPE), known as legumain. VPE is an asparagine-specific endopeptidase that plays important roles in many physiological processes, including the maturation of toll-like receptors 3/7/9. The mature active form of VPE is generated by autoproteolytic maturation at acidic pH. In the three-dimensional structure of the proenzyme, this prodomain is located on top of the protease domain, blocking access to the active site. It shows an entirely alpha-helical fold, with an activation peptide and a region that assemblies into a death domain-like fold at its C-terminal end [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PROLEGUMAIN	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity endopeptidase regulator activity	organic substance metabolic process organonitrogen compound metabolic process proteolysis self proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process multicellular organismal process renal system process system process positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission organic substance metabolic process organonitrogen compound metabolic process proteolysis self proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process multicellular organismal process renal system process system process positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process cell communication long-term synaptic potentiation synaptic signaling positive regulation of long-term synaptic potentiation regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling regulation of biological process regulation of signaling biological regulation cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of long-term synaptic potentiation regulation of cell communication cellular process positive regulation of signaling organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process organic substance catabolic process antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II immune system process antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous antigen behavior learning or memory nervous system process cognition memory neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process developmental process regulation of multicellular organism growth regulation of growth regulation of developmental growth negative regulation of multicellular organism growth regulation of developmental process developmental growth negative regulation of developmental process growth multicellular organism growth negative regulation of developmental growth negative regulation of growth regulation of multicellular organismal process negative regulation of multicellular organismal process cellular response to stimulus cellular response to inorganic substance cellular response to metal ion response to stimulus response to inorganic substance cellular response to chemical stimulus response to metal ion response to chemical cellular response to calcium ion response to calcium ion cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of locomotion regulation of cell motility regulation of response to external stimulus endothelial cell migration positive regulation of chemotaxis positive regulation of cell migration positive regulation of epithelial cell migration positive regulation of response to stimulus tissue migration positive regulation of response to external stimulus taxis ameboidal-type cell migration positive regulation of cell motility regulation of cell migration positive regulation of endothelial cell chemotaxis regulation of endothelial cell migration epithelial cell migration cell migration endothelial cell chemotaxis cell motility locomotion regulation of epithelial cell migration cell chemotaxis chemotaxis regulation of endothelial cell chemotaxis response to external stimulus regulation of chemotaxis epithelium migration regulation of response to stimulus regulation of locomotion positive regulation of endothelial cell migration cellular component organization cell junction organization dendritic spine organization postsynapse organization plasma membrane bounded cell projection organization cell projection organization neuron projection organization synapse organization cellular component organization or biogenesis positive regulation of monocyte chemotaxis regulation of monocyte chemotaxis 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 regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte migration positive regulation of leukocyte chemotaxis monocyte chemotaxis leukocyte migration mononuclear cell migration leukocyte chemotaxis cellular biosynthetic process cellular metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process organic substance biosynthetic process learning associative learning negative regulation of signaling negative regulation of ERBB signaling pathway regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication signal transduction enzyme-linked receptor protein signaling pathway regulation of ERBB signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction ERBB signaling pathway cellular response to endogenous stimulus response to hepatocyte growth factor cellular response to growth factor stimulus cellular response to hepatocyte growth factor stimulus response to endogenous stimulus response to growth factor negative regulation of cellular metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of cell cycle mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle cell cycle regulation of cell cycle response to pH response to abiotic stimulus response to acidic pH cellular response to nitrogen compound response to organic substance response to organonitrogen compound response to oxygen-containing compound response to nitrogen compound cellular response to amyloid-beta cellular response to oxygen-containing compound cellular response to organonitrogen compound cellular response to organic substance response to amyloid-beta receptor catabolic process cellular catabolic process receptor metabolic process	apical part of cell cellular anatomical entity membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle apical part of cell cellular anatomical entity membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular region perinuclear region of cytoplasm endosome intracellular vesicle endomembrane system cytoplasmic vesicle late endosome vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR046427	Legumain prodomain superfamily	Homologous Superfamily
A	IPR048501	Legumain, prodomain	Domain
A	IPR001096	Peptidase C13, legumain	Family
A	IPR043577	Asparaginyl endopeptidase	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	CSX	Parent Component: CYS RESID: AA0451 PSI-MOD : 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380
A	SNN	Parent Component: ASN RESID: AA0451 , AA0302 , AA0593 PSI-MOD : 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380 , L-aspartimide MOD:00307 , 2-(2-aminosuccinimidyl)pentanedioic acid (Asn) MOD:01940 , 2-(2-aminosuccinimidyl)pentanedioic acid (Asp) MOD:01941

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.