4WVP

Crystal structure of an activity-based probe HNE complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth E]	SCOP2B Superfamily	Trypsin-like serine proteases	8038248	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 E]	PF00089	e4wvpE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: PF00089	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth E]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E]	PF00089	Trypsin (Trypsin)	Trypsin	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E]	Neutrophil elastase	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 protein binding binding enzyme binding protease binding cytokine binding transcription corepressor activity 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 protein binding binding enzyme binding protease binding cytokine binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	neutrophil-mediated killing of symbiont cell biological process involved in interspecies interaction between organisms response to stimulus disruption of cell in another organism defense response to Gram-negative bacterium response to biotic stimulus myeloid leukocyte mediated immunity biological process involved in symbiotic interaction defense response to bacterium neutrophil mediated immunity response to stress response to bacterium leukocyte mediated immunity response to external biotic stimulus neutrophil-mediated killing of symbiont cell biological process involved in interspecies interaction between organisms response to stimulus disruption of cell in another organism defense response to Gram-negative bacterium response to biotic stimulus myeloid leukocyte mediated immunity biological process involved in symbiotic interaction defense response to bacterium neutrophil mediated immunity response to stress response to bacterium leukocyte mediated immunity response to external biotic stimulus biological process involved in interaction with symbiont killing of cells of another organism neutrophil-mediated killing of bacterium neutrophil mediated cytotoxicity response to other organism defense response response to external stimulus defense response to symbiont leukocyte mediated cytotoxicity immune effector process killing by host of symbiont cells neutrophil-mediated killing of gram-negative bacterium defense response to other organism immune system process cellular process disruption of anatomical structure in another organism cell killing chemotaxis negative regulation of locomotion regulation of biological process regulation of response to external stimulus negative regulation of response to stimulus biological regulation negative regulation of biological process negative regulation of chemotaxis regulation of chemotaxis taxis regulation of response to stimulus response to chemical regulation of locomotion negative regulation of response to external stimulus locomotion localization import into cell transport phagocytosis endocytosis establishment of localization vesicle-mediated transport immune response inflammatory response acute inflammatory response to antigenic stimulus acute inflammatory response inflammatory response to antigenic stimulus response to yeast response to fungus pyroptosis cell death programmed cell death organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis leukocyte migration cell migration leukocyte migration involved in inflammatory response cell motility multicellular organismal process regulation of cellular process cellular biosynthetic process negative regulation of chemokine production negative regulation of cellular metabolic process regulation of cytokine production organic substance biosynthetic process cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of chemokine production negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process chemokine production regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process regulation of metabolic process positive regulation of interleukin-8 production positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process interleukin-8 production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production positive regulation of cellular biosynthetic process regulation of interleukin-8 production response to light stimulus response to radiation response to abiotic stimulus response to UV cell population proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation negative regulation of interleukin-8 production antibacterial peptide production humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide antimicrobial peptide production biosynthetic process of antibacterial peptides active against Gram-negative bacteria production of molecular mediator of immune response antibacterial humoral response peptide biosynthetic process antibacterial peptide biosynthetic process antimicrobial peptide biosynthetic process peptide metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of response to stimulus positive regulation of immune response regulation of immune response regulation of immune system process positive regulation of immune system process neutrophil-mediated killing of fungus defense response to fungus regulation of defense response negative regulation of inflammatory response regulation of inflammatory response regulation of response to stress negative regulation of defense response cellular component organization cellular component disassembly extracellular matrix disassembly extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction positive regulation of phosphorylation regulation of catalytic activity regulation of signal transduction regulation of transferase activity positive regulation of phosphate metabolic process regulation of MAP kinase activity intracellular signal transduction cell communication positive regulation of protein serine/threonine kinase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process intracellular signaling cassette signal transduction phosphorus metabolic process protein modification process positive regulation of protein phosphorylation positive regulation of MAP kinase activity protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation positive regulation of MAPK cascade regulation of protein metabolic process positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation signaling positive regulation of protein metabolic process positive regulation of molecular function positive regulation of protein modification process regulation of intracellular signal transduction positive regulation of protein kinase activity regulation of signaling positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity MAPK cascade regulation of cell communication regulation of phosphorylation positive regulation of signaling regulation of cell motility positive regulation of leukocyte cell-cell adhesion regulation of leukocyte adhesion to vascular endothelial cell leukocyte cell-cell adhesion leukocyte tethering or rolling positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion positive regulation of leukocyte tethering or rolling cellular extravasation regulation of cell migration regulation of cell-cell adhesion positive regulation of cell adhesion regulation of cell adhesion regulation of leukocyte migration positive regulation of leukocyte adhesion to vascular endothelial cell regulation of leukocyte tethering or rolling leukocyte adhesion to vascular endothelial cell regulation of leukocyte cell-cell adhesion regulation of cellular extravasation proteolysis response to organic substance response to lipid response to oxygen-containing compound response to lipopolysaccharide response to molecule of bacterial origin	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix intracellular anatomical structure cytoplasm cytosol intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle secretory granule secretory vesicle vesicle lumen membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular organelle lumen organelle lumen specific granule lumen specific granule cell surface phagocytic vesicle endocytic vesicle lytic vacuole vacuolar lumen lysosome azurophil granule vacuole azurophil granule lumen primary lysosome protein-containing complex transcription regulator complex transcription repressor complex
B [auth I]	BTN-3V3-NLB-OMT-OIC-3V2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A [auth E]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth E]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A [auth E]	IPR001254	Serine proteases, trypsin domain	Domain
A [auth E]	IPR001314	Peptidase S1A, chymotrypsin family	Family
A [auth E]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth E]	Pharos: P08246	cyclic hematopoiesis neutropenia neutropenia, severe congenital, 1, autosomal dominant severe congenital neutropenia periodic fever syndrome acute lung injury alpha 1-antitrypsin deficiency bronchiectasis Cytopenia lung disease primary biliary cholangitis acute myeloid leukemia atopic eczema congenital anemia hematopoietic and lymphoid system neoplasm cyclic hematopoiesis neutropenia neutropenia, severe congenital, 1, autosomal dominant severe congenital neutropenia periodic fever syndrome acute lung injury alpha 1-antitrypsin deficiency bronchiectasis Cytopenia lung disease primary biliary cholangitis acute myeloid leukemia atopic eczema congenital anemia hematopoietic and lymphoid system neoplasm lymphoplasmacytic lymphoma osteosarcoma psoriasis agranulocytosis autosomal dominant severe congenital neutropenia cystic fibrosis leukopenia

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth I]	3V2
B [auth I]	3V3
B [auth I]	BTN	RESID: AA0117 PSI-MOD : N6-biotinyl-L-lysine MOD:00126
B [auth I]	NLB	Parent Component: LEU RESID: AA0117
B [auth I]	OIC	RESID: AA0117
B [auth I]	OMT	Parent Component: MET RESID: AA0117 , AA0251 PSI-MOD : N6-biotinyl-L-lysine MOD:00126 , L-methionine sulfone MOD:00256

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 R01GM133198.