4OEM | pdb_00004oem

Crystal structure of Cathepsin C in complex with dipeptide substrates

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Dipeptidyl peptidase I (cathepsin C), exclusion domain	8039797	3000840	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	CathepsinC_exc	e4oemA1	A: beta barrels	X: Lipocalins/Streptavidin	H: Dipeptidyl peptidase I (cathepsin C), exclusion domain (From Topology)	T: Dipeptidyl peptidase I (cathepsin C), exclusion domain	F: CathepsinC_exc	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.40.50.170	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Cysteine proteinases. Chain C	CATH (4.3.0)
A	2.40.128.80	Mainly Beta	Beta Barrel	Lipocalin	Cathepsin C, exclusion domain	CATH (4.3.0)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08773	Cathepsin C exclusion domain (CathepsinC_exc)	Cathepsin C exclusion domain	Cathepsin C (dipeptidyl peptidase I) is the physiological activator of a group of serine proteases. This domain corresponds to the exclusion domain whose structure excludes the approach of a polypeptide apart from its termini. It forms an enclosed ...	Cathepsin C (dipeptidyl peptidase I) is the physiological activator of a group of serine proteases. This domain corresponds to the exclusion domain whose structure excludes the approach of a polypeptide apart from its termini. It forms an enclosed beta barrel structure composed from 8 anti-parallel beta strands [1]. Based on a structural comparison and interaction data, it is suggested that the exclusion domain originates from a metallo-protease inhibitor [1].	Domain
A	PF00112	Papain family cysteine protease (Peptidase_C1)	Papain family cysteine protease		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Dipeptidyl peptidase 1 Light chain	peptidase activity catalytic activity, acting on a protein dipeptidyl-peptidase activity hydrolase activity exopeptidase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity protein binding binding peptidase activity catalytic activity, acting on a protein dipeptidyl-peptidase activity hydrolase activity exopeptidase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity protein binding binding protein-folding chaperone binding ion binding anion binding chloride ion binding small molecule binding phosphatase binding enzyme binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity peptidase activator activity involved in apoptotic process identical protein binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction positive regulation of cellular process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of programmed cell death regulation of apoptotic process biological regulation cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication cellular process apoptotic process programmed cell death positive regulation of signaling regulation of apoptotic signaling pathway immune response immune system process catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of proteolysis metabolic process macromolecule metabolic process regulation of metabolic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains T cell mediated cytotoxicity lymphocyte mediated immunity T cell mediated immunity leukocyte mediated cytotoxicity adaptive immune response immune effector process leukocyte mediated immunity cell killing multicellular organismal process negative regulation of nervous system process system process regulation of developmental process regulation of myelination regulation of system process negative regulation of biological process regulation of nervous system development multicellular organism development axon ensheathment ensheathment of neurons anatomical structure development negative regulation of cellular process regulation of multicellular organismal process system development developmental process regulation of multicellular organismal development nervous system process nervous system development regulation of nervous system process myelination negative regulation of myelination negative regulation of multicellular organismal process regulation of macrophage activation regulation of defense response positive regulation of macrophage activation regulation of response to external stimulus regulation of leukocyte activation positive regulation of microglial cell activation regulation of cell activation positive regulation of neuroinflammatory response myeloid leukocyte activation leukocyte activation macrophage activation positive regulation of cell activation positive regulation of response to external stimulus positive regulation of inflammatory response response to stress regulation of response to stress leukocyte activation involved in inflammatory response regulation of neuroinflammatory response positive regulation of leukocyte activation regulation of immune system process positive regulation of immune system process defense response cell activation response to external stimulus regulation of inflammatory response positive regulation of defense response positive regulation of multicellular organismal process microglial cell activation inflammatory response glial cell activation regulation of microglial cell activation neuroinflammatory response	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle centrosome microtubule organizing center cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton intracellular membrane-bounded organelle intracellular vesicle COPII-coated ER to Golgi transport vesicle cytoplasmic vesicle coated vesicle cytoplasm lytic vacuole membrane-enclosed lumen cytoplasmic vesicle lumen vacuolar lumen endomembrane system intracellular organelle lumen lysosome vesicle lumen azurophil granule vacuole secretory granule lumen azurophil granule lumen organelle lumen secretory granule primary lysosome secretory vesicle nucleus nucleoplasm nuclear lumen endoplasmic reticulum lumen endoplasmic reticulum bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment organelle membrane
A	Dipeptidyl peptidase 1 Heavy chain	peptidase activity catalytic activity, acting on a protein dipeptidyl-peptidase activity hydrolase activity exopeptidase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity protein binding binding peptidase activity catalytic activity, acting on a protein dipeptidyl-peptidase activity hydrolase activity exopeptidase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity protein binding binding protein-folding chaperone binding ion binding anion binding chloride ion binding small molecule binding phosphatase binding enzyme binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity peptidase activator activity involved in apoptotic process identical protein binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction positive regulation of cellular process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of programmed cell death regulation of apoptotic process biological regulation cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication cellular process apoptotic process programmed cell death positive regulation of signaling regulation of apoptotic signaling pathway immune response immune system process catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of proteolysis metabolic process macromolecule metabolic process regulation of metabolic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains T cell mediated cytotoxicity lymphocyte mediated immunity T cell mediated immunity leukocyte mediated cytotoxicity adaptive immune response immune effector process leukocyte mediated immunity cell killing multicellular organismal process negative regulation of nervous system process system process regulation of developmental process regulation of myelination regulation of system process negative regulation of biological process regulation of nervous system development multicellular organism development axon ensheathment ensheathment of neurons anatomical structure development negative regulation of cellular process regulation of multicellular organismal process system development developmental process regulation of multicellular organismal development nervous system process nervous system development regulation of nervous system process myelination negative regulation of myelination negative regulation of multicellular organismal process regulation of macrophage activation regulation of defense response positive regulation of macrophage activation regulation of response to external stimulus regulation of leukocyte activation positive regulation of microglial cell activation regulation of cell activation positive regulation of neuroinflammatory response myeloid leukocyte activation leukocyte activation macrophage activation positive regulation of cell activation positive regulation of response to external stimulus positive regulation of inflammatory response response to stress regulation of response to stress leukocyte activation involved in inflammatory response regulation of neuroinflammatory response positive regulation of leukocyte activation regulation of immune system process positive regulation of immune system process defense response cell activation response to external stimulus regulation of inflammatory response positive regulation of defense response positive regulation of multicellular organismal process microglial cell activation inflammatory response glial cell activation regulation of microglial cell activation neuroinflammatory response	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle centrosome microtubule organizing center cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton intracellular membrane-bounded organelle intracellular vesicle COPII-coated ER to Golgi transport vesicle cytoplasmic vesicle coated vesicle cytoplasm lytic vacuole membrane-enclosed lumen cytoplasmic vesicle lumen vacuolar lumen endomembrane system intracellular organelle lumen lysosome vesicle lumen azurophil granule vacuole secretory granule lumen azurophil granule lumen organelle lumen secretory granule primary lysosome secretory vesicle nucleus nucleoplasm nuclear lumen endoplasmic reticulum lumen endoplasmic reticulum bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR025661	Cysteine peptidase, asparagine active site	Active Site
B	IPR000169	Cysteine peptidase, cysteine active site	Active Site
B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
B	IPR013128	Peptidase C1A	Family
B	IPR039412	Cathepsin C	Domain
B	IPR036496	Cathepsin C, exclusion domain superfamily	Homologous Superfamily
B	IPR000668	Peptidase C1A, papain C-terminal	Domain
B	IPR025660	Cysteine peptidase, histidine active site	Active Site
B	IPR014882	Cathepsin C exclusion	Domain
A	IPR025661	Cysteine peptidase, asparagine active site	Active Site
A	IPR000169	Cysteine peptidase, cysteine active site	Active Site
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR013128	Peptidase C1A	Family
A	IPR039412	Cathepsin C	Domain
A	IPR036496	Cathepsin C, exclusion domain superfamily	Homologous Superfamily
A	IPR000668	Peptidase C1A, papain C-terminal	Domain
A	IPR025660	Cysteine peptidase, histidine active site	Active Site
A	IPR014882	Cathepsin C exclusion	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P53634	Haim-Munk syndrome Papillon-Lefevre disease periodontitis, aggressive 1 periodontal disease periodontitis allergic contact dermatitis palmoplantar keratosis gastric carcinoma subependymal giant cell astrocytoma Haim-Monk Syndrome interstitial cystitis large cell medulloblastoma lymphoplasmacytic lymphoma adenoma malignant mesothelioma Haim-Munk syndrome Papillon-Lefevre disease periodontitis, aggressive 1 periodontal disease periodontitis allergic contact dermatitis palmoplantar keratosis gastric carcinoma subependymal giant cell astrocytoma Haim-Monk Syndrome interstitial cystitis large cell medulloblastoma lymphoplasmacytic lymphoma adenoma malignant mesothelioma atopic eczema chronic obstructive pulmonary disease medulloblastoma cutaneous lupus erythematosus ovarian cancer diabetes mellitus pancreatic intraductal papillary-mucinous neoplasm Duchenne muscular dystrophy exocrine pancreatic carcinoma psoriasis gastric neoplasm type 2 diabetes mellitus invasive ductal breast carcinoma lung adenocarcinoma malignant ependymoma atypical teratoid rhabdoid tumor congestive heart failure myocardial ischemia cystic fibrosis ectodermal dysplasia syndrome gastric cancer Sjogren syndrome glioblastoma ulcerative colitis hereditary diffuse gastric adenocarcinoma juvenile dermatomyositis lung carcinoma malignant glioma breast carcinoma malignant pancreatic neoplasm coronary artery disease nasopharyngeal carcinoma dermatomyositis pancreatic ductal adenocarcinoma endometriosis pilocytic astrocytoma
A	Pharos: P53634	Haim-Munk syndrome Papillon-Lefevre disease periodontitis, aggressive 1 periodontal disease periodontitis allergic contact dermatitis palmoplantar keratosis gastric carcinoma subependymal giant cell astrocytoma Haim-Monk Syndrome interstitial cystitis large cell medulloblastoma lymphoplasmacytic lymphoma adenoma malignant mesothelioma Haim-Munk syndrome Papillon-Lefevre disease periodontitis, aggressive 1 periodontal disease periodontitis allergic contact dermatitis palmoplantar keratosis gastric carcinoma subependymal giant cell astrocytoma Haim-Monk Syndrome interstitial cystitis large cell medulloblastoma lymphoplasmacytic lymphoma adenoma malignant mesothelioma atopic eczema chronic obstructive pulmonary disease medulloblastoma cutaneous lupus erythematosus ovarian cancer diabetes mellitus pancreatic intraductal papillary-mucinous neoplasm Duchenne muscular dystrophy exocrine pancreatic carcinoma psoriasis gastric neoplasm type 2 diabetes mellitus invasive ductal breast carcinoma lung adenocarcinoma malignant ependymoma atypical teratoid rhabdoid tumor congestive heart failure myocardial ischemia cystic fibrosis ectodermal dysplasia syndrome gastric cancer Sjogren syndrome glioblastoma ulcerative colitis hereditary diffuse gastric adenocarcinoma juvenile dermatomyositis lung carcinoma malignant glioma breast carcinoma malignant pancreatic neoplasm coronary artery disease nasopharyngeal carcinoma dermatomyositis pancreatic ductal adenocarcinoma endometriosis pilocytic astrocytoma

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.