Annotations: 1K3B

Crystal Structure of Human Dipeptidyl Peptidase I (Cathepsin C): Exclusion Domain Added to an Endopeptidase Framework Creates the Machine for Activation of Granular Serine Proteases

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1k3ba_	All beta proteins	Streptavidin-like	Dipeptidyl peptidase I (cathepsin C), exclusion domain	Dipeptidyl peptidase I (cathepsin C), exclusion domain	Dipeptidyl peptidase I (cathepsin C), exclusion domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1k3b.1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	Cathepsin C (dipeptidyl peptidase I), catalytic domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1k3b.1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	Cathepsin C (dipeptidyl peptidase I), catalytic domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

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	Autotransporter	e1k3bA1	A: alpha arrays	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Autotransporter	ECOD (v295)
C	Flu_M2	e1k3bC1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Flu_M2	ECOD (v295)
B	Penicil_amidase	e1k3bB01	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Penicil_amidase	ECOD (v295)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.128.80	Mainly Beta	Beta Barrel	Lipocalin	Cathepsin C, exclusion domain	CATH (4.3.0)
C	2.40.50.170	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Cysteine proteinases. Chain C	CATH (4.3.0)
B	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 be ...	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
B	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
A	dipeptydil-peptidase I exclusion domain	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	response to stimulus immune response immune system 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 cellular process cell killing proteolysis response to stimulus immune response immune system 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 cellular process cell killing proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle 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 extracellular matrix external encapsulating structure endoplasmic reticulum lumen endoplasmic reticulum bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment organelle membrane
C	dipeptydil-peptidase I 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	response to stimulus immune response immune system 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 cellular process cell killing proteolysis response to stimulus immune response immune system 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 cellular process cell killing proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle 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 extracellular matrix external encapsulating structure endoplasmic reticulum lumen endoplasmic reticulum bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment organelle membrane
B	dipeptydil-peptidase I 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	response to stimulus immune response immune system 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 cellular process cell killing proteolysis response to stimulus immune response immune system 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 cellular process cell killing proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle 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 extracellular matrix external encapsulating structure 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
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
C	IPR025661	Cysteine peptidase, asparagine active site	Active Site
C	IPR000169	Cysteine peptidase, cysteine active site	Active Site
C	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
C	IPR013128	Peptidase C1A	Family
C	IPR039412	Cathepsin C	Domain
C	IPR036496	Cathepsin C, exclusion domain superfamily	Homologous Superfamily
C	IPR000668	Peptidase C1A, papain C-terminal	Domain
C	IPR025660	Cysteine peptidase, histidine active site	Active Site
C	IPR014882	Cathepsin C exclusion	Domain
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: 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 adenoma lymphoplasmacytic lymphoma atopic eczema 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 adenoma lymphoplasmacytic lymphoma atopic eczema malignant mesothelioma 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
C	: 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 adenoma lymphoplasmacytic lymphoma atopic eczema 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 adenoma lymphoplasmacytic lymphoma atopic eczema malignant mesothelioma 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
B	: 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 adenoma lymphoplasmacytic lymphoma atopic eczema 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 adenoma lymphoplasmacytic lymphoma atopic eczema malignant mesothelioma 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