6YYP | pdb_00006yyp

Structure of Cathepsin S in complex with Compound 2

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B [auth BBB]	SCOP2B Superfamily	Cysteine proteinases	8042180	3001808	SCOP2B (2022-06-29)
A [auth AAA]	SCOP2B Superfamily	Cysteine proteinases	8042180	3001808	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)
B [auth BBB]	RNA_pol_Rpb1_5	e6yypBBB1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: RNA_pol_Rpb1_5	ECOD (develop294)
A [auth AAA]	RNA_pol_Rpb1_5	e6yypAAA1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: RNA_pol_Rpb1_5	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth AAA], B [auth BBB]	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 [auth AAA], B [auth BBB]	Cathepsin S	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity collagen binding protein-containing complex binding binding extracellular matrix binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity collagen binding protein-containing complex binding binding extracellular matrix binding protein binding laminin binding fibronectin binding proteoglycan binding carbohydrate derivative binding	collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process regulation of localization positive regulation of cation transmembrane transport regulation of cellular process transport monoatomic ion transmembrane transport positive regulation of biological process regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport monoatomic cation transmembrane transport collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process regulation of localization positive regulation of cation transmembrane transport regulation of cellular process transport monoatomic ion transmembrane transport positive regulation of biological process regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport monoatomic cation transmembrane transport localization positive regulation of molecular function positive regulation of monoatomic ion transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport monoatomic cation transport positive regulation of cellular process regulation of biological process regulation of transport regulation of monoatomic ion transport biological regulation positive regulation of cation channel activity establishment of localization transmembrane transport regulation of molecular function regulation of transmembrane transport positive regulation of transport positive regulation of transporter activity positive regulation of ion transmembrane transporter activity regulation of monoatomic cation transmembrane transport antigen processing and presentation regulation of antigen processing and presentation immune system process regulation of immune system process response to stimulus immune response adaptive immune response antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 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 cellular component organization cellular component disassembly extracellular matrix disassembly basement membrane disassembly extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization basement membrane organization primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing protein metabolic process macromolecule metabolic process cellular response to stimulus response to thyroid hormone response to endogenous stimulus cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical cellular response to thyroid hormone stimulus cellular response to hormone stimulus response to pH response to abiotic stimulus response to acidic pH regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms pattern recognition receptor signaling pathway regulation of response to external stimulus toll-like receptor signaling pathway signaling response to biotic stimulus cell communication positive regulation of response to stimulus immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of immune response regulation of response to stress response to stress innate immune response response to external biotic stimulus signal transduction positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of innate immune response defense response response to other organism regulation of innate immune response defense response to symbiont response to external stimulus regulation of response to stimulus defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response	membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm lysosome intracellular vesicle endomembrane system endolysosome cytoplasmic vesicle endosome lumen vesicle endosome endolysosome lumen phagocytic vesicle endocytic vesicle cell periphery extracellular matrix external encapsulating structure ficolin-1-rich granule ficolin-1-rich granule lumen secretory granule secretory vesicle tertiary granule lumen tertiary granule extracellular region late endosome extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth AAA], B [auth BBB]	IPR025661	Cysteine peptidase, asparagine active site	Active Site
A [auth AAA], B [auth BBB]	IPR000169	Cysteine peptidase, cysteine active site	Active Site
A [auth AAA], B [auth BBB]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A [auth AAA], B [auth BBB]	IPR013128	Peptidase C1A	Family
A [auth AAA], B [auth BBB]	IPR000668	Peptidase C1A, papain C-terminal	Domain
A [auth AAA], B [auth BBB]	IPR013201	Cathepsin propeptide inhibitor domain (I29)	Domain
A [auth AAA], B [auth BBB]	IPR025660	Cysteine peptidase, histidine active site	Active Site
A [auth AAA], B [auth BBB]	IPR039417	Papain-like cysteine endopeptidase	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth AAA], B [auth BBB]	Pharos: P25774	Neoplasm Invasiveness obesity disorder contact dermatitis malignant glioma pancreatic intraductal papillary-mucinous neoplasm Barrett esophagus pilocytic astrocytoma rheumatoid arthritis cystic fibrosis subependymal giant cell astrocytoma glioblastoma interstitial cystitis malignant colon neoplasm malignant pancreatic neoplasm nephrosclerosis Neoplasm Invasiveness obesity disorder contact dermatitis malignant glioma pancreatic intraductal papillary-mucinous neoplasm Barrett esophagus pilocytic astrocytoma rheumatoid arthritis cystic fibrosis subependymal giant cell astrocytoma glioblastoma interstitial cystitis malignant colon neoplasm malignant pancreatic neoplasm nephrosclerosis osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia plasma cell myeloma Crohn disease Sjogren syndrome diabetes mellitus tuberculosis heart disease invasive ductal breast carcinoma lung cancer malignant ependymoma MALT lymphoma non-small cell lung carcinoma ovarian cancer periodontitis prostate carcinoma cutaneous lupus erythematosus skin basal cell carcinoma esophageal adenocarcinoma IgA glomerulonephritis juvenile dermatomyositis lung carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth AAA], B [auth BBB]	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.