4YV8

Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d4yv8a_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin K	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	Cysteine proteinases	8036608	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)
A	Peptidase_C1	e4yv8A1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Cathepsin K	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity collagen binding protein-containing complex binding binding enzyme regulator activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity collagen binding protein-containing complex binding binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity cysteine-type endopeptidase activator activity involved in apoptotic process molecular function regulator activity cysteine-type endopeptidase regulator activity involved in apoptotic process peptidase activator activity peptidase activator activity involved in apoptotic process protein binding fibronectin binding proteoglycan binding carbohydrate derivative binding	collagen catabolic process catabolic process metabolic process collagen metabolic process regulation of hormone levels organic hydroxy compound metabolic process cellular metabolic process biological regulation hormone metabolic process cellular modified amino acid metabolic process thyroid hormone metabolic process phenol-containing compound metabolic process cellular process regulation of biological quality collagen catabolic process catabolic process metabolic process collagen metabolic process regulation of hormone levels organic hydroxy compound metabolic process cellular metabolic process biological regulation hormone metabolic process cellular modified amino acid metabolic process thyroid hormone metabolic process phenol-containing compound metabolic process cellular process regulation of biological quality thyroid hormone generation 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 cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication apoptotic process programmed cell death positive regulation of signaling regulation of apoptotic signaling pathway immune response immune system process cellular response to endogenous stimulus cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to endogenous stimulus response to growth factor proteolysis involved in protein catabolic process proteolysis primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process cellular component organization cellular component disassembly extracellular matrix disassembly extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization multicellular organismal process ossification direct ossification intramembranous ossification response to alcohol response to chemical response to oxygen-containing compound response to ethanol response to peptide cellular response to tumor necrosis factor response to cytokine cellular response to cytokine stimulus response to tumor necrosis factor response to nutrient levels response to zinc ion starvation cellular response to starvation cellular response to nutrient levels cellular response to stress response to stress response to starvation cellular response to zinc ion starvation developmental process cellular developmental process hemopoiesis cell differentiation anatomical structure development cell development mononuclear cell differentiation leukocyte differentiation response to hormone response to peptide hormone response to insulin response to nitrogen compound regulation of cartilage development regulation of multicellular organismal development regulation of developmental process connective tissue development negative regulation of cartilage development negative regulation of developmental process animal organ development negative regulation of biological process tissue development multicellular organism development skeletal system development regulation of multicellular organismal process negative regulation of multicellular organismal process cartilage development system development response to organic cyclic compound cellular catabolic process mitophagy macroautophagy autophagy autophagy of mitochondrion process utilizing autophagic mechanism multicellular organismal-level homeostasis homeostatic process tissue remodeling bone remodeling anatomical structure homeostasis tissue homeostasis bone resorption	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane apical part of cell plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane apical part of cell plasma membrane region apical plasma membrane 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 intracellular vesicle endomembrane system endolysosome cytoplasmic vesicle endosome lumen vesicle endosome endolysosome lumen nucleus nucleoplasm nuclear lumen extracellular region extracellular space
B	Lichostatinal	-	-	-

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	IPR000668	Peptidase C1A, papain C-terminal	Domain
A	IPR013201	Cathepsin propeptide inhibitor domain (I29)	Domain
A	IPR025660	Cysteine peptidase, histidine active site	Active Site
A	IPR039417	Papain-like cysteine endopeptidase	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P43235	pycnodysostosis glioblastoma giant cell glioblastoma osteogenesis imperfecta osteosarcoma pancreatic intraductal papillary-mucinous carcinoma arthritic joint disease skin basal cell carcinoma Chronic hepatitis C ulcerative colitis diabetes mellitus intellectual disability medulloblastoma myopathy osteopetrosis pycnodysostosis glioblastoma giant cell glioblastoma osteogenesis imperfecta osteosarcoma pancreatic intraductal papillary-mucinous carcinoma arthritic joint disease skin basal cell carcinoma Chronic hepatitis C ulcerative colitis diabetes mellitus intellectual disability medulloblastoma myopathy osteopetrosis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia atopic eczema squamous cell carcinoma craniosynostosis Duchenne muscular dystrophy malignant glioma melanoma osteoarthritis osteoporosis pancreatic ductal adenocarcinoma pilocytic astrocytoma Sjogren syndrome breast cancer tuberculosis cystic fibrosis gastric carcinoma heart disease malignant pancreatic neoplasm metabolic syndrome X

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.