7QBM | pdb_00007qbm

Structure of the activation intermediate of cathepsin K in complex with the 3-cyano-3-aza-beta-amino acid inhibitor Gu2602

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	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)
B [auth P]	Peptidase_M4,Peptidase_M4_C	e7qbmP1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_M4,Peptidase_M4_C	ECOD (v294.1)

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 (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth P]	PF08246	Cathepsin propeptide inhibitor domain (I29) (Inhibitor_I29)	Cathepsin propeptide inhibitor domain (I29)	This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin Sw ...	This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin Swiss:Q70SU8. This family is classified as I29 by MEROPS.	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 [auth P]	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 protein binding 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 protein binding fibronectin binding proteoglycan binding carbohydrate derivative binding	collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process regulation of hormone levels phenol-containing compound metabolic process biological regulation modified amino acid metabolic process regulation of biological quality hormone metabolic process thyroid hormone generation thyroid hormone metabolic process cellular component organization collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process regulation of hormone levels phenol-containing compound metabolic process biological regulation modified amino acid metabolic process regulation of biological quality hormone metabolic process thyroid hormone generation thyroid hormone metabolic 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 developmental process multicellular organismal process regulation of cartilage development regulation of multicellular organismal development regulation of biological process 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 anatomical structure development regulation of multicellular organismal process negative regulation of multicellular organismal process cartilage development system development mitophagy macroautophagy autophagy autophagy of mitochondrion process utilizing autophagic mechanism proteolysis primary metabolic process protein metabolic process macromolecule metabolic process multicellular organismal-level homeostasis homeostatic process tissue remodeling bone remodeling anatomical structure homeostasis tissue homeostasis bone resorption	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane apical part of cell plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane apical part of cell plasma membrane region apical plasma membrane 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 organelle lumen organelle cytoplasm lysosome intracellular vesicle endomembrane system endolysosome cytoplasmic vesicle endosome lumen vesicle endosome endolysosome lumen nucleus nucleoplasm nuclear lumen extracellular region
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 protein binding 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 protein binding fibronectin binding proteoglycan binding carbohydrate derivative binding	collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process regulation of hormone levels phenol-containing compound metabolic process biological regulation modified amino acid metabolic process regulation of biological quality hormone metabolic process thyroid hormone generation thyroid hormone metabolic process cellular component organization collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process regulation of hormone levels phenol-containing compound metabolic process biological regulation modified amino acid metabolic process regulation of biological quality hormone metabolic process thyroid hormone generation thyroid hormone metabolic 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 developmental process multicellular organismal process regulation of cartilage development regulation of multicellular organismal development regulation of biological process 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 anatomical structure development regulation of multicellular organismal process negative regulation of multicellular organismal process cartilage development system development mitophagy macroautophagy autophagy autophagy of mitochondrion process utilizing autophagic mechanism proteolysis primary metabolic process protein metabolic process macromolecule metabolic process multicellular organismal-level homeostasis homeostatic process tissue remodeling bone remodeling anatomical structure homeostasis tissue homeostasis bone resorption	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane apical part of cell plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane apical part of cell plasma membrane region apical plasma membrane 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 organelle lumen organelle cytoplasm lysosome intracellular vesicle endomembrane system endolysosome cytoplasmic vesicle endosome lumen vesicle endosome endolysosome lumen nucleus nucleoplasm nuclear lumen extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth P]	IPR025661	Cysteine peptidase, asparagine active site	Active Site
B [auth P]	IPR000169	Cysteine peptidase, cysteine active site	Active Site
B [auth P]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
B [auth P]	IPR013128	Peptidase C1A	Family
B [auth P]	IPR000668	Peptidase C1A, papain C-terminal	Domain
B [auth P]	IPR013201	Cathepsin propeptide inhibitor domain (I29)	Domain
B [auth P]	IPR025660	Cysteine peptidase, histidine active site	Active Site
B [auth P]	IPR039417	Papain-like cysteine endopeptidase	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	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
B [auth P]	Pharos: P43235	pycnodysostosis glioblastoma giant cell glioblastoma osteogenesis imperfecta osteosarcoma pancreatic intraductal papillary-mucinous carcinoma skin basal cell carcinoma arthritic joint disease ulcerative colitis Chronic hepatitis C diabetes mellitus intellectual disability medulloblastoma myopathy osteopetrosis pycnodysostosis glioblastoma giant cell glioblastoma osteogenesis imperfecta osteosarcoma pancreatic intraductal papillary-mucinous carcinoma skin basal cell carcinoma arthritic joint disease ulcerative colitis Chronic hepatitis C diabetes mellitus intellectual disability medulloblastoma myopathy osteopetrosis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia squamous cell carcinoma atopic eczema craniosynostosis Duchenne muscular dystrophy malignant glioma melanoma osteoarthritis osteoporosis pancreatic ductal adenocarcinoma pilocytic astrocytoma Sjogren syndrome tuberculosis breast cancer cystic fibrosis gastric carcinoma heart disease malignant pancreatic neoplasm metabolic syndrome X
A	Pharos: P43235	pycnodysostosis glioblastoma giant cell glioblastoma osteogenesis imperfecta osteosarcoma pancreatic intraductal papillary-mucinous carcinoma skin basal cell carcinoma arthritic joint disease ulcerative colitis Chronic hepatitis C diabetes mellitus intellectual disability medulloblastoma myopathy osteopetrosis pycnodysostosis glioblastoma giant cell glioblastoma osteogenesis imperfecta osteosarcoma pancreatic intraductal papillary-mucinous carcinoma skin basal cell carcinoma arthritic joint disease ulcerative colitis Chronic hepatitis C diabetes mellitus intellectual disability medulloblastoma myopathy osteopetrosis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia squamous cell carcinoma atopic eczema craniosynostosis Duchenne muscular dystrophy malignant glioma melanoma osteoarthritis osteoporosis pancreatic ductal adenocarcinoma pilocytic astrocytoma Sjogren syndrome tuberculosis breast cancer 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.