1CSB | pdb_00001csb

Crystal structure of cathepsin b inhibited with CA030 at 2.1 angstroms resolution: A basis for the design of specific epoxysuccinyl inhibitors

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)
D [auth E]	d1csb.2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin B	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1csb.1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin B	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth D]	d1csb.2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin B	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1csb.1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin B	(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)
D [auth E]	SCOP2B Superfamily	Cysteine proteinases	8042211	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8042211	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)
D [auth E]		e1csbE01	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
B		e1csbB01	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
C [auth D]		e1csbD01	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
A		e1csbA01	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth E]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
B	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
C [auth D]	1.20.5.170	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	1.20.5.170	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D [auth E]	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, D [auth E]	CATHEPSIN B heavy chain	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity collagen binding protein-containing complex binding binding protein 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 biological process involved in interspecies interaction between organisms 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 biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction regulation of biological process regulation of cellular process regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death developmental process epithelium development cellular developmental process cell differentiation anatomical structure development tissue development epithelial cell differentiation multi-multicellular organism process multicellular organismal process placenta development reproductive process maternal process involved in female pregnancy multicellular organismal reproductive process animal organ development developmental process involved in reproduction maternal placenta development female pregnancy multi-organism reproductive process decidualization cellular response to stimulus response to thyroid hormone response to stimulus 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 proteolysis primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle apical part of cell plasma membrane region apical plasma membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle membrane-enclosed lumen lytic vacuole vacuolar lumen endomembrane system intracellular organelle lumen endolysosome endosome lumen lysosome endosome vacuole lysosomal lumen organelle lumen endolysosome lumen extracellular matrix external encapsulating structure ficolin-1-rich granule ficolin-1-rich granule lumen secretory granule secretory vesicle protein-containing complex peptidase inhibitor complex perinuclear region of cytoplasm
A, C [auth D]	CATHEPSIN B light chain	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity collagen binding protein-containing complex binding binding protein 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 biological process involved in interspecies interaction between organisms 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 biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction regulation of biological process regulation of cellular process regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death developmental process epithelium development cellular developmental process cell differentiation anatomical structure development tissue development epithelial cell differentiation multi-multicellular organism process multicellular organismal process placenta development reproductive process maternal process involved in female pregnancy multicellular organismal reproductive process animal organ development developmental process involved in reproduction maternal placenta development female pregnancy multi-organism reproductive process decidualization cellular response to stimulus response to thyroid hormone response to stimulus 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 proteolysis primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle apical part of cell plasma membrane region apical plasma membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle membrane-enclosed lumen lytic vacuole vacuolar lumen endomembrane system intracellular organelle lumen endolysosome endosome lumen lysosome endosome vacuole lysosomal lumen organelle lumen endolysosome lumen extracellular matrix external encapsulating structure ficolin-1-rich granule ficolin-1-rich granule lumen secretory granule secretory vesicle protein-containing complex peptidase inhibitor complex perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D [auth E]	IPR025661	Cysteine peptidase, asparagine active site	Active Site
B, D [auth E]	IPR000169	Cysteine peptidase, cysteine active site	Active Site
B, D [auth E]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
B, D [auth E]	IPR012599	Peptidase C1A, propeptide	Domain
B, D [auth E]	IPR013128	Peptidase C1A	Family
B, D [auth E]	IPR000668	Peptidase C1A, papain C-terminal	Domain
B, D [auth E]	IPR025660	Cysteine peptidase, histidine active site	Active Site
A, C [auth D]	IPR025661	Cysteine peptidase, asparagine active site	Active Site
A, C [auth D]	IPR000169	Cysteine peptidase, cysteine active site	Active Site
A, C [auth D]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, C [auth D]	IPR012599	Peptidase C1A, propeptide	Domain
A, C [auth D]	IPR013128	Peptidase C1A	Family
A, C [auth D]	IPR000668	Peptidase C1A, papain C-terminal	Domain
A, C [auth D]	IPR025660	Cysteine peptidase, histidine active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D [auth E]	Pharos: P07858	myopathy glioblastoma renal cell carcinoma chromophobe renal cell carcinoma collecting duct carcinoma proteinuria sarcomatoid renal cell carcinoma giant cell glioblastoma Necrosis prostate cancer keratolytic winter erythema papillary renal cell carcinoma invasive ductal breast carcinoma large cell medulloblastoma lung carcinoma myopathy glioblastoma renal cell carcinoma chromophobe renal cell carcinoma collecting duct carcinoma proteinuria sarcomatoid renal cell carcinoma giant cell glioblastoma Necrosis prostate cancer keratolytic winter erythema papillary renal cell carcinoma invasive ductal breast carcinoma large cell medulloblastoma lung carcinoma medulloblastoma Alzheimer disease breast cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm polycystic ovary syndrome cystic fibrosis juvenile dermatomyositis leprosy malignant mesothelioma muscle tissue disease astrocytic tumor breast carcinoma ovarian cancer pancreatitis renal carcinoma dilated cardiomyopathy subependymal giant cell astrocytoma Duchenne muscular dystrophy lung cancer malignant pancreatic neoplasm muscular disease atypical teratoid rhabdoid tumor cancer pancreatic ductal adenocarcinoma clear cell renal carcinoma cutaneous lupus erythematosus testicular germ cell tumor gastric carcinoma
A, C [auth D]	Pharos: P07858	myopathy glioblastoma renal cell carcinoma chromophobe renal cell carcinoma collecting duct carcinoma proteinuria sarcomatoid renal cell carcinoma giant cell glioblastoma Necrosis prostate cancer keratolytic winter erythema papillary renal cell carcinoma invasive ductal breast carcinoma large cell medulloblastoma lung carcinoma myopathy glioblastoma renal cell carcinoma chromophobe renal cell carcinoma collecting duct carcinoma proteinuria sarcomatoid renal cell carcinoma giant cell glioblastoma Necrosis prostate cancer keratolytic winter erythema papillary renal cell carcinoma invasive ductal breast carcinoma large cell medulloblastoma lung carcinoma medulloblastoma Alzheimer disease breast cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm polycystic ovary syndrome cystic fibrosis juvenile dermatomyositis leprosy malignant mesothelioma muscle tissue disease astrocytic tumor breast carcinoma ovarian cancer pancreatitis renal carcinoma dilated cardiomyopathy subependymal giant cell astrocytoma Duchenne muscular dystrophy lung cancer malignant pancreatic neoplasm muscular disease atypical teratoid rhabdoid tumor cancer pancreatic ductal adenocarcinoma clear cell renal carcinoma cutaneous lupus erythematosus testicular germ cell tumor gastric carcinoma

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.