3KSE

Unreduced cathepsin L in complex with stefin A

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3ksed_	Alpha and beta proteins (a+b)	Cystatin-like	Cystatin/monellin	Cystatins	Cystatin A (stefin A)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3ksee_	Alpha and beta proteins (a+b)	Cystatin-like	Cystatin/monellin	Cystatins	Cystatin A (stefin A)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3ksef_	Alpha and beta proteins (a+b)	Cystatin-like	Cystatin/monellin	Cystatins	Cystatin A (stefin A)	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)
D	SCOP2B Superfamily	Cystatin/monellin	8043729	3000441	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cystatin/monellin	8043729	3000441	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cystatin/monellin	8043729	3000441	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	PF00112	e3kseA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00112	ECOD (1.6)
B	PF00112	e3kseB1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00112	ECOD (1.6)
C	PF00112	e3kseC1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00112	ECOD (1.6)
D	PF00031	e3kseD1	A: a+b two layers	X: Cystatin-like	H: Cystatin/monellin (From Topology)	T: Cystatin/monellin	F: PF00031	ECOD (1.6)
E	PF00031	e3kseE1	A: a+b two layers	X: Cystatin-like	H: Cystatin/monellin (From Topology)	T: Cystatin/monellin	F: PF00031	ECOD (1.6)
F	PF00031	e3kseF1	A: a+b two layers	X: Cystatin-like	H: Cystatin/monellin (From Topology)	T: Cystatin/monellin	F: PF00031	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)
B	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
C	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
D	3.10.450.10	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
E	3.10.450.10	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
F	3.10.450.10	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00112	Papain family cysteine protease (Peptidase_C1)	Papain family cysteine protease	-	Domain
D, E, F	PF00031	Cystatin domain (Cystatin)	Cystatin domain	Very diverse family. Attempts to define separate sub-families failed. Typically, either the N-terminal or C-terminal end is very divergent. But splitting into two domains would make very short families. All members except Swiss:Q03196 and Swiss:Q1 ...	Very diverse family. Attempts to define separate sub-families failed. Typically, either the N-terminal or C-terminal end is very divergent. But splitting into two domains would make very short families. All members except Swiss:Q03196 and Swiss:Q10993 are found. Pfam:PF00666 are related to this family but have not been included.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Cathepsin L1	protein binding binding histone binding serpin family protein binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity cysteine-type endopeptidase activator activity involved in apoptotic process protein binding binding histone binding serpin family protein binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity 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 fibronectin binding cysteine-type endopeptidase activity endopeptidase activity collagen binding protein-containing complex binding proteoglycan binding carbohydrate derivative binding	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein autoprocessing biosynthetic process proteolysis organic substance biosynthetic process protein processing metabolic process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein autoprocessing biosynthetic process proteolysis organic substance biosynthetic process protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process response to stimulus immune response immune system process adaptive immune response cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction 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 biological regulation 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 organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process organic substance catabolic process response to organic substance 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 organic substance cellular response to thyroid hormone stimulus cellular response to hormone stimulus 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 fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell collagen catabolic process collagen metabolic process peptide hormone processing enkephalin processing signaling receptor ligand precursor processing amide metabolic process regulation of biological quality regulation of hormone levels hormone metabolic process import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport localization endocytosis involved in viral entry into host cell endocytosis receptor-mediated endocytosis transport of virus antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation 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 membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular component organization or biogenesis carbohydrate derivative catabolic process glycoprotein catabolic process elastin catabolic process carbohydrate derivative metabolic process glycoprotein metabolic process elastin metabolic process CD4-positive or CD8-positive, alpha-beta T cell lineage commitment multicellular organismal process cellular developmental process cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation CD4-positive, alpha-beta T cell differentiation leukocyte activation alpha-beta T cell differentiation T cell activation cell differentiation CD4-positive, alpha-beta T cell activation anatomical structure development alpha-beta T cell activation T cell differentiation CD4-positive, alpha-beta T cell lineage commitment developmental process alpha-beta T cell lineage commitment hemopoiesis cell activation T cell lineage commitment positive T cell selection T cell selection cell fate commitment leukocyte differentiation macrophage apoptotic process myeloid cell apoptotic process leukocyte apoptotic process inflammatory cell apoptotic process zymogen activation	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix intracellular anatomical structure intracellular vesicle membrane-enclosed lumen lytic vacuole vacuolar lumen endomembrane system intracellular organelle lumen intracellular organelle endolysosome cytoplasmic vesicle endosome lumen lysosome endosome vacuole intracellular membrane-bounded organelle lysosomal lumen organelle lumen endolysosome lumen cytoplasm Golgi apparatus chromaffin granule secretory granule secretory vesicle apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane late endosome multivesicular body endocytic vesicle lumen endocytic vesicle nucleus
D, E, F	Cystatin-A	enzyme regulator activity molecular function inhibitor activity peptidase regulator activity molecular function regulator activity enzyme inhibitor activity cysteine-type endopeptidase inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity protein binding binding enzyme binding protease binding	developmental process epithelium development epidermal cell differentiation cellular developmental process epidermis development animal organ development tissue development epithelial cell differentiation skin development cell differentiation keratinocyte differentiation anatomical structure development cellular process negative regulation of hydrolase activity developmental process epithelium development epidermal cell differentiation cellular developmental process epidermis development animal organ development tissue development epithelial cell differentiation skin development cell differentiation keratinocyte differentiation anatomical structure development cellular process negative regulation of hydrolase activity negative regulation of proteolysis regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of primary metabolic process negative regulation of peptidase activity organic substance metabolic process regulation of proteolysis proteolysis protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process organonitrogen compound metabolic process regulation of protein metabolic process negative regulation of metabolic process biological regulation negative regulation of molecular function regulation of peptidase activity primary metabolic process regulation of macromolecule metabolic process regulation of molecular function regulation of hydrolase activity metabolic process macromolecule metabolic process regulation of metabolic process cell adhesion cell-cell adhesion peptide cross-linking macromolecule modification protein modification process	protein-containing complex peptidase inhibitor complex cell periphery plasma membrane membrane cellular anatomical entity cornified envelope intracellular anatomical structure cytoplasm cytosol extracellular region extracellular space membrane-bounded organelle nucleus protein-containing complex peptidase inhibitor complex cell periphery plasma membrane membrane cellular anatomical entity cornified envelope intracellular anatomical structure cytoplasm cytosol extracellular region extracellular space membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR025661	Cysteine peptidase, asparagine active site	Active Site
A, B, C	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C	IPR013201	Cathepsin propeptide inhibitor domain (I29)	Domain
A, B, C	IPR000169	Cysteine peptidase, cysteine active site	Active Site
A, B, C	IPR013128	Peptidase C1A	Family
A, B, C	IPR000668	Peptidase C1A, papain C-terminal	Domain
A, B, C	IPR025660	Cysteine peptidase, histidine active site	Active Site
A, B, C	IPR039417	Papain-like cysteine endopeptidase	Domain
D, E, F	IPR018073	Proteinase inhibitor I25, cystatin, conserved site	Conserved Site
D, E, F	IPR001713	Proteinase inhibitor I25A, stefin	Family
D, E, F	IPR000010	Cystatin domain	Domain
D, E, F	IPR046350	Cystatin superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P07711	meningioma secretory meningioma fibrous meningioma intraorbital meningioma meningothelial meningioma olfactory groove meningioma angiomatous meningioma proteinuria cerebral convexity meningioma spinal meningioma intraventricular meningioma microcystic meningioma parasagittal meningioma benign meningioma psammomatous meningioma meningioma secretory meningioma fibrous meningioma intraorbital meningioma meningothelial meningioma olfactory groove meningioma angiomatous meningioma proteinuria cerebral convexity meningioma spinal meningioma intraventricular meningioma microcystic meningioma parasagittal meningioma benign meningioma psammomatous meningioma clear cell meningioma transitional meningioma large cell medulloblastoma Malignant Meningioma multiple sclerosis pancreatic ductal adenocarcinoma breast cancer psoriasis COVID-19 gastric neoplasm tuberculosis lung carcinoma papillary meningioma cutaneous lupus erythematosus gastric cancer glioblastoma hereditary diffuse gastric adenocarcinoma lymphoplasmacyte-rich meningioma ovarian cancer dermatomyositis gastric carcinoma
D, E, F	Pharos: P01040	peeling skin syndrome 4 glioblastoma nasopharyngeal carcinoma psoriasis giant cell glioblastoma Neoplasm Metastasis malignant pancreatic neoplasm nephrolithiasis pancreatic ductal adenocarcinoma peeling skin syndrome acne atypical teratoid rhabdoid tumor spina bifida cystic fibrosis lung cancer peeling skin syndrome 4 glioblastoma nasopharyngeal carcinoma psoriasis giant cell glioblastoma Neoplasm Metastasis malignant pancreatic neoplasm nephrolithiasis pancreatic ductal adenocarcinoma peeling skin syndrome acne atypical teratoid rhabdoid tumor spina bifida cystic fibrosis lung cancer malignant glioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm acral peeling skin syndrome sinusitis B-cell chronic lymphocytic leukemia subependymal giant cell astrocytoma dermatomyositis esophageal adenocarcinoma lung carcinoma malignant mesothelioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pilocytic astrocytoma asthma Sjogren syndrome breast cancer ulcerative colitis exfoliative ichthyosis lung adenocarcinoma malignant ependymoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C	SCH	Parent Component: CYS RESID: AA0101 PSI-MOD : L-cysteine methyl disulfide MOD:00110

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.