3H6S

Structure of clitocypin - cathepsin V complex

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)
A	d3h6sa_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin V	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3h6sb_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin V	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3h6sc_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin V	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3h6sd_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like	(Pro)cathepsin V	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	8033059	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8033059	3001808	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cysteine proteinases	8033059	3001808	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cysteine proteinases	8033059	3001808	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	STI-like	8053737	3000715	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	STI-like	8053737	3000715	SCOP2B (2022-06-29)
G	SCOP2 Family	Clitocypin-like	8044928	4004206	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	STI-like	8053737	3000715	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	STI-like	8053737	3000715	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	e3h6sA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00112	ECOD (1.6)
B	PF00112	e3h6sB1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00112	ECOD (1.6)
C	PF00112	e3h6sC1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00112	ECOD (1.6)
D	PF00112	e3h6sD1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00112	ECOD (1.6)
E	PF10467	e3h6sE1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF10467	ECOD (1.6)
F	PF10467	e3h6sF1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF10467	ECOD (1.6)
G	PF10467	e3h6sG1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF10467	ECOD (1.6)
H	PF10467	e3h6sH1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: PF10467	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	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
E	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
F	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
G	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
H	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00112	Papain family cysteine protease (Peptidase_C1)	Papain family cysteine protease	-	Domain
E, F, G, H	PF10467	Peptidase inhibitor clitocypin (Inhibitor_I48)	Peptidase inhibitor clitocypin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Cathepsin L2	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 cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase 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 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	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 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 biological regulation cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication cellular process apoptotic process programmed cell death positive regulation of signaling regulation of apoptotic signaling pathway immune response immune system process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process 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 cellular component organization cellular component disassembly extracellular matrix disassembly extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization	extracellular region cellular anatomical entity 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 extracellular region cellular anatomical entity 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 extracellular space
E, F, G, H	Clitocypin analog	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	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR025661	Cysteine peptidase, asparagine active site	Active Site
A, B, C, D	IPR000169	Cysteine peptidase, cysteine active site	Active Site
A, B, C, D	IPR013128	Peptidase C1A	Family
A, B, C, D	IPR000668	Peptidase C1A, papain C-terminal	Domain
A, B, C, D	IPR013201	Cathepsin propeptide inhibitor domain (I29)	Domain
A, B, C, D	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C, D	IPR025660	Cysteine peptidase, histidine active site	Active Site
A, B, C, D	IPR039417	Papain-like cysteine endopeptidase	Domain
E, F, G, H	IPR019508	Proteinase inhibitor I48, clitocypin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O60911	atopic eczema Chronic hepatitis C malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm spina bifida atypical teratoid rhabdoid tumor lung adenocarcinoma non-small cell lung carcinoma pituitary cancer ulcerative colitis breast cancer lung cancer osteosarcoma psoriasis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	SCH	Parent Component: CYS RESID: AA0101 PSI-MOD : L-cysteine methyl disulfide MOD:00110
E, F, G, H	SME	Parent Component: MET RESID: AA0101 , AA0581 PSI-MOD : L-cysteine methyl disulfide MOD:00110 , L-methionine (S)-sulfoxide MOD:00721

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.