3H6S | pdb_00003h6s

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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	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)
F	SCOP2B Superfamily	STI-like	8053737	3000715	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	STI-like	8053737	3000715	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cysteine proteinases	8033059	3001808	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cysteine proteinases	8033059	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8033059	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8033059	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)
H	PDEase_I	e3h6sH1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
G	PDEase_I	e3h6sG1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
F	PDEase_I	e3h6sF1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
E	SAM_2	e3h6sE1	A: alpha bundles	X: Cystatin-like	H: Cupredoxin-related	T: Cupredoxin-related	F: SAM_2	ECOD (develop294)
D	PDEase_I	e3h6sD1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
C	PDEase_I	e3h6sC1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
B	PDEase_I	e3h6sB1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (develop294)
A	Peptidase_C1	e3h6sA1	A: alpha bundles	X: Cystatin-like	H: Cupredoxin-related	T: Cupredoxin-related	F: Peptidase_C1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	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)
F	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
E	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
D	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)
B	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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	-	-
A, B, C, D	Cathepsin L2	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	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 immune system process 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 process cellular component organization or biogenesis 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 immune system process 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 process cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization	cellular anatomical structure extracellular region 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 cellular anatomical structure extracellular region 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 extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR019508	Proteinase inhibitor I48, clitocypin	Family
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

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

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.