Entry | Database: PDB / ID: 5qc0 |
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Title | Crystal structure of human Cathepsin-S with bound ligand |
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Components | Cathepsin S |
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Keywords | HYDROLASE / D3R / Cathepsin S / Ligand Docking |
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Function / homology | Function and homology information
cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures ...cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / toll-like receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / laminin binding / phagocytic vesicle / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / positive regulation of apoptotic signaling pathway / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / protein processing / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / tertiary granule lumen / collagen-containing extracellular matrix / adaptive immune response / ficolin-1-rich granule lumen / lysosome / immune response / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular regionSimilarity search - Function Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha BetaSimilarity search - Domain/homology |
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Biological species | Homo sapiens (human) |
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Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å |
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Model details | Structures re-refined for D3R docking challenge |
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Authors | Bembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Yang, H. / Shao, C. / Burley, S.K. |
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Citation | Journal: To be published Title: Crystal structure of human Cathepsin-S with bound ligand Authors: Bembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Yang, H. / Shao, C. / Burley, S.K. |
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History | Deposition | Aug 4, 2017 | Deposition site: RCSB / Processing site: RCSB |
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Revision 1.0 | Dec 20, 2017 | Provider: repository / Type: Initial release |
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Revision 1.1 | Feb 21, 2018 | Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type |
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Revision 2.0 | Jun 6, 2018 | Group: Atomic model / Data collection ...Atomic model / Data collection / Other / Refinement description / Structure summary Category: atom_site / atom_sites ...atom_site / atom_sites / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / refine / refine_hist / refine_ls_shell / reflns Item: _atom_site.occupancy / _atom_sites.fract_transf_matrix[2][1] ..._atom_site.occupancy / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _refine.B_iso_mean / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _refine_ls_shell.d_res_low / _reflns.percent_possible_obs |
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Revision 2.1 | Feb 10, 2021 | Group: Database references / Structure summary / Category: audit_author / citation_author Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID |
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Revision 2.2 | Nov 17, 2021 | Group: Advisory / Database references / Structure summary Category: database_2 / pdbx_deposit_group / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description |
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