Entry Database : PDB / ID : 5qbu Structure visualization Downloads & linksTitle Crystal structure of human Cathepsin-S with bound ligand ComponentsCathepsin S Details Keywords HYDROLASE / D3R / Cathepsin S / Ligand DockingFunction / homology Function and homology informationFunction Domain/homology Component
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 region Similarity 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 Beta Similarity search - Domain/homologyBiological species Homo sapiens (human)Method X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution : 2.78 Å DetailsModel details Structures re-refined for D3R docking challenge Authors Bembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Yang, H. / Shao, C. / Burley, S.K. CitationJournal : To be published Title : Crystal structure of human Cathepsin-S with bound ligandAuthors : Bembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Yang, H. / Shao, C. / Burley, S.K. History Deposition Aug 4, 2017 Deposition site : RCSB / Processing site : RCSBRevision 1.0 Dec 20, 2017 Provider : repository / Type : Initial releaseRevision 1.1 Feb 21, 2018 Group : Structure summary / Category : pdbx_deposit_group / Item : _pdbx_deposit_group.group_typeRevision 2.0 Jun 6, 2018 Group : Atomic model / Data collection ... Atomic model / Data collection / Other / Refinement description Category : atom_site / atom_sites ... atom_site / atom_sites / computing / diffrn_radiation_wavelength / pdbx_nonpoly_scheme / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software 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] / _diffrn_radiation_wavelength.wavelength / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][2] / _refine.aniso_B[2][3] / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _reflns.percent_possible_obs / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.type Revision 2.1 Feb 10, 2021 Group : Database references / Structure summary / Category : audit_author / citation_authorItem : _audit_author.identifier_ORCID / _citation_author.identifier_ORCIDRevision 2.2 Nov 17, 2021 Group : Database references / Structure summary / Category : database_2 / pdbx_deposit_groupItem : _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description
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