data_5QBZ # _entry.id 5QBZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.352 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 5QBZ pdb_00005qbz 10.2210/pdb5qbz/pdb WWPDB D_1001401756 ? ? # _pdbx_database_status.entry_id 5QBZ _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.recvd_initial_deposition_date 2017-08-04 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Bembenek, S.D.' 1 ? 'Ameriks, M.K.' 2 ? 'Mirzadegan, T.' 3 ? 'Yang, H.' 4 ? 'Shao, C.' 5 0000-0001-6817-7476 'Burley, S.K.' 6 0000-0002-2487-9713 # _citation.id primary _citation.journal_abbrev 'To be published' _citation.title 'Crystal structure of human Cathepsin-S with bound ligand' _citation.year ? _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Bembenek, S.D.' 1 ? primary 'Ameriks, M.K.' 2 ? primary 'Mirzadegan, T.' 3 ? primary 'Yang, H.' 4 ? primary 'Shao, C.' 5 0000-0001-6817-7476 primary 'Burley, S.K.' 6 0000-0002-2487-9713 # _cell.entry_id 5QBZ _cell.length_a 70.894 _cell.length_b 70.894 _cell.length_c 89.046 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5QBZ _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Cathepsin S' 24516.471 1 3.4.22.27 C139S ? ? 2 non-polymer syn ;N-{[2-chloro-5-(4-{3-[4-(6-chloro-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propyl}-3-oxo-3,4-dihydropyrazin-2-yl)phenyl]methyl}-4-fluorobenzamide ; 663.569 1 ? ? ? ? 3 water nat water 18.015 37 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;ILPDSVDWREKGCVTEVKYQGSCGASWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYII DNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCT QNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEILQGGG ; _entity_poly.pdbx_seq_one_letter_code_can ;ILPDSVDWREKGCVTEVKYQGSCGASWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYII DNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCT QNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEILQGGG ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ILE n 1 2 LEU n 1 3 PRO n 1 4 ASP n 1 5 SER n 1 6 VAL n 1 7 ASP n 1 8 TRP n 1 9 ARG n 1 10 GLU n 1 11 LYS n 1 12 GLY n 1 13 CYS n 1 14 VAL n 1 15 THR n 1 16 GLU n 1 17 VAL n 1 18 LYS n 1 19 TYR n 1 20 GLN n 1 21 GLY n 1 22 SER n 1 23 CYS n 1 24 GLY n 1 25 ALA n 1 26 SER n 1 27 TRP n 1 28 ALA n 1 29 PHE n 1 30 SER n 1 31 ALA n 1 32 VAL n 1 33 GLY n 1 34 ALA n 1 35 LEU n 1 36 GLU n 1 37 ALA n 1 38 GLN n 1 39 LEU n 1 40 LYS n 1 41 LEU n 1 42 LYS n 1 43 THR n 1 44 GLY n 1 45 LYS n 1 46 LEU n 1 47 VAL n 1 48 SER n 1 49 LEU n 1 50 SER n 1 51 ALA n 1 52 GLN n 1 53 ASN n 1 54 LEU n 1 55 VAL n 1 56 ASP n 1 57 CYS n 1 58 SER n 1 59 THR n 1 60 GLU n 1 61 LYS n 1 62 TYR n 1 63 GLY n 1 64 ASN n 1 65 LYS n 1 66 GLY n 1 67 CYS n 1 68 ASN n 1 69 GLY n 1 70 GLY n 1 71 PHE n 1 72 MET n 1 73 THR n 1 74 THR n 1 75 ALA n 1 76 PHE n 1 77 GLN n 1 78 TYR n 1 79 ILE n 1 80 ILE n 1 81 ASP n 1 82 ASN n 1 83 LYS n 1 84 GLY n 1 85 ILE n 1 86 ASP n 1 87 SER n 1 88 ASP n 1 89 ALA n 1 90 SER n 1 91 TYR n 1 92 PRO n 1 93 TYR n 1 94 LYS n 1 95 ALA n 1 96 MET n 1 97 ASP n 1 98 GLN n 1 99 LYS n 1 100 CYS n 1 101 GLN n 1 102 TYR n 1 103 ASP n 1 104 SER n 1 105 LYS n 1 106 TYR n 1 107 ARG n 1 108 ALA n 1 109 ALA n 1 110 THR n 1 111 CYS n 1 112 SER n 1 113 LYS n 1 114 TYR n 1 115 THR n 1 116 GLU n 1 117 LEU n 1 118 PRO n 1 119 TYR n 1 120 GLY n 1 121 ARG n 1 122 GLU n 1 123 ASP n 1 124 VAL n 1 125 LEU n 1 126 LYS n 1 127 GLU n 1 128 ALA n 1 129 VAL n 1 130 ALA n 1 131 ASN n 1 132 LYS n 1 133 GLY n 1 134 PRO n 1 135 VAL n 1 136 SER n 1 137 VAL n 1 138 GLY n 1 139 VAL n 1 140 ASP n 1 141 ALA n 1 142 ARG n 1 143 HIS n 1 144 PRO n 1 145 SER n 1 146 PHE n 1 147 PHE n 1 148 LEU n 1 149 TYR n 1 150 ARG n 1 151 SER n 1 152 GLY n 1 153 VAL n 1 154 TYR n 1 155 TYR n 1 156 GLU n 1 157 PRO n 1 158 SER n 1 159 CYS n 1 160 THR n 1 161 GLN n 1 162 ASN n 1 163 VAL n 1 164 ASN n 1 165 HIS n 1 166 GLY n 1 167 VAL n 1 168 LEU n 1 169 VAL n 1 170 VAL n 1 171 GLY n 1 172 TYR n 1 173 GLY n 1 174 ASP n 1 175 LEU n 1 176 ASN n 1 177 GLY n 1 178 LYS n 1 179 GLU n 1 180 TYR n 1 181 TRP n 1 182 LEU n 1 183 VAL n 1 184 LYS n 1 185 ASN n 1 186 SER n 1 187 TRP n 1 188 GLY n 1 189 HIS n 1 190 ASN n 1 191 PHE n 1 192 GLY n 1 193 GLU n 1 194 GLU n 1 195 GLY n 1 196 TYR n 1 197 ILE n 1 198 ARG n 1 199 MET n 1 200 ALA n 1 201 ARG n 1 202 ASN n 1 203 LYS n 1 204 GLY n 1 205 ASN n 1 206 HIS n 1 207 CYS n 1 208 GLY n 1 209 ILE n 1 210 ALA n 1 211 SER n 1 212 PHE n 1 213 PRO n 1 214 SER n 1 215 TYR n 1 216 PRO n 1 217 GLU n 1 218 ILE n 1 219 LEU n 1 220 GLN n 1 221 GLY n 1 222 GLY n 1 223 GLY n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 223 _entity_src_gen.gene_src_common_name Human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene CTSS _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Spodoptera frugiperda' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 7108 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type baculovirus _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code CATS_HUMAN _struct_ref.pdbx_db_accession P25774 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;ILPDSVDWREKGCVTEVKYQGSCGACWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYII DNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCT QNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEI ; _struct_ref.pdbx_align_begin 114 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5QBZ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 218 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P25774 _struct_ref_seq.db_align_beg 114 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 331 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 0 _struct_ref_seq.pdbx_auth_seq_align_end 217 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 5QBZ SER A 26 ? UNP P25774 CYS 139 'engineered mutation' 25 1 1 5QBZ LEU A 219 ? UNP P25774 ? ? 'expression tag' 218 2 1 5QBZ GLN A 220 ? UNP P25774 ? ? 'expression tag' 219 3 1 5QBZ GLY A 221 ? UNP P25774 ? ? 'expression tag' 220 4 1 5QBZ GLY A 222 ? UNP P25774 ? ? 'expression tag' 221 5 1 5QBZ GLY A 223 ? UNP P25774 ? ? 'expression tag' 222 6 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 B8Y non-polymer . ;N-{[2-chloro-5-(4-{3-[4-(6-chloro-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propyl}-3-oxo-3,4-dihydropyrazin-2-yl)phenyl]methyl}-4-fluorobenzamide ; ? 'C34 H33 Cl2 F N6 O3' 663.569 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.entry_id 5QBZ _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.33 _exptl_crystal.density_percent_sol 47.25 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.50 _exptl_crystal_grow.pdbx_details ;100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'RIGAKU SATURN 944' _diffrn_detector.pdbx_collection_date 2006-05-10 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.54178 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU MICROMAX-007 HF' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.54178 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 5QBZ _reflns.d_resolution_high 2.8000 _reflns.d_resolution_low 35.4500 _reflns.number_obs 5712 _reflns.percent_possible_obs 99.5000 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? # _refine.entry_id 5QBZ _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_d_res_high 2.8000 _refine.ls_d_res_low 35.4500 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.5000 _refine.ls_number_reflns_obs 5712 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.ls_matrix_type ? _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1852 _refine.ls_R_factor_R_work 0.1821 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2529 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.6000 _refine.ls_number_reflns_R_free 273 _refine.ls_number_reflns_R_work ? _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 33.7910 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 0.0400 _refine.aniso_B[2][2] 0.0400 _refine.aniso_B[3][3] -0.0800 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9370 _refine.correlation_coeff_Fo_to_Fc_free 0.8760 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free 0.3990 _refine.overall_SU_ML 0.2800 _refine.overall_SU_B 14.3290 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 70.620 _refine.B_iso_min 5.670 _refine.pdbx_overall_phase_error ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_R_factor_R_free_error_details ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 2.8000 _refine_hist.d_res_low 35.4500 _refine_hist.pdbx_number_atoms_ligand 46 _refine_hist.number_atoms_solvent 37 _refine_hist.number_atoms_total 1759 _refine_hist.pdbx_number_residues_total 217 _refine_hist.pdbx_B_iso_mean_ligand 38.87 _refine_hist.pdbx_B_iso_mean_solvent 23.55 _refine_hist.pdbx_number_atoms_protein 1676 _refine_hist.pdbx_number_atoms_nucleic_acid 0 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' r_bond_refined_d 1772 0.008 0.019 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 1530 0.002 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 2405 1.165 1.921 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 3560 0.945 2.991 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 216 5.633 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 80 40.470 24.375 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 270 15.376 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 7 17.794 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 239 0.063 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 2008 0.004 0.020 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 380 0.001 0.020 ? ? # _refine_ls_shell.d_res_high 2.7950 _refine_ls_shell.d_res_low 2.8680 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 95.2800 _refine_ls_shell.number_reflns_R_work 381 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2510 _refine_ls_shell.R_factor_R_free 0.3750 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 23 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.number_reflns_all 404 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 5QBZ _struct.title 'Crystal structure of human Cathepsin-S with bound ligand' _struct.pdbx_model_details 'Structures re-refined for D3R docking challenge' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 5QBZ _struct_keywords.text 'D3R, Cathepsin S, Ligand Docking, HYDROLASE' _struct_keywords.pdbx_keywords HYDROLASE # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 ALA A 25 ? GLY A 44 ? ALA A 24 GLY A 43 1 ? 20 HELX_P HELX_P2 AA2 SER A 50 ? SER A 58 ? SER A 49 SER A 57 1 ? 9 HELX_P HELX_P3 AA3 THR A 59 ? GLY A 63 ? THR A 58 GLY A 62 5 ? 5 HELX_P HELX_P4 AA4 LYS A 65 ? GLY A 69 ? LYS A 64 GLY A 68 5 ? 5 HELX_P HELX_P5 AA5 PHE A 71 ? ASN A 82 ? PHE A 70 ASN A 81 1 ? 12 HELX_P HELX_P6 AA6 ASP A 103 ? LYS A 105 ? ASP A 102 LYS A 104 5 ? 3 HELX_P HELX_P7 AA7 ARG A 121 ? LYS A 132 ? ARG A 120 LYS A 131 1 ? 12 HELX_P HELX_P8 AA8 HIS A 143 ? TYR A 149 ? HIS A 142 TYR A 148 1 ? 7 HELX_P HELX_P9 AA9 ASN A 205 ? ILE A 209 ? ASN A 204 ILE A 208 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 23 SG ? ? ? 1_555 A CYS 67 SG ? ? A CYS 22 A CYS 66 1_555 ? ? ? ? ? ? ? 2.028 ? ? disulf2 disulf ? ? A CYS 57 SG ? ? ? 1_555 A CYS 100 SG ? ? A CYS 56 A CYS 99 1_555 ? ? ? ? ? ? ? 2.032 ? ? disulf3 disulf ? ? A CYS 159 SG ? ? ? 1_555 A CYS 207 SG ? ? A CYS 158 A CYS 206 1_555 ? ? ? ? ? ? ? 2.031 ? ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 3 ? AA2 ? 5 ? AA3 ? 2 ? AA4 ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA2 3 4 ? anti-parallel AA2 4 5 ? parallel AA3 1 2 ? anti-parallel AA4 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 VAL A 6 ? ASP A 7 ? VAL A 5 ASP A 6 AA1 2 HIS A 165 ? LEU A 175 ? HIS A 164 LEU A 174 AA1 3 VAL A 135 ? VAL A 139 ? VAL A 134 VAL A 138 AA2 1 VAL A 6 ? ASP A 7 ? VAL A 5 ASP A 6 AA2 2 HIS A 165 ? LEU A 175 ? HIS A 164 LEU A 174 AA2 3 LYS A 178 ? LYS A 184 ? LYS A 177 LYS A 183 AA2 4 TYR A 196 ? ALA A 200 ? TYR A 195 ALA A 199 AA2 5 VAL A 153 ? TYR A 154 ? VAL A 152 TYR A 153 AA3 1 ILE A 85 ? ASP A 86 ? ILE A 84 ASP A 85 AA3 2 ARG A 107 ? ALA A 109 ? ARG A 106 ALA A 108 AA4 1 LYS A 113 ? GLU A 116 ? LYS A 112 GLU A 115 AA4 2 SER A 214 ? GLU A 217 ? SER A 213 GLU A 216 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N VAL A 6 ? N VAL A 5 O TYR A 172 ? O TYR A 171 AA1 2 3 O VAL A 167 ? O VAL A 166 N VAL A 137 ? N VAL A 136 AA2 1 2 N VAL A 6 ? N VAL A 5 O TYR A 172 ? O TYR A 171 AA2 2 3 N LEU A 168 ? N LEU A 167 O LYS A 184 ? O LYS A 183 AA2 3 4 N TRP A 181 ? N TRP A 180 O MET A 199 ? O MET A 198 AA2 4 5 O ARG A 198 ? O ARG A 197 N TYR A 154 ? N TYR A 153 AA3 1 2 N ILE A 85 ? N ILE A 84 O ALA A 108 ? O ALA A 107 AA4 1 2 N THR A 115 ? N THR A 114 O TYR A 215 ? O TYR A 214 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id B8Y _struct_site.pdbx_auth_seq_id 901 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 18 _struct_site.details 'binding site for residue B8Y A 901' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 18 TYR A 19 ? TYR A 18 . ? 4_444 ? 2 AC1 18 GLY A 21 ? GLY A 20 . ? 4_444 ? 3 AC1 18 GLY A 63 ? GLY A 62 . ? 1_555 ? 4 AC1 18 LYS A 65 ? LYS A 64 . ? 1_555 ? 5 AC1 18 ASN A 68 ? ASN A 67 . ? 1_555 ? 6 AC1 18 GLY A 69 ? GLY A 68 . ? 1_555 ? 7 AC1 18 GLY A 70 ? GLY A 69 . ? 1_555 ? 8 AC1 18 PHE A 71 ? PHE A 70 . ? 1_555 ? 9 AC1 18 THR A 74 ? THR A 73 . ? 1_555 ? 10 AC1 18 PHE A 147 ? PHE A 146 . ? 4_444 ? 11 AC1 18 LEU A 148 ? LEU A 147 . ? 4_444 ? 12 AC1 18 VAL A 163 ? VAL A 162 . ? 1_555 ? 13 AC1 18 HIS A 165 ? HIS A 164 . ? 1_555 ? 14 AC1 18 GLY A 166 ? GLY A 165 . ? 1_555 ? 15 AC1 18 TRP A 187 ? TRP A 186 . ? 4_444 ? 16 AC1 18 ASN A 190 ? ASN A 189 . ? 4_444 ? 17 AC1 18 PHE A 212 ? PHE A 211 . ? 1_555 ? 18 AC1 18 HOH C . ? HOH A 1019 . ? 1_555 ? # _atom_sites.entry_id 5QBZ _atom_sites.fract_transf_matrix[1][1] 0.014106 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] -0.000000 _atom_sites.fract_transf_matrix[2][2] 0.014106 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] -0.000000 _atom_sites.fract_transf_matrix[3][3] 0.011230 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C CL F N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 ILE 1 0 ? ? ? A . n A 1 2 LEU 2 1 1 LEU LEU A . n A 1 3 PRO 3 2 2 PRO PRO A . n A 1 4 ASP 4 3 3 ASP ASP A . n A 1 5 SER 5 4 4 SER SER A . n A 1 6 VAL 6 5 5 VAL VAL A . n A 1 7 ASP 7 6 6 ASP ASP A . n A 1 8 TRP 8 7 7 TRP TRP A . n A 1 9 ARG 9 8 8 ARG ARG A . n A 1 10 GLU 10 9 9 GLU GLU A . n A 1 11 LYS 11 10 10 LYS LYS A . n A 1 12 GLY 12 11 11 GLY GLY A . n A 1 13 CYS 13 12 12 CYS CYS A . n A 1 14 VAL 14 13 13 VAL VAL A . n A 1 15 THR 15 14 14 THR THR A . n A 1 16 GLU 16 15 15 GLU GLU A . n A 1 17 VAL 17 16 16 VAL VAL A . n A 1 18 LYS 18 17 17 LYS LYS A . n A 1 19 TYR 19 18 18 TYR TYR A . n A 1 20 GLN 20 19 19 GLN GLN A . n A 1 21 GLY 21 20 20 GLY GLY A . n A 1 22 SER 22 21 21 SER SER A . n A 1 23 CYS 23 22 22 CYS CYS A . n A 1 24 GLY 24 23 23 GLY GLY A . n A 1 25 ALA 25 24 24 ALA ALA A . n A 1 26 SER 26 25 25 SER SER A . n A 1 27 TRP 27 26 26 TRP TRP A . n A 1 28 ALA 28 27 27 ALA ALA A . n A 1 29 PHE 29 28 28 PHE PHE A . n A 1 30 SER 30 29 29 SER SER A . n A 1 31 ALA 31 30 30 ALA ALA A . n A 1 32 VAL 32 31 31 VAL VAL A . n A 1 33 GLY 33 32 32 GLY GLY A . n A 1 34 ALA 34 33 33 ALA ALA A . n A 1 35 LEU 35 34 34 LEU LEU A . n A 1 36 GLU 36 35 35 GLU GLU A . n A 1 37 ALA 37 36 36 ALA ALA A . n A 1 38 GLN 38 37 37 GLN GLN A . n A 1 39 LEU 39 38 38 LEU LEU A . n A 1 40 LYS 40 39 39 LYS LYS A . n A 1 41 LEU 41 40 40 LEU LEU A . n A 1 42 LYS 42 41 41 LYS LYS A . n A 1 43 THR 43 42 42 THR THR A . n A 1 44 GLY 44 43 43 GLY GLY A . n A 1 45 LYS 45 44 44 LYS LYS A . n A 1 46 LEU 46 45 45 LEU LEU A . n A 1 47 VAL 47 46 46 VAL VAL A . n A 1 48 SER 48 47 47 SER SER A . n A 1 49 LEU 49 48 48 LEU LEU A . n A 1 50 SER 50 49 49 SER SER A . n A 1 51 ALA 51 50 50 ALA ALA A . n A 1 52 GLN 52 51 51 GLN GLN A . n A 1 53 ASN 53 52 52 ASN ASN A . n A 1 54 LEU 54 53 53 LEU LEU A . n A 1 55 VAL 55 54 54 VAL VAL A . n A 1 56 ASP 56 55 55 ASP ASP A . n A 1 57 CYS 57 56 56 CYS CYS A . n A 1 58 SER 58 57 57 SER SER A . n A 1 59 THR 59 58 58 THR THR A . n A 1 60 GLU 60 59 59 GLU GLU A . n A 1 61 LYS 61 60 60 LYS LYS A . n A 1 62 TYR 62 61 61 TYR TYR A . n A 1 63 GLY 63 62 62 GLY GLY A . n A 1 64 ASN 64 63 63 ASN ASN A . n A 1 65 LYS 65 64 64 LYS LYS A . n A 1 66 GLY 66 65 65 GLY GLY A . n A 1 67 CYS 67 66 66 CYS CYS A . n A 1 68 ASN 68 67 67 ASN ASN A . n A 1 69 GLY 69 68 68 GLY GLY A . n A 1 70 GLY 70 69 69 GLY GLY A . n A 1 71 PHE 71 70 70 PHE PHE A . n A 1 72 MET 72 71 71 MET MET A . n A 1 73 THR 73 72 72 THR THR A . n A 1 74 THR 74 73 73 THR THR A . n A 1 75 ALA 75 74 74 ALA ALA A . n A 1 76 PHE 76 75 75 PHE PHE A . n A 1 77 GLN 77 76 76 GLN GLN A . n A 1 78 TYR 78 77 77 TYR TYR A . n A 1 79 ILE 79 78 78 ILE ILE A . n A 1 80 ILE 80 79 79 ILE ILE A . n A 1 81 ASP 81 80 80 ASP ASP A . n A 1 82 ASN 82 81 81 ASN ASN A . n A 1 83 LYS 83 82 82 LYS LYS A . n A 1 84 GLY 84 83 83 GLY GLY A . n A 1 85 ILE 85 84 84 ILE ILE A . n A 1 86 ASP 86 85 85 ASP ASP A . n A 1 87 SER 87 86 86 SER SER A . n A 1 88 ASP 88 87 87 ASP ASP A . n A 1 89 ALA 89 88 88 ALA ALA A . n A 1 90 SER 90 89 89 SER SER A . n A 1 91 TYR 91 90 90 TYR TYR A . n A 1 92 PRO 92 91 91 PRO PRO A . n A 1 93 TYR 93 92 92 TYR TYR A . n A 1 94 LYS 94 93 93 LYS LYS A . n A 1 95 ALA 95 94 94 ALA ALA A . n A 1 96 MET 96 95 95 MET MET A . n A 1 97 ASP 97 96 96 ASP ASP A . n A 1 98 GLN 98 97 97 GLN GLN A . n A 1 99 LYS 99 98 98 LYS LYS A . n A 1 100 CYS 100 99 99 CYS CYS A . n A 1 101 GLN 101 100 100 GLN GLN A . n A 1 102 TYR 102 101 101 TYR TYR A . n A 1 103 ASP 103 102 102 ASP ASP A . n A 1 104 SER 104 103 103 SER SER A . n A 1 105 LYS 105 104 104 LYS LYS A . n A 1 106 TYR 106 105 105 TYR TYR A . n A 1 107 ARG 107 106 106 ARG ARG A . n A 1 108 ALA 108 107 107 ALA ALA A . n A 1 109 ALA 109 108 108 ALA ALA A . n A 1 110 THR 110 109 109 THR THR A . n A 1 111 CYS 111 110 110 CYS CYS A . n A 1 112 SER 112 111 111 SER SER A . n A 1 113 LYS 113 112 112 LYS LYS A . n A 1 114 TYR 114 113 113 TYR TYR A . n A 1 115 THR 115 114 114 THR THR A . n A 1 116 GLU 116 115 115 GLU GLU A . n A 1 117 LEU 117 116 116 LEU LEU A . n A 1 118 PRO 118 117 117 PRO PRO A . n A 1 119 TYR 119 118 118 TYR TYR A . n A 1 120 GLY 120 119 119 GLY GLY A . n A 1 121 ARG 121 120 120 ARG ARG A . n A 1 122 GLU 122 121 121 GLU GLU A . n A 1 123 ASP 123 122 122 ASP ASP A . n A 1 124 VAL 124 123 123 VAL VAL A . n A 1 125 LEU 125 124 124 LEU LEU A . n A 1 126 LYS 126 125 125 LYS LYS A . n A 1 127 GLU 127 126 126 GLU GLU A . n A 1 128 ALA 128 127 127 ALA ALA A . n A 1 129 VAL 129 128 128 VAL VAL A . n A 1 130 ALA 130 129 129 ALA ALA A . n A 1 131 ASN 131 130 130 ASN ASN A . n A 1 132 LYS 132 131 131 LYS LYS A . n A 1 133 GLY 133 132 132 GLY GLY A . n A 1 134 PRO 134 133 133 PRO PRO A . n A 1 135 VAL 135 134 134 VAL VAL A . n A 1 136 SER 136 135 135 SER SER A . n A 1 137 VAL 137 136 136 VAL VAL A . n A 1 138 GLY 138 137 137 GLY GLY A . n A 1 139 VAL 139 138 138 VAL VAL A . n A 1 140 ASP 140 139 139 ASP ASP A . n A 1 141 ALA 141 140 140 ALA ALA A . n A 1 142 ARG 142 141 141 ARG ARG A . n A 1 143 HIS 143 142 142 HIS HIS A . n A 1 144 PRO 144 143 143 PRO PRO A . n A 1 145 SER 145 144 144 SER SER A . n A 1 146 PHE 146 145 145 PHE PHE A . n A 1 147 PHE 147 146 146 PHE PHE A . n A 1 148 LEU 148 147 147 LEU LEU A . n A 1 149 TYR 149 148 148 TYR TYR A . n A 1 150 ARG 150 149 149 ARG ARG A . n A 1 151 SER 151 150 150 SER SER A . n A 1 152 GLY 152 151 151 GLY GLY A . n A 1 153 VAL 153 152 152 VAL VAL A . n A 1 154 TYR 154 153 153 TYR TYR A . n A 1 155 TYR 155 154 154 TYR TYR A . n A 1 156 GLU 156 155 155 GLU GLU A . n A 1 157 PRO 157 156 156 PRO PRO A . n A 1 158 SER 158 157 157 SER SER A . n A 1 159 CYS 159 158 158 CYS CYS A . n A 1 160 THR 160 159 159 THR THR A . n A 1 161 GLN 161 160 160 GLN GLN A . n A 1 162 ASN 162 161 161 ASN ASN A . n A 1 163 VAL 163 162 162 VAL VAL A . n A 1 164 ASN 164 163 163 ASN ASN A . n A 1 165 HIS 165 164 164 HIS HIS A . n A 1 166 GLY 166 165 165 GLY GLY A . n A 1 167 VAL 167 166 166 VAL VAL A . n A 1 168 LEU 168 167 167 LEU LEU A . n A 1 169 VAL 169 168 168 VAL VAL A . n A 1 170 VAL 170 169 169 VAL VAL A . n A 1 171 GLY 171 170 170 GLY GLY A . n A 1 172 TYR 172 171 171 TYR TYR A . n A 1 173 GLY 173 172 172 GLY GLY A . n A 1 174 ASP 174 173 173 ASP ASP A . n A 1 175 LEU 175 174 174 LEU LEU A . n A 1 176 ASN 176 175 175 ASN ASN A . n A 1 177 GLY 177 176 176 GLY GLY A . n A 1 178 LYS 178 177 177 LYS LYS A . n A 1 179 GLU 179 178 178 GLU GLU A . n A 1 180 TYR 180 179 179 TYR TYR A . n A 1 181 TRP 181 180 180 TRP TRP A . n A 1 182 LEU 182 181 181 LEU LEU A . n A 1 183 VAL 183 182 182 VAL VAL A . n A 1 184 LYS 184 183 183 LYS LYS A . n A 1 185 ASN 185 184 184 ASN ASN A . n A 1 186 SER 186 185 185 SER SER A . n A 1 187 TRP 187 186 186 TRP TRP A . n A 1 188 GLY 188 187 187 GLY GLY A . n A 1 189 HIS 189 188 188 HIS HIS A . n A 1 190 ASN 190 189 189 ASN ASN A . n A 1 191 PHE 191 190 190 PHE PHE A . n A 1 192 GLY 192 191 191 GLY GLY A . n A 1 193 GLU 193 192 192 GLU GLU A . n A 1 194 GLU 194 193 193 GLU GLU A . n A 1 195 GLY 195 194 194 GLY GLY A . n A 1 196 TYR 196 195 195 TYR TYR A . n A 1 197 ILE 197 196 196 ILE ILE A . n A 1 198 ARG 198 197 197 ARG ARG A . n A 1 199 MET 199 198 198 MET MET A . n A 1 200 ALA 200 199 199 ALA ALA A . n A 1 201 ARG 201 200 200 ARG ARG A . n A 1 202 ASN 202 201 201 ASN ASN A . n A 1 203 LYS 203 202 202 LYS LYS A . n A 1 204 GLY 204 203 203 GLY GLY A . n A 1 205 ASN 205 204 204 ASN ASN A . n A 1 206 HIS 206 205 205 HIS HIS A . n A 1 207 CYS 207 206 206 CYS CYS A . n A 1 208 GLY 208 207 207 GLY GLY A . n A 1 209 ILE 209 208 208 ILE ILE A . n A 1 210 ALA 210 209 209 ALA ALA A . n A 1 211 SER 211 210 210 SER SER A . n A 1 212 PHE 212 211 211 PHE PHE A . n A 1 213 PRO 213 212 212 PRO PRO A . n A 1 214 SER 214 213 213 SER SER A . n A 1 215 TYR 215 214 214 TYR TYR A . n A 1 216 PRO 216 215 215 PRO PRO A . n A 1 217 GLU 217 216 216 GLU GLU A . n A 1 218 ILE 218 217 217 ILE ILE A . n A 1 219 LEU 219 218 ? ? ? A . n A 1 220 GLN 220 219 ? ? ? A . n A 1 221 GLY 221 220 ? ? ? A . n A 1 222 GLY 222 221 ? ? ? A . n A 1 223 GLY 223 222 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 B8Y 1 901 901 B8Y 030 A . C 3 HOH 1 1001 12 HOH HOH A . C 3 HOH 2 1002 37 HOH HOH A . C 3 HOH 3 1003 29 HOH HOH A . C 3 HOH 4 1004 28 HOH HOH A . C 3 HOH 5 1005 5 HOH HOH A . C 3 HOH 6 1006 25 HOH HOH A . C 3 HOH 7 1007 27 HOH HOH A . C 3 HOH 8 1008 32 HOH HOH A . C 3 HOH 9 1009 10 HOH HOH A . C 3 HOH 10 1010 19 HOH HOH A . C 3 HOH 11 1011 8 HOH HOH A . C 3 HOH 12 1012 7 HOH HOH A . C 3 HOH 13 1013 14 HOH HOH A . C 3 HOH 14 1014 4 HOH HOH A . C 3 HOH 15 1015 35 HOH HOH A . C 3 HOH 16 1016 3 HOH HOH A . C 3 HOH 17 1017 33 HOH HOH A . C 3 HOH 18 1018 31 HOH HOH A . C 3 HOH 19 1019 30 HOH HOH A . C 3 HOH 20 1020 18 HOH HOH A . C 3 HOH 21 1021 13 HOH HOH A . C 3 HOH 22 1022 26 HOH HOH A . C 3 HOH 23 1023 20 HOH HOH A . C 3 HOH 24 1024 21 HOH HOH A . C 3 HOH 25 1025 11 HOH HOH A . C 3 HOH 26 1026 15 HOH HOH A . C 3 HOH 27 1027 22 HOH HOH A . C 3 HOH 28 1028 17 HOH HOH A . C 3 HOH 29 1029 6 HOH HOH A . C 3 HOH 30 1030 23 HOH HOH A . C 3 HOH 31 1031 36 HOH HOH A . C 3 HOH 32 1032 2 HOH HOH A . C 3 HOH 33 1033 39 HOH HOH A . C 3 HOH 34 1034 24 HOH HOH A . C 3 HOH 35 1035 40 HOH HOH A . C 3 HOH 36 1036 38 HOH HOH A . C 3 HOH 37 1037 16 HOH HOH A . # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? monomeric 1 2 author_defined_assembly ? monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C 2 1 A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 1036 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id C _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2017-12-20 2 'Structure model' 1 1 2018-02-21 3 'Structure model' 1 2 2021-02-10 4 'Structure model' 1 3 2021-11-17 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Structure summary' 2 3 'Structure model' 'Database references' 3 3 'Structure model' 'Structure summary' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' pdbx_deposit_group 2 3 'Structure model' audit_author 3 3 'Structure model' citation_author 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_deposit_group # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_pdbx_deposit_group.group_type' 2 3 'Structure model' '_audit_author.identifier_ORCID' 3 3 'Structure model' '_citation_author.identifier_ORCID' 4 4 'Structure model' '_database_2.pdbx_DOI' 5 4 'Structure model' '_database_2.pdbx_database_accession' 6 4 'Structure model' '_pdbx_deposit_group.group_description' # _phasing.method MR # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 REFMAC 5.8.0158 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 2 PDB_EXTRACT 3.23 'Dec. 13, 2016' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 MOSFLM . ? ? ? ? 'data reduction' ? ? ? 4 SCALA . ? ? ? ? 'data scaling' ? ? ? # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 THR A 58 ? ? -114.23 -118.07 2 1 TYR A 90 ? ? -155.79 69.30 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A LYS 60 ? CD ? A LYS 61 CD 2 1 Y 1 A LYS 60 ? CE ? A LYS 61 CE 3 1 Y 1 A LYS 60 ? NZ ? A LYS 61 NZ 4 1 Y 1 A LYS 82 ? CE ? A LYS 83 CE 5 1 Y 1 A LYS 82 ? NZ ? A LYS 83 NZ 6 1 Y 1 A LYS 98 ? CG ? A LYS 99 CG 7 1 Y 1 A LYS 98 ? CD ? A LYS 99 CD 8 1 Y 1 A LYS 98 ? CE ? A LYS 99 CE 9 1 Y 1 A LYS 98 ? NZ ? A LYS 99 NZ # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A ILE 0 ? A ILE 1 2 1 Y 1 A LEU 218 ? A LEU 219 3 1 Y 1 A GLN 219 ? A GLN 220 4 1 Y 1 A GLY 220 ? A GLY 221 5 1 Y 1 A GLY 221 ? A GLY 222 6 1 Y 1 A GLY 222 ? A GLY 223 # _pdbx_deposit_group.group_id G_1002040 _pdbx_deposit_group.group_description 'Ligand binding to Cathepsin S' _pdbx_deposit_group.group_title 'Ligand binding to Cathepsin S' _pdbx_deposit_group.group_type undefined # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 ;N-{[2-chloro-5-(4-{3-[4-(6-chloro-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propyl}-3-oxo-3,4-dihydropyrazin-2-yl)phenyl]methyl}-4-fluorobenzamide ; B8Y 3 water HOH #