data_3OVZ # _entry.id 3OVZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.289 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3OVZ RCSB RCSB061640 WWPDB D_1000061640 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3OVX _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3OVZ _pdbx_database_status.recvd_initial_deposition_date 2010-09-17 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Fradera, X.' 1 'van Zeeland, M.' 2 'Uitdehaag, J.C.M.' 3 # _citation.id primary _citation.title 'Trifluoromethylphenyl as P2 for ketoamide-based cathepsin S inhibitors.' _citation.journal_abbrev Bioorg.Med.Chem.Lett. _citation.journal_volume 20 _citation.page_first 6890 _citation.page_last 6894 _citation.year 2010 _citation.journal_id_ASTM BMCLE8 _citation.country UK _citation.journal_id_ISSN 0960-894X _citation.journal_id_CSD 1127 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21030256 _citation.pdbx_database_id_DOI 10.1016/j.bmcl.2010.10.012 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Cai, J.' 1 primary 'Robinson, J.' 2 primary 'Belshaw, S.' 3 primary 'Everett, K.' 4 primary 'Fradera, X.' 5 primary 'van Zeeland, M.' 6 primary 'van Berkom, L.' 7 primary 'van Rijnsbergen, P.' 8 primary 'Popplestone, L.' 9 primary 'Baugh, M.' 10 primary 'Dempster, M.' 11 primary 'Bruin, J.' 12 primary 'Hamilton, W.' 13 primary 'Kinghorn, E.' 14 primary 'Westwood, P.' 15 primary 'Kerr, J.' 16 primary 'Rankovic, Z.' 17 primary 'Arbuckle, W.' 18 primary 'Bennett, D.J.' 19 primary 'Jones, P.S.' 20 primary 'Long, C.' 21 primary 'Martin, I.' 22 primary 'Uitdehaag, J.C.' 23 primary 'Meulemans, T.' 24 # _cell.entry_id 3OVZ _cell.length_a 55.741 _cell.length_b 55.741 _cell.length_c 128.916 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3OVZ _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # 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 K' 23355.287 1 3.4.22.38 ? 'UNP residues 121-329' ? 2 non-polymer syn 'N-[(1S)-3-amino-1-ethyl-2,3-dioxopropyl]-2-chloro-4-(pyridin-2-ylmethoxy)-3-(trifluoromethyl)benzamide' 443.804 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 2 ? ? ? ? 4 water nat water 18.015 79 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Cathepsin O, Cathepsin O2, Cathepsin X' # _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 ;DSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGID SEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNH AVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM ; _entity_poly.pdbx_seq_one_letter_code_can ;DSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGID SEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNH AVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM ; _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 ASP n 1 2 SER n 1 3 VAL n 1 4 ASP n 1 5 TYR n 1 6 ARG n 1 7 LYS n 1 8 LYS n 1 9 GLY n 1 10 TYR n 1 11 VAL n 1 12 THR n 1 13 PRO n 1 14 VAL n 1 15 LYS n 1 16 ASN n 1 17 GLN n 1 18 GLY n 1 19 GLN n 1 20 CYS n 1 21 GLY n 1 22 SER n 1 23 CYS n 1 24 TRP n 1 25 ALA n 1 26 PHE n 1 27 SER n 1 28 SER n 1 29 VAL n 1 30 GLY n 1 31 ALA n 1 32 LEU n 1 33 GLU n 1 34 GLY n 1 35 GLN n 1 36 LEU n 1 37 LYS n 1 38 LYS n 1 39 LYS n 1 40 THR n 1 41 GLY n 1 42 LYS n 1 43 LEU n 1 44 LEU n 1 45 ASN n 1 46 LEU n 1 47 SER n 1 48 PRO n 1 49 GLN n 1 50 ASN n 1 51 LEU n 1 52 VAL n 1 53 ASP n 1 54 CYS n 1 55 VAL n 1 56 SER n 1 57 GLU n 1 58 ASN n 1 59 ASP n 1 60 GLY n 1 61 CYS n 1 62 GLY n 1 63 GLY n 1 64 GLY n 1 65 TYR n 1 66 MET n 1 67 THR n 1 68 ASN n 1 69 ALA n 1 70 PHE n 1 71 GLN n 1 72 TYR n 1 73 VAL n 1 74 GLN n 1 75 LYS n 1 76 ASN n 1 77 ARG n 1 78 GLY n 1 79 ILE n 1 80 ASP n 1 81 SER n 1 82 GLU n 1 83 ASP n 1 84 ALA n 1 85 TYR n 1 86 PRO n 1 87 TYR n 1 88 VAL n 1 89 GLY n 1 90 GLN n 1 91 GLU n 1 92 GLU n 1 93 SER n 1 94 CYS n 1 95 MET n 1 96 TYR n 1 97 ASN n 1 98 PRO n 1 99 THR n 1 100 GLY n 1 101 LYS n 1 102 ALA n 1 103 ALA n 1 104 LYS n 1 105 CYS n 1 106 ARG n 1 107 GLY n 1 108 TYR n 1 109 ARG n 1 110 GLU n 1 111 ILE n 1 112 PRO n 1 113 GLU n 1 114 GLY n 1 115 ASN n 1 116 GLU n 1 117 LYS n 1 118 ALA n 1 119 LEU n 1 120 LYS n 1 121 ARG n 1 122 ALA n 1 123 VAL n 1 124 ALA n 1 125 ARG n 1 126 VAL n 1 127 GLY n 1 128 PRO n 1 129 VAL n 1 130 SER n 1 131 VAL n 1 132 ALA n 1 133 ILE n 1 134 ASP n 1 135 ALA n 1 136 SER n 1 137 LEU n 1 138 THR n 1 139 SER n 1 140 PHE n 1 141 GLN n 1 142 PHE n 1 143 TYR n 1 144 SER n 1 145 LYS n 1 146 GLY n 1 147 VAL n 1 148 TYR n 1 149 TYR n 1 150 ASP n 1 151 GLU n 1 152 SER n 1 153 CYS n 1 154 ASN n 1 155 SER n 1 156 ASP n 1 157 ASN n 1 158 LEU n 1 159 ASN n 1 160 HIS n 1 161 ALA n 1 162 VAL n 1 163 LEU n 1 164 ALA n 1 165 VAL n 1 166 GLY n 1 167 TYR n 1 168 GLY n 1 169 ILE n 1 170 GLN n 1 171 LYS n 1 172 GLY n 1 173 ASN n 1 174 LYS n 1 175 HIS n 1 176 TRP n 1 177 ILE n 1 178 ILE n 1 179 LYS n 1 180 ASN n 1 181 SER n 1 182 TRP n 1 183 GLY n 1 184 GLU n 1 185 ASN n 1 186 TRP n 1 187 GLY n 1 188 ASN n 1 189 LYS n 1 190 GLY n 1 191 TYR n 1 192 ILE n 1 193 LEU n 1 194 MET n 1 195 ALA n 1 196 ARG n 1 197 ASN n 1 198 LYS n 1 199 ASN n 1 200 ASN n 1 201 ALA n 1 202 CYS n 1 203 GLY n 1 204 ILE n 1 205 ALA n 1 206 ASN n 1 207 LEU n 1 208 ALA n 1 209 SER n 1 210 PHE n 1 211 PRO n 1 212 LYS n 1 213 MET 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 ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'CTSK, CTSO, CTSO2' _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 ? _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ? _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 ? _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 CATK_HUMAN _struct_ref.pdbx_db_accession P43235 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;YRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDA YPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLA VGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM ; _struct_ref.pdbx_align_begin 121 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3OVZ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 5 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 213 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P43235 _struct_ref_seq.db_align_beg 121 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 329 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 7 _struct_ref_seq.pdbx_auth_seq_align_end 215 # 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 3OVZ ASP A 1 ? UNP P43235 ? ? 'EXPRESSION TAG' 3 1 1 3OVZ SER A 2 ? UNP P43235 ? ? 'EXPRESSION TAG' 4 2 1 3OVZ VAL A 3 ? UNP P43235 ? ? 'EXPRESSION TAG' 5 3 1 3OVZ ASP A 4 ? UNP P43235 ? ? 'EXPRESSION TAG' 6 4 # 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 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 O96 non-polymer . 'N-[(1S)-3-amino-1-ethyl-2,3-dioxopropyl]-2-chloro-4-(pyridin-2-ylmethoxy)-3-(trifluoromethyl)benzamide' ? 'C19 H17 Cl F3 N3 O4' 443.804 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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.entry_id 3OVZ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.02 _exptl_crystal.density_percent_sol 38.61 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 298.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;0 mM NaAcetate pH=4.0, 0.3 M NaCl, 20% PEG4000, 0.2 M (NH4)2SO4, pH=2.9, 4% Methanol, Cryoprotectant composition:20% PEG4000, 0.1M (NH4)2SO4 pH=2.9, 4% Methanol, 20% PEG 400, pH 5, cocrystallization, hanging drop, temperature 398K ; # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2008-02-12 _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 1.5418 _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 1.5418 _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 3OVZ _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 55.740 _reflns.d_resolution_high 2.020 _reflns.number_obs 14051 _reflns.number_all ? _reflns.percent_possible_obs 100.0 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.02 _reflns_shell.d_res_low 2.09 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.7 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.0 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3OVZ _refine.ls_number_reflns_obs 13991 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 51.16 _refine.ls_d_res_high 2.02 _refine.ls_percent_reflns_obs 99.7 _refine.ls_R_factor_obs 0.247 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.244 _refine.ls_R_factor_R_free 0.308 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 698 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.934 _refine.correlation_coeff_Fo_to_Fc_free 0.902 _refine.B_iso_mean 35.26 _refine.aniso_B[1][1] 0.99000 _refine.aniso_B[2][2] 0.99000 _refine.aniso_B[3][3] -1.98000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 'In-house cathepsin K structure' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.204 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 7.597 _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.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_ESU_R ? _refine.pdbx_TLS_residual_ADP_flag ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1637 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 40 _refine_hist.number_atoms_solvent 79 _refine_hist.number_atoms_total 1756 _refine_hist.d_res_high 2.02 _refine_hist.d_res_low 51.16 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.016 0.022 ? 1738 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 1176 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.785 1.966 ? 2355 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.052 3.005 ? 2859 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.198 5.000 ? 219 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 40.592 25.366 ? 82 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 18.138 15.000 ? 288 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 13.198 15.000 ? 7 'X-RAY DIFFRACTION' ? r_chiral_restr 0.104 0.200 ? 236 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.006 0.020 ? 1976 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 344 'X-RAY DIFFRACTION' ? r_nbd_refined 0.215 0.200 ? 355 'X-RAY DIFFRACTION' ? r_nbd_other 0.211 0.200 ? 1190 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.187 0.200 ? 824 'X-RAY DIFFRACTION' ? r_nbtor_other 0.092 0.200 ? 878 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.160 0.200 ? 84 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.276 0.200 ? 21 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.300 0.200 ? 48 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.257 0.200 ? 7 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 0.917 1.500 ? 1366 'X-RAY DIFFRACTION' ? r_mcbond_other 0.171 1.500 ? 449 'X-RAY DIFFRACTION' ? r_mcangle_it 1.106 2.000 ? 1686 'X-RAY DIFFRACTION' ? r_scbond_it 1.891 3.000 ? 831 'X-RAY DIFFRACTION' ? r_scangle_it 2.502 4.500 ? 665 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.02 _refine_ls_shell.d_res_low 2.07 _refine_ls_shell.number_reflns_R_work 975 _refine_ls_shell.R_factor_R_work 0.307 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.4290 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 55 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 3OVZ _struct.title 'Cathepsin K in complex with a covalent inhibitor with a ketoamide warhead' _struct.pdbx_descriptor 'Cathepsin K (E.C.3.4.22.38)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3OVZ _struct_keywords.pdbx_keywords 'HYDROLASE/HYDROLASE INHIBITOR' _struct_keywords.text ;Cathepsin K, hydrolase, covalent inhibitor, ketoamide warhead, Ligand forms covalent bond to Cys25, Lysosomes, HYDROLASE-HYDROLASE INHIBITOR complex ; # 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 ? D N N 3 ? E N N 4 ? # _struct_biol.id 1 _struct_biol.details ? # 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 1 ARG A 6 ? GLY A 9 ? ARG A 8 GLY A 11 5 ? 4 HELX_P HELX_P2 2 SER A 22 ? GLY A 41 ? SER A 24 GLY A 43 1 ? 20 HELX_P HELX_P3 3 SER A 47 ? VAL A 55 ? SER A 49 VAL A 57 1 ? 9 HELX_P HELX_P4 4 ASP A 59 ? GLY A 63 ? ASP A 61 GLY A 65 5 ? 5 HELX_P HELX_P5 5 TYR A 65 ? ASN A 76 ? TYR A 67 ASN A 78 1 ? 12 HELX_P HELX_P6 6 ASN A 97 ? THR A 99 ? ASN A 99 THR A 101 5 ? 3 HELX_P HELX_P7 7 ASN A 115 ? VAL A 126 ? ASN A 117 VAL A 128 1 ? 12 HELX_P HELX_P8 8 LEU A 137 ? PHE A 142 ? LEU A 139 PHE A 144 1 ? 6 HELX_P HELX_P9 9 ASN A 200 ? ILE A 204 ? ASN A 202 ILE A 206 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 disulf1 disulf ? ? A CYS 20 SG ? ? ? 1_555 A CYS 61 SG ? ? A CYS 22 A CYS 63 1_555 ? ? ? ? ? ? ? 2.023 ? disulf2 disulf ? ? A CYS 54 SG ? ? ? 1_555 A CYS 94 SG ? ? A CYS 56 A CYS 96 1_555 ? ? ? ? ? ? ? 2.008 ? disulf3 disulf ? ? A CYS 153 SG ? ? ? 1_555 A CYS 202 SG ? ? A CYS 155 A CYS 204 1_555 ? ? ? ? ? ? ? 2.010 ? # _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 A ? 3 ? B ? 5 ? C ? 2 ? D ? 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 A 1 2 ? anti-parallel A 2 3 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? parallel C 1 2 ? anti-parallel D 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 A 1 VAL A 3 ? ASP A 4 ? VAL A 5 ASP A 6 A 2 HIS A 160 ? GLN A 170 ? HIS A 162 GLN A 172 A 3 VAL A 129 ? ILE A 133 ? VAL A 131 ILE A 135 B 1 VAL A 3 ? ASP A 4 ? VAL A 5 ASP A 6 B 2 HIS A 160 ? GLN A 170 ? HIS A 162 GLN A 172 B 3 ASN A 173 ? LYS A 179 ? ASN A 175 LYS A 181 B 4 TYR A 191 ? ALA A 195 ? TYR A 193 ALA A 197 B 5 VAL A 147 ? TYR A 148 ? VAL A 149 TYR A 150 C 1 ILE A 79 ? ASP A 80 ? ILE A 81 ASP A 82 C 2 LYS A 101 ? ALA A 103 ? LYS A 103 ALA A 105 D 1 TYR A 108 ? GLU A 110 ? TYR A 110 GLU A 112 D 2 SER A 209 ? PRO A 211 ? SER A 211 PRO A 213 # 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 A 1 2 N VAL A 3 ? N VAL A 5 O TYR A 167 ? O TYR A 169 A 2 3 O VAL A 162 ? O VAL A 164 N VAL A 131 ? N VAL A 133 B 1 2 N VAL A 3 ? N VAL A 5 O TYR A 167 ? O TYR A 169 B 2 3 N GLN A 170 ? N GLN A 172 O ASN A 173 ? O ASN A 175 B 3 4 N ILE A 178 ? N ILE A 180 O ILE A 192 ? O ILE A 194 B 4 5 O LEU A 193 ? O LEU A 195 N TYR A 148 ? N TYR A 150 C 1 2 N ILE A 79 ? N ILE A 81 O ALA A 102 ? O ALA A 104 D 1 2 N ARG A 109 ? N ARG A 111 O PHE A 210 ? O PHE A 212 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 16 'BINDING SITE FOR RESIDUE O96 A 1' AC2 Software ? ? ? ? 7 'BINDING SITE FOR RESIDUE SO4 A 216' AC3 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE SO4 A 2' # 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 16 GLN A 17 ? GLN A 19 . ? 1_555 ? 2 AC1 16 GLY A 21 ? GLY A 23 . ? 1_555 ? 3 AC1 16 SER A 22 ? SER A 24 . ? 1_555 ? 4 AC1 16 CYS A 23 ? CYS A 25 . ? 1_555 ? 5 AC1 16 TRP A 24 ? TRP A 26 . ? 1_555 ? 6 AC1 16 GLY A 63 ? GLY A 65 . ? 1_555 ? 7 AC1 16 GLY A 64 ? GLY A 66 . ? 1_555 ? 8 AC1 16 TYR A 65 ? TYR A 67 . ? 1_555 ? 9 AC1 16 LYS A 101 ? LYS A 103 . ? 5_554 ? 10 AC1 16 ALA A 132 ? ALA A 134 . ? 1_555 ? 11 AC1 16 LEU A 158 ? LEU A 160 . ? 1_555 ? 12 AC1 16 ASN A 159 ? ASN A 161 . ? 1_555 ? 13 AC1 16 HIS A 160 ? HIS A 162 . ? 1_555 ? 14 AC1 16 ALA A 161 ? ALA A 163 . ? 1_555 ? 15 AC1 16 LEU A 207 ? LEU A 209 . ? 1_555 ? 16 AC1 16 HOH E . ? HOH A 242 . ? 1_555 ? 17 AC2 7 ASN A 16 ? ASN A 18 . ? 1_555 ? 18 AC2 7 ARG A 106 ? ARG A 108 . ? 4_545 ? 19 AC2 7 ARG A 109 ? ARG A 111 . ? 4_545 ? 20 AC2 7 GLY A 183 ? GLY A 185 . ? 1_555 ? 21 AC2 7 GLU A 184 ? GLU A 186 . ? 1_555 ? 22 AC2 7 ASN A 185 ? ASN A 187 . ? 1_555 ? 23 AC2 7 LYS A 212 ? LYS A 214 . ? 4_545 ? 24 AC3 4 LYS A 120 ? LYS A 122 . ? 1_555 ? 25 AC3 4 LYS A 174 ? LYS A 176 . ? 1_555 ? 26 AC3 4 ARG A 196 ? ARG A 198 . ? 1_555 ? 27 AC3 4 ASN A 197 ? ASN A 199 . ? 1_555 ? # _database_PDB_matrix.entry_id 3OVZ _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 3OVZ _atom_sites.fract_transf_matrix[1][1] 0.017940 _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] 0.017940 _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] 0.007757 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # 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 ASP 1 3 3 ASP ASP A . n A 1 2 SER 2 4 4 SER SER A . n A 1 3 VAL 3 5 5 VAL VAL A . n A 1 4 ASP 4 6 6 ASP ASP A . n A 1 5 TYR 5 7 7 TYR TYR A . n A 1 6 ARG 6 8 8 ARG ARG A . n A 1 7 LYS 7 9 9 LYS LYS A . n A 1 8 LYS 8 10 10 LYS LYS A . n A 1 9 GLY 9 11 11 GLY GLY A . n A 1 10 TYR 10 12 12 TYR TYR A . n A 1 11 VAL 11 13 13 VAL VAL A . n A 1 12 THR 12 14 14 THR THR A . n A 1 13 PRO 13 15 15 PRO PRO A . n A 1 14 VAL 14 16 16 VAL VAL A . n A 1 15 LYS 15 17 17 LYS LYS A . n A 1 16 ASN 16 18 18 ASN ASN A . n A 1 17 GLN 17 19 19 GLN GLN A . n A 1 18 GLY 18 20 20 GLY GLY A . n A 1 19 GLN 19 21 21 GLN GLN A . n A 1 20 CYS 20 22 22 CYS CYS A . n A 1 21 GLY 21 23 23 GLY GLY A . n A 1 22 SER 22 24 24 SER SER A . n A 1 23 CYS 23 25 25 CYS CYS A . n A 1 24 TRP 24 26 26 TRP TRP A . n A 1 25 ALA 25 27 27 ALA ALA A . n A 1 26 PHE 26 28 28 PHE PHE A . n A 1 27 SER 27 29 29 SER SER A . n A 1 28 SER 28 30 30 SER SER A . n A 1 29 VAL 29 31 31 VAL VAL A . n A 1 30 GLY 30 32 32 GLY GLY A . n A 1 31 ALA 31 33 33 ALA ALA A . n A 1 32 LEU 32 34 34 LEU LEU A . n A 1 33 GLU 33 35 35 GLU GLU A . n A 1 34 GLY 34 36 36 GLY GLY A . n A 1 35 GLN 35 37 37 GLN GLN A . n A 1 36 LEU 36 38 38 LEU LEU A . n A 1 37 LYS 37 39 39 LYS LYS A . n A 1 38 LYS 38 40 40 LYS LYS A . n A 1 39 LYS 39 41 41 LYS LYS A . n A 1 40 THR 40 42 42 THR THR A . n A 1 41 GLY 41 43 43 GLY GLY A . n A 1 42 LYS 42 44 44 LYS LYS A . n A 1 43 LEU 43 45 45 LEU LEU A . n A 1 44 LEU 44 46 46 LEU LEU A . n A 1 45 ASN 45 47 47 ASN ASN A . n A 1 46 LEU 46 48 48 LEU LEU A . n A 1 47 SER 47 49 49 SER SER A . n A 1 48 PRO 48 50 50 PRO PRO A . n A 1 49 GLN 49 51 51 GLN GLN A . n A 1 50 ASN 50 52 52 ASN ASN A . n A 1 51 LEU 51 53 53 LEU LEU A . n A 1 52 VAL 52 54 54 VAL VAL A . n A 1 53 ASP 53 55 55 ASP ASP A . n A 1 54 CYS 54 56 56 CYS CYS A . n A 1 55 VAL 55 57 57 VAL VAL A . n A 1 56 SER 56 58 58 SER SER A . n A 1 57 GLU 57 59 59 GLU GLU A . n A 1 58 ASN 58 60 60 ASN ASN A . n A 1 59 ASP 59 61 61 ASP ASP A . n A 1 60 GLY 60 62 62 GLY GLY A . n A 1 61 CYS 61 63 63 CYS CYS A . n A 1 62 GLY 62 64 64 GLY GLY A . n A 1 63 GLY 63 65 65 GLY GLY A . n A 1 64 GLY 64 66 66 GLY GLY A . n A 1 65 TYR 65 67 67 TYR TYR A . n A 1 66 MET 66 68 68 MET MET A . n A 1 67 THR 67 69 69 THR THR A . n A 1 68 ASN 68 70 70 ASN ASN A . n A 1 69 ALA 69 71 71 ALA ALA A . n A 1 70 PHE 70 72 72 PHE PHE A . n A 1 71 GLN 71 73 73 GLN GLN A . n A 1 72 TYR 72 74 74 TYR TYR A . n A 1 73 VAL 73 75 75 VAL VAL A . n A 1 74 GLN 74 76 76 GLN GLN A . n A 1 75 LYS 75 77 77 LYS LYS A . n A 1 76 ASN 76 78 78 ASN ASN A . n A 1 77 ARG 77 79 79 ARG ARG A . n A 1 78 GLY 78 80 80 GLY GLY A . n A 1 79 ILE 79 81 81 ILE ILE A . n A 1 80 ASP 80 82 82 ASP ASP A . n A 1 81 SER 81 83 83 SER SER A . n A 1 82 GLU 82 84 84 GLU GLU A . n A 1 83 ASP 83 85 85 ASP ASP A . n A 1 84 ALA 84 86 86 ALA ALA A . n A 1 85 TYR 85 87 87 TYR TYR A . n A 1 86 PRO 86 88 88 PRO PRO A . n A 1 87 TYR 87 89 89 TYR TYR A . n A 1 88 VAL 88 90 90 VAL VAL A . n A 1 89 GLY 89 91 91 GLY GLY A . n A 1 90 GLN 90 92 92 GLN GLN A . n A 1 91 GLU 91 93 93 GLU GLU A . n A 1 92 GLU 92 94 94 GLU GLU A . n A 1 93 SER 93 95 95 SER SER A . n A 1 94 CYS 94 96 96 CYS CYS A . n A 1 95 MET 95 97 97 MET MET A . n A 1 96 TYR 96 98 98 TYR TYR A . n A 1 97 ASN 97 99 99 ASN ASN A . n A 1 98 PRO 98 100 100 PRO PRO A . n A 1 99 THR 99 101 101 THR THR A . n A 1 100 GLY 100 102 102 GLY GLY A . n A 1 101 LYS 101 103 103 LYS LYS A . n A 1 102 ALA 102 104 104 ALA ALA A . n A 1 103 ALA 103 105 105 ALA ALA A . n A 1 104 LYS 104 106 106 LYS LYS A . n A 1 105 CYS 105 107 107 CYS CYS A . n A 1 106 ARG 106 108 108 ARG ARG A . n A 1 107 GLY 107 109 109 GLY GLY A . n A 1 108 TYR 108 110 110 TYR TYR A . n A 1 109 ARG 109 111 111 ARG ARG A . n A 1 110 GLU 110 112 112 GLU GLU A . n A 1 111 ILE 111 113 113 ILE ILE A . n A 1 112 PRO 112 114 114 PRO PRO A . n A 1 113 GLU 113 115 115 GLU GLU A . n A 1 114 GLY 114 116 116 GLY GLY A . n A 1 115 ASN 115 117 117 ASN ASN A . n A 1 116 GLU 116 118 118 GLU GLU A . n A 1 117 LYS 117 119 119 LYS LYS A . n A 1 118 ALA 118 120 120 ALA ALA A . n A 1 119 LEU 119 121 121 LEU LEU A . n A 1 120 LYS 120 122 122 LYS LYS A . n A 1 121 ARG 121 123 123 ARG ARG A . n A 1 122 ALA 122 124 124 ALA ALA A . n A 1 123 VAL 123 125 125 VAL VAL A . n A 1 124 ALA 124 126 126 ALA ALA A . n A 1 125 ARG 125 127 127 ARG ARG A . n A 1 126 VAL 126 128 128 VAL VAL A . n A 1 127 GLY 127 129 129 GLY GLY A . n A 1 128 PRO 128 130 130 PRO PRO A . n A 1 129 VAL 129 131 131 VAL VAL A . n A 1 130 SER 130 132 132 SER SER A . n A 1 131 VAL 131 133 133 VAL VAL A . n A 1 132 ALA 132 134 134 ALA ALA A . n A 1 133 ILE 133 135 135 ILE ILE A . n A 1 134 ASP 134 136 136 ASP ASP A . n A 1 135 ALA 135 137 137 ALA ALA A . n A 1 136 SER 136 138 138 SER SER A . n A 1 137 LEU 137 139 139 LEU LEU A . n A 1 138 THR 138 140 140 THR THR A . n A 1 139 SER 139 141 141 SER SER A . n A 1 140 PHE 140 142 142 PHE PHE A . n A 1 141 GLN 141 143 143 GLN GLN A . n A 1 142 PHE 142 144 144 PHE PHE A . n A 1 143 TYR 143 145 145 TYR TYR A . n A 1 144 SER 144 146 146 SER SER A . n A 1 145 LYS 145 147 147 LYS LYS A . n A 1 146 GLY 146 148 148 GLY GLY A . n A 1 147 VAL 147 149 149 VAL VAL A . n A 1 148 TYR 148 150 150 TYR TYR A . n A 1 149 TYR 149 151 151 TYR TYR A . n A 1 150 ASP 150 152 152 ASP ASP A . n A 1 151 GLU 151 153 153 GLU GLU A . n A 1 152 SER 152 154 154 SER SER A . n A 1 153 CYS 153 155 155 CYS CYS A . n A 1 154 ASN 154 156 156 ASN ASN A . n A 1 155 SER 155 157 157 SER SER A . n A 1 156 ASP 156 158 158 ASP ASP A . n A 1 157 ASN 157 159 159 ASN ASN A . n A 1 158 LEU 158 160 160 LEU LEU A . n A 1 159 ASN 159 161 161 ASN ASN A . n A 1 160 HIS 160 162 162 HIS HIS A . n A 1 161 ALA 161 163 163 ALA ALA A . n A 1 162 VAL 162 164 164 VAL VAL A . n A 1 163 LEU 163 165 165 LEU LEU A . n A 1 164 ALA 164 166 166 ALA ALA A . n A 1 165 VAL 165 167 167 VAL VAL A . n A 1 166 GLY 166 168 168 GLY GLY A . n A 1 167 TYR 167 169 169 TYR TYR A . n A 1 168 GLY 168 170 170 GLY GLY A . n A 1 169 ILE 169 171 171 ILE ILE A . n A 1 170 GLN 170 172 172 GLN GLN A . n A 1 171 LYS 171 173 173 LYS LYS A . n A 1 172 GLY 172 174 174 GLY GLY A . n A 1 173 ASN 173 175 175 ASN ASN A . n A 1 174 LYS 174 176 176 LYS LYS A . n A 1 175 HIS 175 177 177 HIS HIS A . n A 1 176 TRP 176 178 178 TRP TRP A . n A 1 177 ILE 177 179 179 ILE ILE A . n A 1 178 ILE 178 180 180 ILE ILE A . n A 1 179 LYS 179 181 181 LYS LYS A . n A 1 180 ASN 180 182 182 ASN ASN A . n A 1 181 SER 181 183 183 SER SER A . n A 1 182 TRP 182 184 184 TRP TRP A . n A 1 183 GLY 183 185 185 GLY GLY A . n A 1 184 GLU 184 186 186 GLU GLU A . n A 1 185 ASN 185 187 187 ASN ASN A . n A 1 186 TRP 186 188 188 TRP TRP A . n A 1 187 GLY 187 189 189 GLY GLY A . n A 1 188 ASN 188 190 190 ASN ASN A . n A 1 189 LYS 189 191 191 LYS LYS A . n A 1 190 GLY 190 192 192 GLY GLY A . n A 1 191 TYR 191 193 193 TYR TYR A . n A 1 192 ILE 192 194 194 ILE ILE A . n A 1 193 LEU 193 195 195 LEU LEU A . n A 1 194 MET 194 196 196 MET MET A . n A 1 195 ALA 195 197 197 ALA ALA A . n A 1 196 ARG 196 198 198 ARG ARG A . n A 1 197 ASN 197 199 199 ASN ASN A . n A 1 198 LYS 198 200 200 LYS LYS A . n A 1 199 ASN 199 201 201 ASN ASN A . n A 1 200 ASN 200 202 202 ASN ASN A . n A 1 201 ALA 201 203 203 ALA ALA A . n A 1 202 CYS 202 204 204 CYS CYS A . n A 1 203 GLY 203 205 205 GLY GLY A . n A 1 204 ILE 204 206 206 ILE ILE A . n A 1 205 ALA 205 207 207 ALA ALA A . n A 1 206 ASN 206 208 208 ASN ASN A . n A 1 207 LEU 207 209 209 LEU LEU A . n A 1 208 ALA 208 210 210 ALA ALA A . n A 1 209 SER 209 211 211 SER SER A . n A 1 210 PHE 210 212 212 PHE PHE A . n A 1 211 PRO 211 213 213 PRO PRO A . n A 1 212 LYS 212 214 214 LYS LYS A . n A 1 213 MET 213 215 215 MET MET 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 O96 1 1 1 O96 O96 A . C 3 SO4 1 216 1 SO4 SO4 A . D 3 SO4 1 2 2 SO4 SO4 A . E 4 HOH 1 217 1 HOH HOH A . E 4 HOH 2 218 2 HOH HOH A . E 4 HOH 3 219 3 HOH HOH A . E 4 HOH 4 220 4 HOH HOH A . E 4 HOH 5 221 5 HOH HOH A . E 4 HOH 6 222 6 HOH HOH A . E 4 HOH 7 223 7 HOH HOH A . E 4 HOH 8 224 9 HOH HOH A . E 4 HOH 9 225 10 HOH HOH A . E 4 HOH 10 226 11 HOH HOH A . E 4 HOH 11 227 12 HOH HOH A . E 4 HOH 12 228 13 HOH HOH A . E 4 HOH 13 229 14 HOH HOH A . E 4 HOH 14 230 15 HOH HOH A . E 4 HOH 15 231 16 HOH HOH A . E 4 HOH 16 232 17 HOH HOH A . E 4 HOH 17 233 18 HOH HOH A . E 4 HOH 18 234 19 HOH HOH A . E 4 HOH 19 235 20 HOH HOH A . E 4 HOH 20 236 21 HOH HOH A . E 4 HOH 21 237 22 HOH HOH A . E 4 HOH 22 238 23 HOH HOH A . E 4 HOH 23 239 24 HOH HOH A . E 4 HOH 24 240 25 HOH HOH A . E 4 HOH 25 241 26 HOH HOH A . E 4 HOH 26 242 27 HOH HOH A . E 4 HOH 27 243 28 HOH HOH A . E 4 HOH 28 244 29 HOH HOH A . E 4 HOH 29 245 30 HOH HOH A . E 4 HOH 30 246 31 HOH HOH A . E 4 HOH 31 247 32 HOH HOH A . E 4 HOH 32 248 33 HOH HOH A . E 4 HOH 33 249 34 HOH HOH A . E 4 HOH 34 250 35 HOH HOH A . E 4 HOH 35 251 36 HOH HOH A . E 4 HOH 36 252 37 HOH HOH A . E 4 HOH 37 253 38 HOH HOH A . E 4 HOH 38 254 39 HOH HOH A . E 4 HOH 39 255 40 HOH HOH A . E 4 HOH 40 256 41 HOH HOH A . E 4 HOH 41 257 42 HOH HOH A . E 4 HOH 42 258 43 HOH HOH A . E 4 HOH 43 259 44 HOH HOH A . E 4 HOH 44 260 45 HOH HOH A . E 4 HOH 45 261 47 HOH HOH A . E 4 HOH 46 262 48 HOH HOH A . E 4 HOH 47 263 49 HOH HOH A . E 4 HOH 48 264 50 HOH HOH A . E 4 HOH 49 265 51 HOH HOH A . E 4 HOH 50 266 53 HOH HOH A . E 4 HOH 51 267 54 HOH HOH A . E 4 HOH 52 268 55 HOH HOH A . E 4 HOH 53 269 56 HOH HOH A . E 4 HOH 54 270 57 HOH HOH A . E 4 HOH 55 271 58 HOH HOH A . E 4 HOH 56 272 59 HOH HOH A . E 4 HOH 57 273 60 HOH HOH A . E 4 HOH 58 274 61 HOH HOH A . E 4 HOH 59 275 62 HOH HOH A . E 4 HOH 60 276 63 HOH HOH A . E 4 HOH 61 277 64 HOH HOH A . E 4 HOH 62 278 65 HOH HOH A . E 4 HOH 63 279 67 HOH HOH A . E 4 HOH 64 280 69 HOH HOH A . E 4 HOH 65 281 70 HOH HOH A . E 4 HOH 66 282 71 HOH HOH A . E 4 HOH 67 283 72 HOH HOH A . E 4 HOH 68 284 73 HOH HOH A . E 4 HOH 69 285 74 HOH HOH A . E 4 HOH 70 286 75 HOH HOH A . E 4 HOH 71 287 76 HOH HOH A . E 4 HOH 72 288 77 HOH HOH A . E 4 HOH 73 289 78 HOH HOH A . E 4 HOH 74 290 79 HOH HOH A . E 4 HOH 75 291 80 HOH HOH A . E 4 HOH 76 292 81 HOH HOH A . E 4 HOH 77 293 82 HOH HOH A . E 4 HOH 78 294 84 HOH HOH A . E 4 HOH 79 295 85 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _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 # 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 2010-12-22 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2011-10-12 4 'Structure model' 1 3 2012-05-09 5 'Structure model' 1 4 2018-01-31 # _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 ? # 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' 'Version format compliance' 2 3 'Structure model' 'Derived calculations' 3 4 'Structure model' 'Data collection' 4 5 'Structure model' 'Experimental preparation' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 5 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category exptl_crystal_grow # 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 5 'Structure model' '_exptl_crystal_grow.pdbx_details' 2 5 'Structure model' '_exptl_crystal_grow.temp' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CrystalClear 'data collection' . ? 1 MOLREP phasing . ? 2 REFMAC refinement 5.2.0019 ? 3 d*TREK 'data reduction' . ? 4 d*TREK 'data scaling' . ? 5 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 SG _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 CYS _pdbx_validate_close_contact.auth_seq_id_1 25 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 C5 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 O96 _pdbx_validate_close_contact.auth_seq_id_2 1 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.14 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CA A LEU 38 ? ? CB A LEU 38 ? ? CG A LEU 38 ? ? 129.60 115.30 14.30 2.30 N 2 1 NE A ARG 127 ? ? CZ A ARG 127 ? ? NH1 A ARG 127 ? ? 124.61 120.30 4.31 0.50 N 3 1 NE A ARG 127 ? ? CZ A ARG 127 ? ? NH2 A ARG 127 ? ? 117.04 120.30 -3.26 0.50 N # 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 LYS A 173 ? ? 36.95 54.53 2 1 ASN A 199 ? ? 70.34 31.87 3 1 LYS A 200 ? ? -119.22 50.98 4 1 LEU A 209 ? ? -147.48 53.11 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'N-[(1S)-3-amino-1-ethyl-2,3-dioxopropyl]-2-chloro-4-(pyridin-2-ylmethoxy)-3-(trifluoromethyl)benzamide' O96 3 'SULFATE ION' SO4 4 water HOH #