data_3KAF # _model_server_result.job_id 42yxG3NvoGwQelN8q3qX3g _model_server_result.datetime_utc '2025-03-26 02:29:17' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3kaf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":164}' # _entry.id 3KAF # _exptl.entry_id 3KAF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 365.406 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-(1H-benzimidazol-2-yl)-N-(1-benzothiophen-2-ylcarbonyl)-D-alanine _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 3KAF _cell.length_a 67.937 _cell.length_b 67.937 _cell.length_c 79.247 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KAF _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C19 H15 N3 O3 S' _chem_comp.formula_weight 365.406 _chem_comp.id 4D9 _chem_comp.mon_nstd_flag . _chem_comp.name 3-(1H-benzimidazol-2-yl)-N-(1-benzothiophen-2-ylcarbonyl)-D-alanine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(R)-2-[(Benzo[b]thiophene-2-carbonyl)-amino]-3-(1H-benzoimidazol-2-yl)-propionic acid' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C6 C1 4D9 doub 1 n y C2 C1 4D9 sing 2 n y C1 H1 4D9 sing 3 n n C3 C2 4D9 doub 4 n y C2 H2 4D9 sing 5 n n C4 C3 4D9 sing 6 n y C3 H3 4D9 sing 7 n n C4 C7 4D9 doub 8 n y C4 H4 4D9 sing 9 n n C9 N5 4D9 sing 10 n y N5 C6 4D9 sing 11 n y C7 C6 4D9 sing 12 n y N8 C7 4D9 sing 13 n y N8 C9 4D9 doub 14 n y C10 C9 4D9 sing 15 n n C11 C10 4D9 sing 16 n n C10 H10 4D9 sing 17 n n C10 H10A 4D9 sing 18 n n N13 C11 4D9 sing 19 n n C12 C11 4D9 sing 20 n n C11 H11 4D9 sing 21 n n O14 C12 4D9 doub 22 n n C12 O15 4D9 sing 23 n n C16 N13 4D9 sing 24 n n N13 HN13 4D9 sing 25 n n O15 HO15 4D9 sing 26 n n C17 C16 4D9 sing 27 n n C16 O18 4D9 doub 28 n n C19 C17 4D9 doub 29 n y S20 C17 4D9 sing 30 n y C22 C19 4D9 sing 31 n y C19 H19 4D9 sing 32 n n C21 S20 4D9 sing 33 n y C26 C21 4D9 doub 34 n y C22 C21 4D9 sing 35 n y C23 C22 4D9 doub 36 n y C24 C23 4D9 sing 37 n y C23 H23 4D9 sing 38 n n C24 C25 4D9 doub 39 n y C24 H24 4D9 sing 40 n n C25 C26 4D9 sing 41 n y C25 H25 4D9 sing 42 n n C26 H26 4D9 sing 43 n n N5 HN5 4D9 sing 44 n n # _atom_sites.entry_id 3KAF _atom_sites.fract_transf_matrix[1][1] 0.014719 _atom_sites.fract_transf_matrix[1][2] 0.008498 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016997 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012619 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code B 2 4D9 A 1 164 1 4D9 4D9 . C 3 HOH A 1 165 1 HOH HOH . C 3 HOH A 2 166 2 HOH HOH . C 3 HOH A 3 167 3 HOH HOH . C 3 HOH A 4 168 4 HOH HOH . C 3 HOH A 5 169 5 HOH HOH . C 3 HOH A 6 170 6 HOH HOH . C 3 HOH A 7 171 8 HOH HOH . C 3 HOH A 8 172 11 HOH HOH . C 3 HOH A 9 173 12 HOH HOH . C 3 HOH A 10 174 14 HOH HOH . C 3 HOH A 11 175 15 HOH HOH . C 3 HOH A 12 176 16 HOH HOH . C 3 HOH A 13 177 17 HOH HOH . C 3 HOH A 14 178 18 HOH HOH . C 3 HOH A 15 179 19 HOH HOH . C 3 HOH A 16 180 20 HOH HOH . C 3 HOH A 17 181 22 HOH HOH . C 3 HOH A 18 182 25 HOH HOH . C 3 HOH A 19 183 26 HOH HOH . C 3 HOH A 20 184 27 HOH HOH . C 3 HOH A 21 185 28 HOH HOH . C 3 HOH A 22 186 29 HOH HOH . C 3 HOH A 23 187 30 HOH HOH . C 3 HOH A 24 188 32 HOH HOH . C 3 HOH A 25 189 37 HOH HOH . C 3 HOH A 26 190 39 HOH HOH . C 3 HOH A 27 191 40 HOH HOH . C 3 HOH A 28 192 43 HOH HOH . C 3 HOH A 29 193 45 HOH HOH . C 3 HOH A 30 194 47 HOH HOH . C 3 HOH A 31 195 51 HOH HOH . C 3 HOH A 32 196 52 HOH HOH . C 3 HOH A 33 197 57 HOH HOH . C 3 HOH A 34 198 59 HOH HOH . C 3 HOH A 35 199 60 HOH HOH . C 3 HOH A 36 200 61 HOH HOH . C 3 HOH A 37 201 62 HOH HOH . C 3 HOH A 38 202 63 HOH HOH . C 3 HOH A 39 203 64 HOH HOH . C 3 HOH A 40 204 65 HOH HOH . C 3 HOH A 41 205 66 HOH HOH . C 3 HOH A 42 206 67 HOH HOH . C 3 HOH A 43 207 68 HOH HOH . C 3 HOH A 44 208 69 HOH HOH . C 3 HOH A 45 209 70 HOH HOH . C 3 HOH A 46 210 71 HOH HOH . C 3 HOH A 47 211 72 HOH HOH . C 3 HOH A 48 212 73 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 4D9 . . . B 2 39.425 -18.644 13.843 0.8 59.24 ? C1 4D9 164 A 1 HETATM 2 C C2 4D9 . . . B 2 39.592 -20.011 13.663 0.8 58.52 ? C2 4D9 164 A 1 HETATM 3 C C3 4D9 . . . B 2 39.395 -20.572 12.398 0.8 60.95 ? C3 4D9 164 A 1 HETATM 4 C C4 4D9 . . . B 2 39.044 -19.819 11.272 0.8 60.58 ? C4 4D9 164 A 1 HETATM 5 N N5 4D9 . . . B 2 38.848 -16.537 12.612 0.8 59.59 ? N5 4D9 164 A 1 HETATM 6 C C6 4D9 . . . B 2 39.075 -17.842 12.762 0.8 59.97 ? C6 4D9 164 A 1 HETATM 7 C C7 4D9 . . . B 2 38.881 -18.458 11.431 0.8 60.62 ? C7 4D9 164 A 1 HETATM 8 N N8 4D9 . . . B 2 38.554 -17.461 10.615 0.8 61.31 ? N8 4D9 164 A 1 HETATM 9 C C9 4D9 . . . B 2 38.537 -16.302 11.327 0.8 61.46 ? C9 4D9 164 A 1 HETATM 10 C C10 4D9 . . . B 2 38.223 -14.944 10.732 0.8 63.28 ? C10 4D9 164 A 1 HETATM 11 C C11 4D9 . . . B 2 39.459 -14.065 10.447 0.8 64.93 ? C11 4D9 164 A 1 HETATM 12 C C12 4D9 . . . B 2 38.988 -12.768 9.82 0.8 66.49 ? C12 4D9 164 A 1 HETATM 13 N N13 4D9 . . . B 2 40.563 -14.625 9.661 0.8 65.82 ? N13 4D9 164 A 1 HETATM 14 O O14 4D9 . . . B 2 38.725 -12.723 8.582 0.8 65.3 ? O14 4D9 164 A 1 HETATM 15 O O15 4D9 . . . B 2 38.87 -11.77 10.582 0.8 66.72 ? O15 4D9 164 A 1 HETATM 16 C C16 4D9 . . . B 2 40.811 -15.895 9.28 0.8 67.25 ? C16 4D9 164 A 1 HETATM 17 C C17 4D9 . . . B 2 40.564 -16.258 7.846 0.8 67.72 ? C17 4D9 164 A 1 HETATM 18 O O18 4D9 . . . B 2 41.242 -16.745 10.049 0.8 67.59 ? O18 4D9 164 A 1 HETATM 19 C C19 4D9 . . . B 2 40.061 -15.457 6.799 0.8 67.73 ? C19 4D9 164 A 1 HETATM 20 S S20 4D9 . . . B 2 40.932 -17.919 7.354 0.8 68.51 ? S20 4D9 164 A 1 HETATM 21 C C21 4D9 . . . B 2 40.451 -17.643 5.751 0.8 68.85 ? C21 4D9 164 A 1 HETATM 22 C C22 4D9 . . . B 2 39.991 -16.232 5.581 0.8 68.33 ? C22 4D9 164 A 1 HETATM 23 C C23 4D9 . . . B 2 39.544 -15.799 4.326 0.8 68.86 ? C23 4D9 164 A 1 HETATM 24 C C24 4D9 . . . B 2 39.544 -16.72 3.273 0.8 69.82 ? C24 4D9 164 A 1 HETATM 25 C C25 4D9 . . . B 2 39.987 -18.055 3.445 0.8 70.54 ? C25 4D9 164 A 1 HETATM 26 C C26 4D9 . . . B 2 40.455 -18.541 4.678 0.8 69.12 ? C26 4D9 164 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 26 #