data_3KAD # _model_server_result.job_id LPpnkXM54q47-0knce51mw _model_server_result.datetime_utc '2024-12-03 17:59:21' _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 3kad # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":164}' # _entry.id 3KAD # _exptl.entry_id 3KAD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 337.372 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-(1H-benzimidazol-2-yl)-N-(3-phenylpropanoyl)-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 3KAD _cell.length_a 68.211 _cell.length_b 68.211 _cell.length_c 79.55 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KAD _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,D _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 H19 N3 O3' _chem_comp.formula_weight 337.372 _chem_comp.id 4C0 _chem_comp.mon_nstd_flag . _chem_comp.name 3-(1H-benzimidazol-2-yl)-N-(3-phenylpropanoyl)-D-alanine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(R)-3-(1H-Benzoimidazol-2-yl)-2-(3-phenyl-propionylamino)-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 C2 C1 4C0 doub 87 n y C1 C4 4C0 sing 88 n y C1 H1 4C0 sing 89 n n C3 C2 4C0 sing 90 n y C2 H2 4C0 sing 91 n n C3 C6 4C0 doub 92 n y C3 H3 4C0 sing 93 n n C5 C4 4C0 doub 94 n y C4 H4 4C0 sing 95 n n C6 C5 4C0 sing 96 n y C5 N9 4C0 sing 97 n y N7 C6 4C0 sing 98 n y N7 C8 4C0 sing 99 n y C10 C8 4C0 sing 100 n n C8 N9 4C0 doub 101 n y C11 C10 4C0 sing 102 n n C10 H10 4C0 sing 103 n n C10 H10A 4C0 sing 104 n n N12 C11 4C0 sing 105 n n C11 C23 4C0 sing 106 n n C11 H11 4C0 sing 107 n n C13 N12 4C0 sing 108 n n N12 HN12 4C0 sing 109 n n C15 C13 4C0 sing 110 n n C13 O14 4C0 doub 111 n n C16 C15 4C0 sing 112 n n C15 H15 4C0 sing 113 n n C15 H15A 4C0 sing 114 n n C17 C16 4C0 sing 115 n n C16 H16 4C0 sing 116 n n C16 H16A 4C0 sing 117 n n C18 C17 4C0 doub 118 n y C22 C17 4C0 sing 119 n y C19 C18 4C0 sing 120 n y C18 H18 4C0 sing 121 n n C20 C19 4C0 doub 122 n y C19 H19 4C0 sing 123 n n C20 C21 4C0 sing 124 n y C20 H20 4C0 sing 125 n n C21 C22 4C0 doub 126 n y C21 H21 4C0 sing 127 n n C22 H22 4C0 sing 128 n n O24 C23 4C0 doub 129 n n C23 O25 4C0 sing 130 n n O25 HO25 4C0 sing 131 n n N7 HN7 4C0 sing 132 n n # _atom_sites.entry_id 3KAD _atom_sites.fract_transf_matrix[1][1] 0.01466 _atom_sites.fract_transf_matrix[1][2] 0.008464 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016928 _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] 0.012571 _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 4C0 A 1 164 1 4C0 4C0 . C 3 12P A 1 165 1 12P 12P . D 4 HOH A 1 166 166 HOH HOH . D 4 HOH A 2 167 167 HOH HOH . D 4 HOH A 3 168 168 HOH HOH . D 4 HOH A 4 169 169 HOH HOH . D 4 HOH A 5 170 170 HOH HOH . D 4 HOH A 6 171 171 HOH HOH . D 4 HOH A 7 172 172 HOH HOH . D 4 HOH A 8 173 173 HOH HOH . D 4 HOH A 9 174 174 HOH HOH . D 4 HOH A 10 175 175 HOH HOH . D 4 HOH A 11 176 176 HOH HOH . D 4 HOH A 12 177 177 HOH HOH . D 4 HOH A 13 178 178 HOH HOH . D 4 HOH A 14 179 179 HOH HOH . D 4 HOH A 15 180 180 HOH HOH . D 4 HOH A 16 181 181 HOH HOH . D 4 HOH A 17 182 182 HOH HOH . D 4 HOH A 18 183 183 HOH HOH . D 4 HOH A 19 184 184 HOH HOH . D 4 HOH A 20 185 185 HOH HOH . D 4 HOH A 21 186 186 HOH HOH . D 4 HOH A 22 187 187 HOH HOH . D 4 HOH A 23 188 188 HOH HOH . D 4 HOH A 24 189 189 HOH HOH . D 4 HOH A 25 190 190 HOH HOH . D 4 HOH A 26 191 191 HOH HOH . D 4 HOH A 27 192 192 HOH HOH . D 4 HOH A 28 193 193 HOH HOH . D 4 HOH A 29 194 194 HOH HOH . D 4 HOH A 30 195 195 HOH HOH . D 4 HOH A 31 196 196 HOH HOH . D 4 HOH A 32 197 197 HOH HOH . D 4 HOH A 33 198 198 HOH HOH . D 4 HOH A 34 199 199 HOH HOH . D 4 HOH A 35 200 200 HOH HOH . D 4 HOH A 36 201 201 HOH HOH . D 4 HOH A 37 202 202 HOH HOH . D 4 HOH A 38 203 1 HOH HOH . D 4 HOH A 39 204 2 HOH HOH . D 4 HOH A 40 205 3 HOH HOH . D 4 HOH A 41 206 4 HOH HOH . D 4 HOH A 42 207 5 HOH HOH . D 4 HOH A 43 208 6 HOH HOH . D 4 HOH A 44 209 7 HOH HOH . D 4 HOH A 45 210 8 HOH HOH . D 4 HOH A 46 211 10 HOH HOH . D 4 HOH A 47 212 11 HOH HOH . D 4 HOH A 48 213 13 HOH HOH . D 4 HOH A 49 214 14 HOH HOH . D 4 HOH A 50 215 15 HOH HOH . D 4 HOH A 51 216 16 HOH HOH . D 4 HOH A 52 217 18 HOH HOH . D 4 HOH A 53 218 20 HOH HOH . D 4 HOH A 54 219 21 HOH HOH . D 4 HOH A 55 220 22 HOH HOH . D 4 HOH A 56 221 23 HOH HOH . D 4 HOH A 57 222 24 HOH HOH . D 4 HOH A 58 223 25 HOH HOH . D 4 HOH A 59 224 26 HOH HOH . D 4 HOH A 60 225 27 HOH HOH . D 4 HOH A 61 226 28 HOH HOH . D 4 HOH A 62 227 29 HOH HOH . D 4 HOH A 63 228 30 HOH HOH . D 4 HOH A 64 229 31 HOH HOH . D 4 HOH A 65 230 33 HOH HOH . D 4 HOH A 66 231 34 HOH HOH . D 4 HOH A 67 232 35 HOH HOH . D 4 HOH A 68 233 36 HOH HOH . D 4 HOH A 69 234 37 HOH HOH . D 4 HOH A 70 235 38 HOH HOH . D 4 HOH A 71 236 39 HOH HOH . D 4 HOH A 72 237 40 HOH HOH . D 4 HOH A 73 238 41 HOH HOH . D 4 HOH A 74 239 42 HOH HOH . D 4 HOH A 75 240 43 HOH HOH . D 4 HOH A 76 241 44 HOH HOH . D 4 HOH A 77 242 46 HOH HOH . D 4 HOH A 78 243 47 HOH HOH . D 4 HOH A 79 244 48 HOH HOH . D 4 HOH A 80 245 50 HOH HOH . D 4 HOH A 81 246 51 HOH HOH . D 4 HOH A 82 247 52 HOH HOH . D 4 HOH A 83 248 54 HOH HOH . D 4 HOH A 84 249 55 HOH HOH . D 4 HOH A 85 250 56 HOH HOH . D 4 HOH A 86 251 57 HOH HOH . D 4 HOH A 87 252 58 HOH HOH . D 4 HOH A 88 253 59 HOH HOH . D 4 HOH A 89 254 60 HOH HOH . D 4 HOH A 90 255 61 HOH HOH . D 4 HOH A 91 256 62 HOH HOH . D 4 HOH A 92 257 63 HOH HOH . D 4 HOH A 93 258 64 HOH HOH . D 4 HOH A 94 259 65 HOH HOH . D 4 HOH A 95 260 66 HOH HOH . D 4 HOH A 96 261 67 HOH HOH . D 4 HOH A 97 262 69 HOH HOH . D 4 HOH A 98 263 70 HOH HOH . D 4 HOH A 99 264 71 HOH HOH . D 4 HOH A 100 265 72 HOH HOH . D 4 HOH A 101 266 73 HOH HOH . D 4 HOH A 102 267 75 HOH HOH . D 4 HOH A 103 268 76 HOH HOH . D 4 HOH A 104 269 77 HOH HOH . D 4 HOH A 105 270 78 HOH HOH . D 4 HOH A 106 271 79 HOH HOH . D 4 HOH A 107 272 80 HOH HOH . D 4 HOH A 108 273 82 HOH HOH . D 4 HOH A 109 274 83 HOH HOH . D 4 HOH A 110 275 84 HOH HOH . D 4 HOH A 111 276 85 HOH HOH . D 4 HOH A 112 277 86 HOH HOH . D 4 HOH A 113 278 87 HOH HOH . D 4 HOH A 114 279 89 HOH HOH . D 4 HOH A 115 280 90 HOH HOH . D 4 HOH A 116 281 91 HOH HOH . D 4 HOH A 117 282 92 HOH HOH . D 4 HOH A 118 283 95 HOH HOH . D 4 HOH A 119 284 96 HOH HOH . D 4 HOH A 120 285 98 HOH HOH . D 4 HOH A 121 286 99 HOH HOH . D 4 HOH A 122 287 100 HOH HOH . D 4 HOH A 123 288 101 HOH HOH . D 4 HOH A 124 289 102 HOH HOH . D 4 HOH A 125 290 103 HOH HOH . D 4 HOH A 126 291 104 HOH HOH . D 4 HOH A 127 292 105 HOH HOH . D 4 HOH A 128 293 106 HOH HOH . D 4 HOH A 129 294 107 HOH HOH . D 4 HOH A 130 295 108 HOH HOH . D 4 HOH A 131 296 109 HOH HOH . D 4 HOH A 132 297 110 HOH HOH . D 4 HOH A 133 298 111 HOH HOH . D 4 HOH A 134 299 114 HOH HOH . D 4 HOH A 135 300 115 HOH HOH . D 4 HOH A 136 301 116 HOH HOH . D 4 HOH A 137 302 117 HOH HOH . D 4 HOH A 138 303 119 HOH HOH . D 4 HOH A 139 304 121 HOH HOH . D 4 HOH A 140 305 122 HOH HOH . D 4 HOH A 141 306 123 HOH HOH . D 4 HOH A 142 307 124 HOH HOH . D 4 HOH A 143 308 126 HOH HOH . D 4 HOH A 144 309 127 HOH HOH . D 4 HOH A 145 310 128 HOH HOH . D 4 HOH A 146 311 132 HOH HOH . D 4 HOH A 147 312 134 HOH HOH . D 4 HOH A 148 313 135 HOH HOH . D 4 HOH A 149 314 138 HOH HOH . D 4 HOH A 150 315 143 HOH HOH . D 4 HOH A 151 316 145 HOH HOH . D 4 HOH A 152 317 148 HOH HOH . D 4 HOH A 153 318 150 HOH HOH . D 4 HOH A 154 319 154 HOH HOH . D 4 HOH A 155 320 155 HOH HOH . D 4 HOH A 156 321 156 HOH HOH . D 4 HOH A 157 322 157 HOH HOH . D 4 HOH A 158 323 158 HOH HOH . D 4 HOH A 159 324 159 HOH HOH . D 4 HOH A 160 325 160 HOH HOH . D 4 HOH A 161 326 161 HOH HOH . D 4 HOH A 162 327 162 HOH HOH . D 4 HOH A 163 328 163 HOH HOH . D 4 HOH A 164 329 164 HOH HOH . D 4 HOH A 165 330 165 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 4C0 . . . B 2 31.466 -15.067 -0.188 1 31.75 ? C1 4C0 164 A 1 HETATM 2 C C2 4C0 . . . B 2 31.941 -15.366 -1.46 1 30.55 ? C2 4C0 164 A 1 HETATM 3 C C3 4C0 . . . B 2 31.236 -16.24 -2.279 1 28.98 ? C3 4C0 164 A 1 HETATM 4 C C4 4C0 . . . B 2 30.285 -15.643 0.266 1 30.37 ? C4 4C0 164 A 1 HETATM 5 C C5 4C0 . . . B 2 29.581 -16.517 -0.554 1 31.72 ? C5 4C0 164 A 1 HETATM 6 C C6 4C0 . . . B 2 30.055 -16.815 -1.823 1 29.29 ? C6 4C0 164 A 1 HETATM 7 N N7 4C0 . . . B 2 29.185 -17.677 -2.388 1 31.51 ? N7 4C0 164 A 1 HETATM 8 C C8 4C0 . . . B 2 28.191 -17.916 -1.503 1 34.85 ? C8 4C0 164 A 1 HETATM 9 N N9 4C0 . . . B 2 28.434 -17.206 -0.379 1 29.75 ? N9 4C0 164 A 1 HETATM 10 C C10 4C0 . . . B 2 27.008 -18.826 -1.731 1 37.33 ? C10 4C0 164 A 1 HETATM 11 C C11 4C0 . . . B 2 25.853 -18.021 -2.313 1 46.42 ? C11 4C0 164 A 1 HETATM 12 N N12 4C0 . . . B 2 26.137 -17.671 -3.692 1 48.19 ? N12 4C0 164 A 1 HETATM 13 C C13 4C0 . . . B 2 26.437 -16.425 -4.045 1 51.76 ? C13 4C0 164 A 1 HETATM 14 O O14 4C0 . . . B 2 26.47 -15.499 -3.251 1 54.2 ? O14 4C0 164 A 1 HETATM 15 C C15 4C0 . . . B 2 26.742 -16.193 -5.505 1 48.27 ? C15 4C0 164 A 1 HETATM 16 C C16 4C0 . . . B 2 28.057 -15.433 -5.635 1 49.11 ? C16 4C0 164 A 1 HETATM 17 C C17 4C0 . . . B 2 28.596 -15.595 -7.037 1 49.13 ? C17 4C0 164 A 1 HETATM 18 C C18 4C0 . . . B 2 28.201 -16.679 -7.813 1 46.94 ? C18 4C0 164 A 1 HETATM 19 C C19 4C0 . . . B 2 28.697 -16.828 -9.103 1 44.49 ? C19 4C0 164 A 1 HETATM 20 C C20 4C0 . . . B 2 29.588 -15.893 -9.617 1 42.86 ? C20 4C0 164 A 1 HETATM 21 C C21 4C0 . . . B 2 29.983 -14.809 -8.841 1 47.75 ? C21 4C0 164 A 1 HETATM 22 C C22 4C0 . . . B 2 29.487 -14.66 -7.551 1 48.78 ? C22 4C0 164 A 1 HETATM 23 C C23 4C0 . . . B 2 24.583 -18.811 -2.194 1 47.72 ? C23 4C0 164 A 1 HETATM 24 O O24 4C0 . . . B 2 24.112 -19.341 -3.223 1 50.03 ? O24 4C0 164 A 1 HETATM 25 O O25 4C0 . . . B 2 24.044 -18.908 -1.071 1 51.86 ? O25 4C0 164 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 219 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #