data_5R87 # _model_server_result.job_id V5ogQ_46t9C2b1ZZ3zyjMw _model_server_result.datetime_utc '2024-11-26 00:12:16' _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 5r87 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 5R87 # _exptl.entry_id 5R87 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 213.235 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "N-phenyl-N'-pyridin-3-ylurea" _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 90 _cell.entry_id 5R87 _cell.length_a 54.65 _cell.length_b 54.65 _cell.length_c 75.05 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5R87 _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43' # _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,E _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 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C12 H11 N3 O' _chem_comp.formula_weight 213.235 _chem_comp.id K0G _chem_comp.mon_nstd_flag . _chem_comp.name "N-phenyl-N'-pyridin-3-ylurea" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C4 C3 K0G doub 173 n y C4 C5 K0G sing 174 n y C3 C2 K0G sing 175 n y C5 C6 K0G doub 176 n y C2 C1 K0G doub 177 n y C6 C1 K0G sing 178 n y C1 N K0G sing 179 n n N C K0G sing 180 n n C O K0G doub 181 n n C N1 K0G sing 182 n n N1 C7 K0G sing 183 n n C7 C8 K0G doub 184 n y C7 C11 K0G sing 185 n y C8 C9 K0G sing 186 n y C11 N2 K0G doub 187 n y C9 C10 K0G doub 188 n y N2 C10 K0G sing 189 n y N1 H1 K0G sing 190 n n C4 H2 K0G sing 191 n n C5 H3 K0G sing 192 n n C6 H4 K0G sing 193 n n C8 H5 K0G sing 194 n n C10 H6 K0G sing 195 n n N H7 K0G sing 196 n n C11 H8 K0G sing 197 n n C2 H9 K0G sing 198 n n C3 H10 K0G sing 199 n n C9 H11 K0G sing 200 n n # _atom_sites.entry_id 5R87 _atom_sites.fract_transf_matrix[1][1] 0.018298 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018298 _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] 0.013324 _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 SO4 A 1 201 160 SO4 SO4 . C 2 SO4 A 1 202 161 SO4 SO4 . D 3 K0G A 1 203 401 K0G LIG . E 4 HOH A 1 301 29 HOH HOH . E 4 HOH A 2 302 235 HOH HOH . E 4 HOH A 3 303 326 HOH HOH . E 4 HOH A 4 304 241 HOH HOH . E 4 HOH A 5 305 271 HOH HOH . E 4 HOH A 6 306 247 HOH HOH . E 4 HOH A 7 307 303 HOH HOH . E 4 HOH A 8 308 262 HOH HOH . E 4 HOH A 9 309 214 HOH HOH . E 4 HOH A 10 310 243 HOH HOH . E 4 HOH A 11 311 34 HOH HOH . E 4 HOH A 12 312 239 HOH HOH . E 4 HOH A 13 313 267 HOH HOH . E 4 HOH A 14 314 325 HOH HOH . E 4 HOH A 15 315 276 HOH HOH . E 4 HOH A 16 316 237 HOH HOH . E 4 HOH A 17 317 287 HOH HOH . E 4 HOH A 18 318 220 HOH HOH . E 4 HOH A 19 319 208 HOH HOH . E 4 HOH A 20 320 213 HOH HOH . E 4 HOH A 21 321 322 HOH HOH . E 4 HOH A 22 322 232 HOH HOH . E 4 HOH A 23 323 238 HOH HOH . E 4 HOH A 24 324 19 HOH HOH . E 4 HOH A 25 325 28 HOH HOH . E 4 HOH A 26 326 18 HOH HOH . E 4 HOH A 27 327 257 HOH HOH . E 4 HOH A 28 328 211 HOH HOH . E 4 HOH A 29 329 203 HOH HOH . E 4 HOH A 30 330 200 HOH HOH . E 4 HOH A 31 331 343 HOH HOH . E 4 HOH A 32 332 240 HOH HOH . E 4 HOH A 33 333 334 HOH HOH . E 4 HOH A 34 334 216 HOH HOH . E 4 HOH A 35 335 223 HOH HOH . E 4 HOH A 36 336 21 HOH HOH . E 4 HOH A 37 337 204 HOH HOH . E 4 HOH A 38 338 218 HOH HOH . E 4 HOH A 39 339 228 HOH HOH . E 4 HOH A 40 340 227 HOH HOH . E 4 HOH A 41 341 229 HOH HOH . E 4 HOH A 42 342 277 HOH HOH . E 4 HOH A 43 343 294 HOH HOH . E 4 HOH A 44 344 275 HOH HOH . E 4 HOH A 45 345 201 HOH HOH . E 4 HOH A 46 346 209 HOH HOH . E 4 HOH A 47 347 202 HOH HOH . E 4 HOH A 48 348 244 HOH HOH . E 4 HOH A 49 349 269 HOH HOH . E 4 HOH A 50 350 226 HOH HOH . E 4 HOH A 51 351 215 HOH HOH . E 4 HOH A 52 352 318 HOH HOH . E 4 HOH A 53 353 245 HOH HOH . E 4 HOH A 54 354 248 HOH HOH . E 4 HOH A 55 355 23 HOH HOH . E 4 HOH A 56 356 321 HOH HOH . E 4 HOH A 57 357 346 HOH HOH . E 4 HOH A 58 358 206 HOH HOH . E 4 HOH A 59 359 233 HOH HOH . E 4 HOH A 60 360 255 HOH HOH . E 4 HOH A 61 361 312 HOH HOH . E 4 HOH A 62 362 338 HOH HOH . E 4 HOH A 63 363 348 HOH HOH . E 4 HOH A 64 364 251 HOH HOH . E 4 HOH A 65 365 272 HOH HOH . E 4 HOH A 66 366 246 HOH HOH . E 4 HOH A 67 367 13 HOH HOH . E 4 HOH A 68 368 207 HOH HOH . E 4 HOH A 69 369 225 HOH HOH . E 4 HOH A 70 370 305 HOH HOH . E 4 HOH A 71 371 298 HOH HOH . E 4 HOH A 72 372 284 HOH HOH . E 4 HOH A 73 373 254 HOH HOH . E 4 HOH A 74 374 286 HOH HOH . E 4 HOH A 75 375 297 HOH HOH . E 4 HOH A 76 376 266 HOH HOH . E 4 HOH A 77 377 323 HOH HOH . E 4 HOH A 78 378 205 HOH HOH . E 4 HOH A 79 379 307 HOH HOH . E 4 HOH A 80 380 270 HOH HOH . E 4 HOH A 81 381 345 HOH HOH . E 4 HOH A 82 382 242 HOH HOH . E 4 HOH A 83 383 224 HOH HOH . E 4 HOH A 84 384 250 HOH HOH . E 4 HOH A 85 385 221 HOH HOH . E 4 HOH A 86 386 252 HOH HOH . E 4 HOH A 87 387 217 HOH HOH . E 4 HOH A 88 388 290 HOH HOH . E 4 HOH A 89 389 302 HOH HOH . E 4 HOH A 90 390 212 HOH HOH . E 4 HOH A 91 391 210 HOH HOH . E 4 HOH A 92 392 285 HOH HOH . E 4 HOH A 93 393 317 HOH HOH . E 4 HOH A 94 394 219 HOH HOH . E 4 HOH A 95 395 268 HOH HOH . E 4 HOH A 96 396 282 HOH HOH . E 4 HOH A 97 397 25 HOH HOH . E 4 HOH A 98 398 16 HOH HOH . E 4 HOH A 99 399 333 HOH HOH . E 4 HOH A 100 400 31 HOH HOH . E 4 HOH A 101 401 314 HOH HOH . E 4 HOH A 102 402 22 HOH HOH . E 4 HOH A 103 403 14 HOH HOH . E 4 HOH A 104 404 27 HOH HOH . E 4 HOH A 105 405 258 HOH HOH . E 4 HOH A 106 406 2 HOH HOH . E 4 HOH A 107 407 304 HOH HOH . E 4 HOH A 108 408 347 HOH HOH . E 4 HOH A 109 409 311 HOH HOH . E 4 HOH A 110 410 256 HOH HOH . E 4 HOH A 111 411 231 HOH HOH . E 4 HOH A 112 412 20 HOH HOH . E 4 HOH A 113 413 310 HOH HOH . E 4 HOH A 114 414 11 HOH HOH . E 4 HOH A 115 415 332 HOH HOH . E 4 HOH A 116 416 291 HOH HOH . E 4 HOH A 117 417 32 HOH HOH . E 4 HOH A 118 418 260 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 N N1 K0G . . . D 3 41.941 26.274 67.364 0.37 42.87 ? N1 K0G 203 A 1 HETATM 2 C C4 K0G . . . D 3 39.541 24.772 61.621 0.37 48.3 ? C4 K0G 203 A 1 HETATM 3 C C5 K0G . . . D 3 39.259 26.071 62.04 0.37 50.16 ? C5 K0G 203 A 1 HETATM 4 C C6 K0G . . . D 3 39.641 26.519 63.3 0.37 50.02 ? C6 K0G 203 A 1 HETATM 5 C C7 K0G . . . D 3 43.059 26.234 68.215 0.37 42.17 ? C7 K0G 203 A 1 HETATM 6 C C8 K0G . . . D 3 43.316 27.252 69.113 0.37 40.94 ? C8 K0G 203 A 1 HETATM 7 C C10 K0G . . . D 3 45.19 25.991 69.876 0.37 40.93 ? C10 K0G 203 A 1 HETATM 8 N N K0G . . . D 3 40.643 25.992 65.464 0.37 46.22 ? N K0G 203 A 1 HETATM 9 C C K0G . . . D 3 41.932 25.892 66.016 0.37 43.45 ? C K0G 203 A 1 HETATM 10 O O K0G . . . D 3 42.933 25.554 65.392 0.37 41 ? O K0G 203 A 1 HETATM 11 C C1 K0G . . . D 3 40.314 25.64 64.145 0.37 49.73 ? C1 K0G 203 A 1 HETATM 12 C C11 K0G . . . D 3 43.912 25.106 68.198 0.37 41.09 ? C11 K0G 203 A 1 HETATM 13 C C2 K0G . . . D 3 40.617 24.332 63.735 0.37 50.47 ? C2 K0G 203 A 1 HETATM 14 C C3 K0G . . . D 3 40.222 23.912 62.464 0.37 48 ? C3 K0G 203 A 1 HETATM 15 C C9 K0G . . . D 3 44.407 27.124 69.944 0.37 42.44 ? C9 K0G 203 A 1 HETATM 16 N N2 K0G . . . D 3 44.964 24.978 69.02 0.37 40.97 ? N2 K0G 203 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 16 #