data_1QGS # _model_server_result.job_id hvjcZ31c1zLx2k0TL-FVdA _model_server_result.datetime_utc '2024-12-21 15:47:19' _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 1qgs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":311}' # _entry.id 1QGS # _exptl.entry_id 1QGS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 1QGS _cell.length_a 47.42 _cell.length_b 141.997 _cell.length_c 81.439 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1QGS _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 154 A CYS 155 1_555 A SG CYS 242 A CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc1 A OD2 ASP 98 A ASP 99 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc2 B MG MG . A MG 301 1_555 E O2 GOL . A GOL 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc3 B MG MG . A MG 301 1_555 D O1B UDP . A UDP 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc4 B MG MG . A MG 301 1_555 F O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc5 B MG MG . A MG 301 1_555 F O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? metalc ? metalc6 B MG MG . A MG 301 1_555 F O HOH . A HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc7 B MG MG . A MG 301 1_555 F O HOH . A HOH 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc8 C MG MG . A MG 302 1_555 D O3B UDP . A UDP 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 N1 C2 UDP sing 371 n n N1 C6 UDP sing 372 n n N1 C1' UDP sing 373 n n C2 N3 UDP sing 374 n n C2 O2 UDP doub 375 n n N3 C4 UDP sing 376 n n N3 HN3 UDP sing 377 n n C4 C5 UDP sing 378 n n C4 O4 UDP doub 379 n n C5 C6 UDP doub 380 n n C5 H5 UDP sing 381 n n C6 H6 UDP sing 382 n n C1' C2' UDP sing 383 n n C1' O4' UDP sing 384 n n C1' H1' UDP sing 385 n n C2' O2' UDP sing 386 n n C2' C3' UDP sing 387 n n C2' H2' UDP sing 388 n n O2' HO2' UDP sing 389 n n C3' C4' UDP sing 390 n n C3' O3' UDP sing 391 n n C3' H3' UDP sing 392 n n C4' O4' UDP sing 393 n n C4' C5' UDP sing 394 n n C4' H4' UDP sing 395 n n O3' HO3' UDP sing 396 n n C5' O5' UDP sing 397 n n C5' "H5'1" UDP sing 398 n n C5' "H5'2" UDP sing 399 n n O5' PA UDP sing 400 n n PA O1A UDP doub 401 n n PA O2A UDP sing 402 n n PA O3A UDP sing 403 n n O2A HOA2 UDP sing 404 n n O3A PB UDP sing 405 n n PB O1B UDP doub 406 n n PB O2B UDP sing 407 n n PB O3B UDP sing 408 n n O2B HOB2 UDP sing 409 n n O3B HOB3 UDP sing 410 n n # _atom_sites.entry_id 1QGS _atom_sites.fract_transf_matrix[1][1] 0.021088 _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] 0.007042 _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] 0.012279 _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 MG A 1 301 301 MG IUM . C 2 MG A 1 302 302 MG IUM . D 3 UDP A 1 311 1 UDP UDP . E 4 GOL A 1 310 310 GOL GOL . F 5 HOH A 1 312 1 HOH HOH . F 5 HOH A 2 313 2 HOH HOH . F 5 HOH A 3 314 3 HOH HOH . F 5 HOH A 4 315 1 HOH HOH . F 5 HOH A 5 316 2 HOH HOH . F 5 HOH A 6 317 3 HOH HOH . F 5 HOH A 7 318 4 HOH HOH . F 5 HOH A 8 319 5 HOH HOH . F 5 HOH A 9 320 6 HOH HOH . F 5 HOH A 10 321 7 HOH HOH . F 5 HOH A 11 322 8 HOH HOH . F 5 HOH A 12 323 9 HOH HOH . F 5 HOH A 13 324 10 HOH HOH . F 5 HOH A 14 325 11 HOH HOH . F 5 HOH A 15 326 12 HOH HOH . F 5 HOH A 16 327 13 HOH HOH . F 5 HOH A 17 328 14 HOH HOH . F 5 HOH A 18 329 15 HOH HOH . F 5 HOH A 19 330 16 HOH HOH . F 5 HOH A 20 331 17 HOH HOH . F 5 HOH A 21 332 18 HOH HOH . F 5 HOH A 22 333 19 HOH HOH . F 5 HOH A 23 334 20 HOH HOH . F 5 HOH A 24 335 21 HOH HOH . F 5 HOH A 25 336 22 HOH HOH . F 5 HOH A 26 337 23 HOH HOH . F 5 HOH A 27 338 24 HOH HOH . F 5 HOH A 28 339 25 HOH HOH . F 5 HOH A 29 340 26 HOH HOH . F 5 HOH A 30 341 27 HOH HOH . F 5 HOH A 31 342 28 HOH HOH . F 5 HOH A 32 343 29 HOH HOH . F 5 HOH A 33 344 30 HOH HOH . F 5 HOH A 34 345 31 HOH HOH . F 5 HOH A 35 346 32 HOH HOH . F 5 HOH A 36 347 33 HOH HOH . F 5 HOH A 37 348 34 HOH HOH . F 5 HOH A 38 349 35 HOH HOH . F 5 HOH A 39 350 36 HOH HOH . F 5 HOH A 40 351 37 HOH HOH . F 5 HOH A 41 352 38 HOH HOH . F 5 HOH A 42 353 39 HOH HOH . F 5 HOH A 43 354 40 HOH HOH . F 5 HOH A 44 355 41 HOH HOH . F 5 HOH A 45 356 42 HOH HOH . F 5 HOH A 46 357 43 HOH HOH . F 5 HOH A 47 358 44 HOH HOH . F 5 HOH A 48 359 45 HOH HOH . F 5 HOH A 49 360 46 HOH HOH . F 5 HOH A 50 361 47 HOH HOH . F 5 HOH A 51 362 48 HOH HOH . F 5 HOH A 52 363 49 HOH HOH . F 5 HOH A 53 364 50 HOH HOH . F 5 HOH A 54 365 51 HOH HOH . F 5 HOH A 55 366 52 HOH HOH . F 5 HOH A 56 367 53 HOH HOH . F 5 HOH A 57 368 54 HOH HOH . F 5 HOH A 58 369 55 HOH HOH . F 5 HOH A 59 370 56 HOH HOH . F 5 HOH A 60 371 57 HOH HOH . F 5 HOH A 61 372 58 HOH HOH . F 5 HOH A 62 373 59 HOH HOH . F 5 HOH A 63 374 60 HOH HOH . F 5 HOH A 64 375 61 HOH HOH . F 5 HOH A 65 376 62 HOH HOH . F 5 HOH A 66 377 63 HOH HOH . F 5 HOH A 67 378 64 HOH HOH . F 5 HOH A 68 379 65 HOH HOH . F 5 HOH A 69 380 66 HOH HOH . F 5 HOH A 70 381 67 HOH HOH . F 5 HOH A 71 382 68 HOH HOH . F 5 HOH A 72 383 69 HOH HOH . F 5 HOH A 73 384 70 HOH HOH . F 5 HOH A 74 385 71 HOH HOH . F 5 HOH A 75 386 72 HOH HOH . F 5 HOH A 76 387 73 HOH HOH . F 5 HOH A 77 388 74 HOH HOH . F 5 HOH A 78 389 75 HOH HOH . F 5 HOH A 79 390 76 HOH HOH . F 5 HOH A 80 391 77 HOH HOH . F 5 HOH A 81 392 78 HOH HOH . F 5 HOH A 82 393 79 HOH HOH . F 5 HOH A 83 394 80 HOH HOH . F 5 HOH A 84 395 81 HOH HOH . F 5 HOH A 85 396 82 HOH HOH . F 5 HOH A 86 397 83 HOH HOH . F 5 HOH A 87 398 84 HOH HOH . F 5 HOH A 88 399 85 HOH HOH . F 5 HOH A 89 400 86 HOH HOH . F 5 HOH A 90 401 87 HOH HOH . F 5 HOH A 91 402 88 HOH HOH . F 5 HOH A 92 403 89 HOH HOH . F 5 HOH A 93 404 90 HOH HOH . F 5 HOH A 94 405 91 HOH HOH . F 5 HOH A 95 406 92 HOH HOH . F 5 HOH A 96 407 93 HOH HOH . F 5 HOH A 97 408 94 HOH HOH . F 5 HOH A 98 409 95 HOH HOH . F 5 HOH A 99 410 96 HOH HOH . F 5 HOH A 100 411 97 HOH HOH . F 5 HOH A 101 412 98 HOH HOH . F 5 HOH A 102 413 99 HOH HOH . F 5 HOH A 103 414 100 HOH HOH . F 5 HOH A 104 415 101 HOH HOH . F 5 HOH A 105 416 102 HOH HOH . F 5 HOH A 106 417 103 HOH HOH . F 5 HOH A 107 418 104 HOH HOH . F 5 HOH A 108 419 105 HOH HOH . F 5 HOH A 109 420 106 HOH HOH . F 5 HOH A 110 421 107 HOH HOH . F 5 HOH A 111 422 108 HOH HOH . F 5 HOH A 112 423 109 HOH HOH . F 5 HOH A 113 424 110 HOH HOH . F 5 HOH A 114 425 111 HOH HOH . F 5 HOH A 115 426 112 HOH HOH . F 5 HOH A 116 427 114 HOH HOH . F 5 HOH A 117 428 115 HOH HOH . F 5 HOH A 118 429 116 HOH HOH . F 5 HOH A 119 430 117 HOH HOH . F 5 HOH A 120 431 118 HOH HOH . F 5 HOH A 121 432 119 HOH HOH . F 5 HOH A 122 433 120 HOH HOH . F 5 HOH A 123 434 121 HOH HOH . F 5 HOH A 124 435 122 HOH HOH . F 5 HOH A 125 436 123 HOH HOH . F 5 HOH A 126 437 124 HOH HOH . F 5 HOH A 127 438 125 HOH HOH . F 5 HOH A 128 439 126 HOH HOH . F 5 HOH A 129 440 127 HOH HOH . F 5 HOH A 130 441 128 HOH HOH . F 5 HOH A 131 442 129 HOH HOH . F 5 HOH A 132 443 130 HOH HOH . F 5 HOH A 133 444 131 HOH HOH . F 5 HOH A 134 445 132 HOH HOH . F 5 HOH A 135 446 133 HOH HOH . F 5 HOH A 136 447 134 HOH HOH . F 5 HOH A 137 448 135 HOH HOH . F 5 HOH A 138 449 136 HOH HOH . F 5 HOH A 139 450 137 HOH HOH . F 5 HOH A 140 451 138 HOH HOH . F 5 HOH A 141 452 139 HOH HOH . F 5 HOH A 142 453 140 HOH HOH . F 5 HOH A 143 454 141 HOH HOH . F 5 HOH A 144 455 142 HOH HOH . F 5 HOH A 145 456 143 HOH HOH . F 5 HOH A 146 457 144 HOH HOH . F 5 HOH A 147 458 145 HOH HOH . F 5 HOH A 148 459 146 HOH HOH . F 5 HOH A 149 460 147 HOH HOH . F 5 HOH A 150 461 149 HOH HOH . F 5 HOH A 151 462 150 HOH HOH . F 5 HOH A 152 463 151 HOH HOH . F 5 HOH A 153 464 152 HOH HOH . F 5 HOH A 154 465 153 HOH HOH . F 5 HOH A 155 466 154 HOH HOH . F 5 HOH A 156 467 155 HOH HOH . F 5 HOH A 157 468 156 HOH HOH . F 5 HOH A 158 469 157 HOH HOH . F 5 HOH A 159 470 158 HOH HOH . F 5 HOH A 160 471 159 HOH HOH . F 5 HOH A 161 472 160 HOH HOH . F 5 HOH A 162 473 161 HOH HOH . F 5 HOH A 163 474 162 HOH HOH . F 5 HOH A 164 475 163 HOH HOH . F 5 HOH A 165 476 164 HOH HOH . F 5 HOH A 166 477 165 HOH HOH . F 5 HOH A 167 478 166 HOH HOH . F 5 HOH A 168 479 167 HOH HOH . F 5 HOH A 169 480 168 HOH HOH . F 5 HOH A 170 481 169 HOH HOH . F 5 HOH A 171 482 170 HOH HOH . F 5 HOH A 172 483 171 HOH HOH . F 5 HOH A 173 484 172 HOH HOH . F 5 HOH A 174 485 173 HOH HOH . F 5 HOH A 175 486 174 HOH HOH . F 5 HOH A 176 487 175 HOH HOH . F 5 HOH A 177 488 176 HOH HOH . F 5 HOH A 178 489 178 HOH HOH . F 5 HOH A 179 490 179 HOH HOH . F 5 HOH A 180 491 180 HOH HOH . F 5 HOH A 181 492 181 HOH HOH . F 5 HOH A 182 493 182 HOH HOH . F 5 HOH A 183 494 183 HOH HOH . F 5 HOH A 184 495 184 HOH HOH . F 5 HOH A 185 496 185 HOH HOH . F 5 HOH A 186 497 186 HOH HOH . F 5 HOH A 187 498 187 HOH HOH . F 5 HOH A 188 499 189 HOH HOH . F 5 HOH A 189 500 190 HOH HOH . F 5 HOH A 190 501 192 HOH HOH . F 5 HOH A 191 502 193 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 UDP . . . D 3 18.382 19.553 33.565 1 36.02 ? N1 UDP 311 A 1 HETATM 2 C C2 UDP . . . D 3 18.893 20.808 33.292 1 35.83 ? C2 UDP 311 A 1 HETATM 3 N N3 UDP . . . D 3 20.205 20.965 32.935 1 34.26 ? N3 UDP 311 A 1 HETATM 4 C C4 UDP . . . D 3 21.145 19.93 32.803 1 34.74 ? C4 UDP 311 A 1 HETATM 5 C C5 UDP . . . D 3 20.557 18.653 33.098 1 34.83 ? C5 UDP 311 A 1 HETATM 6 C C6 UDP . . . D 3 19.277 18.495 33.436 1 35.73 ? C6 UDP 311 A 1 HETATM 7 O O2 UDP . . . D 3 18.249 21.852 33.357 1 35.17 ? O2 UDP 311 A 1 HETATM 8 O O4 UDP . . . D 3 22.29 20.213 32.476 1 32.65 ? O4 UDP 311 A 1 HETATM 9 C C1' UDP . . . D 3 16.963 19.393 33.865 1 36.15 ? C1' UDP 311 A 1 HETATM 10 C C2' UDP . . . D 3 16.178 18.378 33.021 1 35.38 ? C2' UDP 311 A 1 HETATM 11 O O2' UDP . . . D 3 15.816 18.994 31.824 1 33.69 ? O2' UDP 311 A 1 HETATM 12 C C3' UDP . . . D 3 14.982 18.01 33.918 1 36.38 ? C3' UDP 311 A 1 HETATM 13 C C4' UDP . . . D 3 15.523 18.212 35.327 1 39.44 ? C4' UDP 311 A 1 HETATM 14 O O4' UDP . . . D 3 16.795 18.926 35.186 1 39.37 ? O4' UDP 311 A 1 HETATM 15 O O3' UDP . . . D 3 13.87 18.887 33.734 1 33.56 ? O3' UDP 311 A 1 HETATM 16 C C5' UDP . . . D 3 15.704 16.954 36.154 1 43.94 ? C5' UDP 311 A 1 HETATM 17 O O5' UDP . . . D 3 16.724 16.158 35.594 1 50.86 ? O5' UDP 311 A 1 HETATM 18 P PA UDP . . . D 3 16.84 14.697 35.016 1 55.19 ? PA UDP 311 A 1 HETATM 19 O O1A UDP . . . D 3 15.601 14.468 34.213 1 54.83 ? O1A UDP 311 A 1 HETATM 20 O O2A UDP . . . D 3 18.171 14.549 34.338 1 55.33 ? O2A UDP 311 A 1 HETATM 21 O O3A UDP . . . D 3 16.781 13.9 36.392 1 55.67 ? O3A UDP 311 A 1 HETATM 22 P PB UDP . . . D 3 15.832 12.734 36.943 1 56.56 ? PB UDP 311 A 1 HETATM 23 O O1B UDP . . . D 3 15.488 13.167 38.451 1 55.89 ? O1B UDP 311 A 1 HETATM 24 O O2B UDP . . . D 3 16.736 11.544 36.87 1 57.6 ? O2B UDP 311 A 1 HETATM 25 O O3B UDP . . . D 3 14.507 12.619 36.275 1 56.34 ? O3B UDP 311 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #