data_1C3J # _model_server_result.job_id nDkWP12h-e9acemj5nLM2g _model_server_result.datetime_utc '2024-10-18 15:25:01' _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 1c3j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":353}' # _entry.id 1C3J # _exptl.entry_id 1C3J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _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 1C3J _cell.length_a 151.7 _cell.length_b 52.26 _cell.length_c 52.65 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1C3J _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _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 '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 345 n n N1 C6 UDP sing 346 n n N1 C1' UDP sing 347 n n C2 N3 UDP sing 348 n n C2 O2 UDP doub 349 n n N3 C4 UDP sing 350 n n N3 HN3 UDP sing 351 n n C4 C5 UDP sing 352 n n C4 O4 UDP doub 353 n n C5 C6 UDP doub 354 n n C5 H5 UDP sing 355 n n C6 H6 UDP sing 356 n n C1' C2' UDP sing 357 n n C1' O4' UDP sing 358 n n C1' H1' UDP sing 359 n n C2' O2' UDP sing 360 n n C2' C3' UDP sing 361 n n C2' H2' UDP sing 362 n n O2' HO2' UDP sing 363 n n C3' C4' UDP sing 364 n n C3' O3' UDP sing 365 n n C3' H3' UDP sing 366 n n C4' O4' UDP sing 367 n n C4' C5' UDP sing 368 n n C4' H4' UDP sing 369 n n O3' HO3' UDP sing 370 n n C5' O5' UDP sing 371 n n C5' "H5'1" UDP sing 372 n n C5' "H5'2" UDP sing 373 n n O5' PA UDP sing 374 n n PA O1A UDP doub 375 n n PA O2A UDP sing 376 n n PA O3A UDP sing 377 n n O2A HOA2 UDP sing 378 n n O3A PB UDP sing 379 n n PB O1B UDP doub 380 n n PB O2B UDP sing 381 n n PB O3B UDP sing 382 n n O2B HOB2 UDP sing 383 n n O3B HOB3 UDP sing 384 n n # _atom_sites.entry_id 1C3J _atom_sites.fract_transf_matrix[1][1] 0.006592 _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] 0.019135 _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] 0.018993 _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 UDP A 1 353 353 UDP UDP . C 3 HOH A 1 354 1 HOH HOH . C 3 HOH A 2 355 2 HOH HOH . C 3 HOH A 3 356 3 HOH HOH . C 3 HOH A 4 357 4 HOH HOH . C 3 HOH A 5 358 5 HOH HOH . C 3 HOH A 6 359 6 HOH HOH . C 3 HOH A 7 360 7 HOH HOH . C 3 HOH A 8 361 8 HOH HOH . C 3 HOH A 9 362 9 HOH HOH . C 3 HOH A 10 363 10 HOH HOH . C 3 HOH A 11 364 11 HOH HOH . C 3 HOH A 12 365 12 HOH HOH . C 3 HOH A 13 366 13 HOH HOH . C 3 HOH A 14 367 14 HOH HOH . C 3 HOH A 15 368 15 HOH HOH . C 3 HOH A 16 369 16 HOH HOH . C 3 HOH A 17 370 17 HOH HOH . C 3 HOH A 18 371 18 HOH HOH . C 3 HOH A 19 372 19 HOH HOH . C 3 HOH A 20 373 20 HOH HOH . C 3 HOH A 21 374 21 HOH HOH . C 3 HOH A 22 375 22 HOH HOH . C 3 HOH A 23 376 23 HOH HOH . C 3 HOH A 24 377 24 HOH HOH . C 3 HOH A 25 378 25 HOH HOH . C 3 HOH A 26 379 26 HOH HOH . C 3 HOH A 27 380 27 HOH HOH . C 3 HOH A 28 381 28 HOH HOH . C 3 HOH A 29 382 29 HOH HOH . C 3 HOH A 30 383 30 HOH HOH . C 3 HOH A 31 384 31 HOH HOH . C 3 HOH A 32 385 32 HOH HOH . C 3 HOH A 33 386 33 HOH HOH . C 3 HOH A 34 387 34 HOH HOH . C 3 HOH A 35 388 35 HOH HOH . C 3 HOH A 36 389 36 HOH HOH . C 3 HOH A 37 390 37 HOH HOH . C 3 HOH A 38 391 38 HOH HOH . C 3 HOH A 39 392 39 HOH HOH . C 3 HOH A 40 393 40 HOH HOH . C 3 HOH A 41 394 41 HOH HOH . C 3 HOH A 42 395 42 HOH HOH . C 3 HOH A 43 396 43 HOH HOH . C 3 HOH A 44 397 44 HOH HOH . C 3 HOH A 45 398 45 HOH HOH . C 3 HOH A 46 399 46 HOH HOH . C 3 HOH A 47 400 47 HOH HOH . C 3 HOH A 48 401 48 HOH HOH . C 3 HOH A 49 402 49 HOH HOH . C 3 HOH A 50 403 50 HOH HOH . C 3 HOH A 51 404 51 HOH HOH . C 3 HOH A 52 405 52 HOH HOH . C 3 HOH A 53 406 53 HOH HOH . C 3 HOH A 54 407 54 HOH HOH . C 3 HOH A 55 408 55 HOH HOH . C 3 HOH A 56 409 56 HOH HOH . C 3 HOH A 57 410 57 HOH HOH . C 3 HOH A 58 411 58 HOH HOH . C 3 HOH A 59 412 59 HOH HOH . C 3 HOH A 60 413 60 HOH HOH . C 3 HOH A 61 414 61 HOH HOH . C 3 HOH A 62 415 62 HOH HOH . C 3 HOH A 63 416 63 HOH HOH . C 3 HOH A 64 417 64 HOH HOH . C 3 HOH A 65 418 65 HOH HOH . C 3 HOH A 66 419 66 HOH HOH . C 3 HOH A 67 420 67 HOH HOH . C 3 HOH A 68 421 68 HOH HOH . C 3 HOH A 69 422 69 HOH HOH . C 3 HOH A 70 423 70 HOH HOH . C 3 HOH A 71 424 71 HOH HOH . C 3 HOH A 72 425 72 HOH HOH . C 3 HOH A 73 426 73 HOH HOH . C 3 HOH A 74 427 74 HOH HOH . C 3 HOH A 75 428 75 HOH HOH . C 3 HOH A 76 429 76 HOH HOH . C 3 HOH A 77 430 77 HOH HOH . C 3 HOH A 78 431 78 HOH HOH . C 3 HOH A 79 432 79 HOH HOH . C 3 HOH A 80 433 80 HOH HOH . C 3 HOH A 81 434 81 HOH HOH . C 3 HOH A 82 435 82 HOH HOH . C 3 HOH A 83 436 83 HOH HOH . C 3 HOH A 84 437 84 HOH HOH . C 3 HOH A 85 438 85 HOH HOH . C 3 HOH A 86 439 86 HOH HOH . C 3 HOH A 87 440 87 HOH HOH . C 3 HOH A 88 441 88 HOH HOH . C 3 HOH A 89 442 89 HOH HOH . C 3 HOH A 90 443 90 HOH HOH . C 3 HOH A 91 444 91 HOH HOH . C 3 HOH A 92 445 92 HOH HOH . C 3 HOH A 93 446 93 HOH HOH . C 3 HOH A 94 447 94 HOH HOH . C 3 HOH A 95 448 95 HOH HOH . C 3 HOH A 96 449 96 HOH HOH . C 3 HOH A 97 450 97 HOH HOH . C 3 HOH A 98 451 98 HOH HOH . C 3 HOH A 99 452 99 HOH HOH . C 3 HOH A 100 453 100 HOH HOH . C 3 HOH A 101 454 101 HOH HOH . C 3 HOH A 102 455 102 HOH HOH . C 3 HOH A 103 456 103 HOH HOH . C 3 HOH A 104 457 104 HOH HOH . C 3 HOH A 105 458 105 HOH HOH . C 3 HOH A 106 459 106 HOH HOH . C 3 HOH A 107 460 107 HOH HOH . C 3 HOH A 108 461 108 HOH HOH . C 3 HOH A 109 462 109 HOH HOH . C 3 HOH A 110 463 110 HOH HOH . C 3 HOH A 111 464 111 HOH HOH . C 3 HOH A 112 465 112 HOH HOH . C 3 HOH A 113 466 113 HOH HOH . C 3 HOH A 114 467 114 HOH HOH . C 3 HOH A 115 468 115 HOH HOH . C 3 HOH A 116 469 116 HOH HOH . C 3 HOH A 117 470 117 HOH HOH . C 3 HOH A 118 471 118 HOH HOH . C 3 HOH A 119 472 119 HOH HOH . C 3 HOH A 120 473 120 HOH HOH . C 3 HOH A 121 474 121 HOH HOH . C 3 HOH A 122 475 122 HOH HOH . C 3 HOH A 123 476 123 HOH HOH . C 3 HOH A 124 477 124 HOH HOH . C 3 HOH A 125 478 125 HOH HOH . C 3 HOH A 126 479 126 HOH HOH . C 3 HOH A 127 480 127 HOH HOH . C 3 HOH A 128 481 128 HOH HOH . C 3 HOH A 129 482 129 HOH HOH . C 3 HOH A 130 483 130 HOH HOH . C 3 HOH A 131 484 131 HOH HOH . C 3 HOH A 132 485 132 HOH HOH . C 3 HOH A 133 486 133 HOH HOH . C 3 HOH A 134 487 134 HOH HOH . C 3 HOH A 135 488 135 HOH HOH . C 3 HOH A 136 489 136 HOH HOH . C 3 HOH A 137 490 137 HOH HOH . C 3 HOH A 138 491 138 HOH HOH . C 3 HOH A 139 492 139 HOH HOH . C 3 HOH A 140 493 140 HOH HOH . C 3 HOH A 141 494 141 HOH HOH . C 3 HOH A 142 495 142 HOH HOH . C 3 HOH A 143 496 143 HOH HOH . C 3 HOH A 144 497 144 HOH HOH . C 3 HOH A 145 498 145 HOH HOH . C 3 HOH A 146 499 146 HOH HOH . C 3 HOH A 147 500 147 HOH HOH . C 3 HOH A 148 501 148 HOH HOH . C 3 HOH A 149 502 149 HOH HOH . C 3 HOH A 150 503 150 HOH HOH . C 3 HOH A 151 504 151 HOH HOH . C 3 HOH A 152 505 152 HOH HOH . C 3 HOH A 153 506 153 HOH HOH . C 3 HOH A 154 507 154 HOH HOH . C 3 HOH A 155 508 155 HOH HOH . C 3 HOH A 156 509 156 HOH HOH . C 3 HOH A 157 510 157 HOH HOH . C 3 HOH A 158 511 158 HOH HOH . C 3 HOH A 159 512 159 HOH HOH . C 3 HOH A 160 513 160 HOH HOH . C 3 HOH A 161 514 161 HOH HOH . C 3 HOH A 162 515 162 HOH HOH . C 3 HOH A 163 516 163 HOH HOH . C 3 HOH A 164 517 164 HOH HOH . C 3 HOH A 165 518 165 HOH HOH . C 3 HOH A 166 519 166 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 . . . B 2 15.539 -9.182 16.794 1 16.06 ? N1 UDP 353 A 1 HETATM 2 C C2 UDP . . . B 2 14.226 -8.833 17.075 1 16.12 ? C2 UDP 353 A 1 HETATM 3 N N3 UDP . . . B 2 13.739 -9.254 18.297 1 14.38 ? N3 UDP 353 A 1 HETATM 4 C C4 UDP . . . B 2 14.428 -9.979 19.259 1 14.29 ? C4 UDP 353 A 1 HETATM 5 C C5 UDP . . . B 2 15.8 -10.294 18.906 1 14.69 ? C5 UDP 353 A 1 HETATM 6 C C6 UDP . . . B 2 16.307 -9.895 17.699 1 15.86 ? C6 UDP 353 A 1 HETATM 7 O O2 UDP . . . B 2 13.565 -8.128 16.32 1 15.9 ? O2 UDP 353 A 1 HETATM 8 O O4 UDP . . . B 2 13.868 -10.33 20.274 1 14.59 ? O4 UDP 353 A 1 HETATM 9 C C1' UDP . . . B 2 16.06 -8.806 15.48 1 11.36 ? C1' UDP 353 A 1 HETATM 10 C C2' UDP . . . B 2 16.901 -7.568 15.584 1 12.91 ? C2' UDP 353 A 1 HETATM 11 O O2' UDP . . . B 2 16.614 -6.665 14.498 1 11.05 ? O2' UDP 353 A 1 HETATM 12 C C3' UDP . . . B 2 18.303 -8.109 15.485 1 12.41 ? C3' UDP 353 A 1 HETATM 13 C C4' UDP . . . B 2 18.144 -9.299 14.636 1 11.09 ? C4' UDP 353 A 1 HETATM 14 O O4' UDP . . . B 2 16.892 -9.849 14.999 1 9.35 ? O4' UDP 353 A 1 HETATM 15 O O3' UDP . . . B 2 19.207 -7.182 14.895 1 11.49 ? O3' UDP 353 A 1 HETATM 16 C C5' UDP . . . B 2 19.251 -10.275 14.888 1 12.72 ? C5' UDP 353 A 1 HETATM 17 O O5' UDP . . . B 2 19.263 -11.289 13.895 1 12.9 ? O5' UDP 353 A 1 HETATM 18 P PA UDP . . . B 2 20.26 -12.549 13.994 1 13.33 ? PA UDP 353 A 1 HETATM 19 O O1A UDP . . . B 2 20.061 -13.367 12.765 1 15.34 ? O1A UDP 353 A 1 HETATM 20 O O2A UDP . . . B 2 20.041 -13.203 15.3 1 15.93 ? O2A UDP 353 A 1 HETATM 21 O O3A UDP . . . B 2 21.743 -11.891 14.008 1 14.08 ? O3A UDP 353 A 1 HETATM 22 P PB UDP . . . B 2 22.64 -11.043 12.965 1 12.7 ? PB UDP 353 A 1 HETATM 23 O O1B UDP . . . B 2 23.124 -12.025 11.972 1 12.99 ? O1B UDP 353 A 1 HETATM 24 O O2B UDP . . . B 2 21.77 -10.01 12.411 1 13.28 ? O2B UDP 353 A 1 HETATM 25 O O3B UDP . . . B 2 23.69 -10.497 13.825 1 15.46 ? O3B UDP 353 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #