data_2BGU # _model_server_result.job_id 7-8Gmo_GDItmANruSpY1sA _model_server_result.datetime_utc '2024-11-09 02:48:09' _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 2bgu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":353}' # _entry.id 2BGU # _exptl.entry_id 2BGU _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 2BGU _cell.length_a 151.92 _cell.length_b 52.26 _cell.length_c 52.74 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BGU _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 2BGU _atom_sites.fract_transf_matrix[1][1] 0.006582 _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] 0.018961 _atom_sites.fract_transf_vector[1] -0.25 _atom_sites.fract_transf_vector[2] -0.25 _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 1 355 355 HOH HOH . C 3 HOH A 2 356 356 HOH HOH . C 3 HOH A 3 357 357 HOH HOH . C 3 HOH A 4 358 358 HOH HOH . C 3 HOH A 5 359 359 HOH HOH . C 3 HOH A 6 360 360 HOH HOH . C 3 HOH A 7 361 361 HOH HOH . C 3 HOH A 8 362 362 HOH HOH . C 3 HOH A 9 363 363 HOH HOH . C 3 HOH A 10 364 364 HOH HOH . C 3 HOH A 11 365 365 HOH HOH . C 3 HOH A 12 366 366 HOH HOH . C 3 HOH A 13 367 367 HOH HOH . C 3 HOH A 14 368 368 HOH HOH . C 3 HOH A 15 369 369 HOH HOH . C 3 HOH A 16 370 370 HOH HOH . C 3 HOH A 17 371 371 HOH HOH . C 3 HOH A 18 372 372 HOH HOH . C 3 HOH A 19 373 373 HOH HOH . C 3 HOH A 20 374 374 HOH HOH . C 3 HOH A 21 375 375 HOH HOH . C 3 HOH A 22 376 376 HOH HOH . C 3 HOH A 23 377 377 HOH HOH . C 3 HOH A 24 378 378 HOH HOH . C 3 HOH A 25 379 379 HOH HOH . C 3 HOH A 26 380 380 HOH HOH . C 3 HOH A 27 381 381 HOH HOH . C 3 HOH A 28 382 382 HOH HOH . C 3 HOH A 29 383 383 HOH HOH . C 3 HOH A 30 384 384 HOH HOH . C 3 HOH A 31 385 385 HOH HOH . C 3 HOH A 32 387 387 HOH HOH . C 3 HOH A 33 388 388 HOH HOH . C 3 HOH A 34 389 389 HOH HOH . C 3 HOH A 35 390 390 HOH HOH . C 3 HOH A 36 391 391 HOH HOH . C 3 HOH A 37 392 392 HOH HOH . C 3 HOH A 38 393 393 HOH HOH . C 3 HOH A 39 394 394 HOH HOH . C 3 HOH A 40 395 395 HOH HOH . C 3 HOH A 41 396 396 HOH HOH . C 3 HOH A 42 397 397 HOH HOH . C 3 HOH A 43 398 398 HOH HOH . C 3 HOH A 44 399 399 HOH HOH . C 3 HOH A 45 400 400 HOH HOH . C 3 HOH A 46 401 401 HOH HOH . C 3 HOH A 47 402 402 HOH HOH . C 3 HOH A 48 403 403 HOH HOH . C 3 HOH A 49 404 404 HOH HOH . C 3 HOH A 50 405 405 HOH HOH . C 3 HOH A 51 406 406 HOH HOH . C 3 HOH A 52 407 407 HOH HOH . C 3 HOH A 53 408 408 HOH HOH . C 3 HOH A 54 409 409 HOH HOH . C 3 HOH A 55 410 410 HOH HOH . C 3 HOH A 56 411 411 HOH HOH . C 3 HOH A 57 412 412 HOH HOH . C 3 HOH A 58 413 413 HOH HOH . C 3 HOH A 59 414 414 HOH HOH . C 3 HOH A 60 415 415 HOH HOH . C 3 HOH A 61 416 416 HOH HOH . C 3 HOH A 62 417 417 HOH HOH . C 3 HOH A 63 418 418 HOH HOH . C 3 HOH A 64 419 419 HOH HOH . C 3 HOH A 65 420 420 HOH HOH . C 3 HOH A 66 421 421 HOH HOH . C 3 HOH A 67 422 422 HOH HOH . C 3 HOH A 68 423 423 HOH HOH . C 3 HOH A 69 424 424 HOH HOH . C 3 HOH A 70 425 425 HOH HOH . C 3 HOH A 71 426 426 HOH HOH . C 3 HOH A 72 427 427 HOH HOH . C 3 HOH A 73 428 428 HOH HOH . C 3 HOH A 74 429 429 HOH HOH . C 3 HOH A 75 430 430 HOH HOH . C 3 HOH A 76 431 431 HOH HOH . C 3 HOH A 77 433 433 HOH HOH . C 3 HOH A 78 434 434 HOH HOH . C 3 HOH A 79 435 435 HOH HOH . C 3 HOH A 80 436 436 HOH HOH . C 3 HOH A 81 437 437 HOH HOH . C 3 HOH A 82 438 438 HOH HOH . C 3 HOH A 83 439 439 HOH HOH . C 3 HOH A 84 440 440 HOH HOH . C 3 HOH A 85 441 441 HOH HOH . C 3 HOH A 86 442 442 HOH HOH . C 3 HOH A 87 443 443 HOH HOH . C 3 HOH A 88 444 444 HOH HOH . C 3 HOH A 89 445 445 HOH HOH . C 3 HOH A 90 446 446 HOH HOH . C 3 HOH A 91 449 449 HOH HOH . C 3 HOH A 92 450 450 HOH HOH . C 3 HOH A 93 451 451 HOH HOH . C 3 HOH A 94 452 452 HOH HOH . C 3 HOH A 95 453 453 HOH HOH . C 3 HOH A 96 454 454 HOH HOH . C 3 HOH A 97 455 455 HOH HOH . C 3 HOH A 98 456 456 HOH HOH . C 3 HOH A 99 457 457 HOH HOH . C 3 HOH A 100 461 461 HOH HOH . C 3 HOH A 101 462 462 HOH HOH . C 3 HOH A 102 463 463 HOH HOH . C 3 HOH A 103 464 464 HOH HOH . C 3 HOH A 104 465 465 HOH HOH . C 3 HOH A 105 466 466 HOH HOH . C 3 HOH A 106 467 467 HOH HOH . C 3 HOH A 107 468 468 HOH HOH . C 3 HOH A 108 469 469 HOH HOH . C 3 HOH A 109 470 470 HOH HOH . C 3 HOH A 110 471 471 HOH HOH . C 3 HOH A 111 472 472 HOH HOH . C 3 HOH A 112 473 473 HOH HOH . C 3 HOH A 113 474 474 HOH HOH . C 3 HOH A 114 475 475 HOH HOH . C 3 HOH A 115 476 476 HOH HOH . C 3 HOH A 116 477 477 HOH HOH . C 3 HOH A 117 478 478 HOH HOH . C 3 HOH A 118 479 479 HOH HOH . C 3 HOH A 119 480 480 HOH HOH . C 3 HOH A 120 481 481 HOH HOH . C 3 HOH A 121 482 482 HOH HOH . C 3 HOH A 122 483 483 HOH HOH . C 3 HOH A 123 484 484 HOH HOH . C 3 HOH A 124 485 485 HOH HOH . C 3 HOH A 125 486 486 HOH HOH . C 3 HOH A 126 487 487 HOH HOH . C 3 HOH A 127 488 488 HOH HOH . C 3 HOH A 128 489 489 HOH HOH . C 3 HOH A 129 490 490 HOH HOH . C 3 HOH A 130 491 491 HOH HOH . C 3 HOH A 131 492 492 HOH HOH . C 3 HOH A 132 493 493 HOH HOH . C 3 HOH A 133 494 494 HOH HOH . C 3 HOH A 134 495 495 HOH HOH . C 3 HOH A 135 496 496 HOH HOH . C 3 HOH A 136 497 497 HOH HOH . C 3 HOH A 137 498 498 HOH HOH . C 3 HOH A 138 499 499 HOH HOH . C 3 HOH A 139 500 500 HOH HOH . C 3 HOH A 140 501 501 HOH HOH . C 3 HOH A 141 502 502 HOH HOH . C 3 HOH A 142 503 503 HOH HOH . C 3 HOH A 143 504 504 HOH HOH . C 3 HOH A 144 505 505 HOH HOH . C 3 HOH A 145 506 506 HOH HOH . C 3 HOH A 146 507 507 HOH HOH . C 3 HOH A 147 508 508 HOH HOH . C 3 HOH A 148 509 509 HOH HOH . C 3 HOH A 149 510 510 HOH HOH . C 3 HOH A 150 511 511 HOH HOH . C 3 HOH A 151 512 512 HOH HOH . C 3 HOH A 152 513 513 HOH HOH . C 3 HOH A 153 514 514 HOH HOH . C 3 HOH A 154 515 515 HOH HOH . C 3 HOH A 155 516 516 HOH HOH . C 3 HOH A 156 517 517 HOH HOH . C 3 HOH A 157 518 518 HOH HOH . C 3 HOH A 158 519 519 HOH HOH . C 3 HOH A 159 520 520 HOH HOH . C 3 HOH A 160 521 521 HOH HOH . C 3 HOH A 161 522 522 HOH HOH . C 3 HOH A 162 523 523 HOH HOH . C 3 HOH A 163 524 524 HOH HOH . C 3 HOH A 164 525 525 HOH HOH . C 3 HOH A 165 526 526 HOH HOH . C 3 HOH A 166 527 527 HOH HOH . C 3 HOH A 167 528 528 HOH HOH . C 3 HOH A 168 529 529 HOH HOH . C 3 HOH A 169 530 530 HOH HOH . C 3 HOH A 170 531 531 HOH HOH . C 3 HOH A 171 532 532 HOH HOH . C 3 HOH A 172 533 533 HOH HOH . C 3 HOH A 173 534 534 HOH HOH . C 3 HOH A 174 535 535 HOH HOH . C 3 HOH A 175 536 536 HOH HOH . C 3 HOH A 176 537 537 HOH HOH . C 3 HOH A 177 538 538 HOH HOH . C 3 HOH A 178 539 539 HOH HOH . C 3 HOH A 179 540 540 HOH HOH . C 3 HOH A 180 541 541 HOH HOH . C 3 HOH A 181 542 542 HOH HOH . C 3 HOH A 182 543 543 HOH HOH . C 3 HOH A 183 544 544 HOH HOH . C 3 HOH A 184 545 545 HOH HOH . C 3 HOH A 185 546 546 HOH HOH . C 3 HOH A 186 547 547 HOH HOH . C 3 HOH A 187 548 548 HOH HOH . C 3 HOH A 188 549 549 HOH HOH . C 3 HOH A 189 550 550 HOH HOH . C 3 HOH A 190 551 551 HOH HOH . C 3 HOH A 191 552 552 HOH HOH . C 3 HOH A 192 553 553 HOH HOH . C 3 HOH A 193 554 554 HOH HOH . C 3 HOH A 194 555 555 HOH HOH . C 3 HOH A 195 556 556 HOH HOH . C 3 HOH A 196 557 557 HOH HOH . C 3 HOH A 197 558 558 HOH HOH . C 3 HOH A 198 559 559 HOH HOH . C 3 HOH A 199 560 560 HOH HOH . C 3 HOH A 200 561 561 HOH HOH . C 3 HOH A 201 562 562 HOH HOH . C 3 HOH A 202 563 563 HOH HOH . C 3 HOH A 203 564 564 HOH HOH . C 3 HOH A 204 565 565 HOH HOH . C 3 HOH A 205 566 566 HOH HOH . C 3 HOH A 206 567 567 HOH HOH . C 3 HOH A 207 568 568 HOH HOH . C 3 HOH A 208 569 569 HOH HOH . C 3 HOH A 209 570 570 HOH HOH . C 3 HOH A 210 571 571 HOH HOH . C 3 HOH A 211 572 572 HOH HOH . C 3 HOH A 212 573 573 HOH HOH . C 3 HOH A 213 574 574 HOH HOH . C 3 HOH A 214 575 575 HOH HOH . C 3 HOH A 215 576 576 HOH HOH . C 3 HOH A 216 577 577 HOH HOH . C 3 HOH A 217 578 578 HOH HOH . C 3 HOH A 218 579 579 HOH HOH . C 3 HOH A 219 580 580 HOH HOH . C 3 HOH A 220 581 581 HOH HOH . C 3 HOH A 221 582 582 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 53.589 3.867 16.708 1 16.74 ? N1 UDP 353 A 1 HETATM 2 C C2 UDP . . . B 2 52.309 4.22 17.054 1 17.25 ? C2 UDP 353 A 1 HETATM 3 N N3 UDP . . . B 2 51.815 3.785 18.251 1 17.83 ? N3 UDP 353 A 1 HETATM 4 C C4 UDP . . . B 2 52.531 3.01 19.119 1 17.84 ? C4 UDP 353 A 1 HETATM 5 C C5 UDP . . . B 2 53.98 2.701 18.907 1 17.3 ? C5 UDP 353 A 1 HETATM 6 C C6 UDP . . . B 2 54.442 3.079 17.691 1 17.21 ? C6 UDP 353 A 1 HETATM 7 O O2 UDP . . . B 2 51.615 4.928 16.329 1 17.27 ? O2 UDP 353 A 1 HETATM 8 O O4 UDP . . . B 2 51.988 2.5 20.096 1 18.48 ? O4 UDP 353 A 1 HETATM 9 C C1' UDP . . . B 2 54.116 4.214 15.37 1 15.8 ? C1' UDP 353 A 1 HETATM 10 C C2' UDP . . . B 2 54.939 5.421 15.521 1 15.59 ? C2' UDP 353 A 1 HETATM 11 O O2' UDP . . . B 2 54.677 6.386 14.502 1 15.55 ? O2' UDP 353 A 1 HETATM 12 C C3' UDP . . . B 2 56.347 4.889 15.578 1 15.42 ? C3' UDP 353 A 1 HETATM 13 C C4' UDP . . . B 2 56.278 3.787 14.663 1 15.34 ? C4' UDP 353 A 1 HETATM 14 O O4' UDP . . . B 2 55.037 3.175 15.022 1 15.66 ? O4' UDP 353 A 1 HETATM 15 O O3' UDP . . . B 2 57.319 5.836 15.158 1 16.08 ? O3' UDP 353 A 1 HETATM 16 C C5' UDP . . . B 2 57.402 2.857 14.892 1 15.54 ? C5' UDP 353 A 1 HETATM 17 O O5' UDP . . . B 2 57.229 1.693 14.024 1 15.36 ? O5' UDP 353 A 1 HETATM 18 P PA UDP . . . B 2 58.275 0.48 14.125 1 15.45 ? PA UDP 353 A 1 HETATM 19 O O1A UDP . . . B 2 58.086 -0.181 15.378 1 15.26 ? O1A UDP 353 A 1 HETATM 20 O O2A UDP . . . B 2 57.889 -0.442 13.054 1 15.61 ? O2A UDP 353 A 1 HETATM 21 O O3A UDP . . . B 2 59.775 0.951 13.952 1 15.39 ? O3A UDP 353 A 1 HETATM 22 P PB UDP . . . B 2 60.687 1.928 13.093 1 15.37 ? PB UDP 353 A 1 HETATM 23 O O1B UDP . . . B 2 59.942 2.979 12.601 1 15.61 ? O1B UDP 353 A 1 HETATM 24 O O2B UDP . . . B 2 61.188 1.123 11.964 1 15.64 ? O2B UDP 353 A 1 HETATM 25 O O3B UDP . . . B 2 61.693 2.586 13.976 1 15.68 ? O3B UDP 353 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #