data_3KVK # _model_server_result.job_id MCIemLRNKX8CZ34v6TlAmA _model_server_result.datetime_utc '2024-11-08 16:51:49' _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 3kvk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":399}' # _entry.id 3KVK # _exptl.entry_id 3KVK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 158.112 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID' _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 3KVK _cell.length_a 90.908 _cell.length_b 90.908 _cell.length_c 123.077 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KVK _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 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,E,F,G _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C5 H6 N2 O4' _chem_comp.formula_weight 158.112 _chem_comp.id DOR _chem_comp.mon_nstd_flag . _chem_comp.name '(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'DIHYDROOROTIC 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 O2 C2 DOR doub 145 n n C2 N1 DOR sing 146 n n C2 N3 DOR sing 147 n n N1 C6 DOR sing 148 n n N1 HN1 DOR sing 149 n n N3 C4 DOR sing 150 n n N3 HN3 DOR sing 151 n n C4 O4 DOR doub 152 n n C4 C5 DOR sing 153 n n C5 C6 DOR sing 154 n n C5 H51 DOR sing 155 n n C5 H52 DOR sing 156 n n C6 C7 DOR sing 157 n n C6 H6 DOR sing 158 n n C7 O72 DOR sing 159 n n C7 O71 DOR doub 160 n n O72 H72 DOR sing 161 n n # _atom_sites.entry_id 3KVK _atom_sites.fract_transf_matrix[1][1] 0.011 _atom_sites.fract_transf_matrix[1][2] 0.006351 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012702 _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] 0.008125 _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 1 397 397 SO4 SO4 . C 3 FMN A 1 398 398 FMN FMN . D 4 DOR A 1 399 399 DOR DOR . E 5 DET A 1 400 400 DET DET . F 6 6X1 A 1 401 401 6X1 6X1 . G 7 HOH A 1 402 402 HOH HOH . G 7 HOH A 2 403 403 HOH HOH . G 7 HOH A 3 404 404 HOH HOH . G 7 HOH A 4 405 405 HOH HOH . G 7 HOH A 5 406 406 HOH HOH . G 7 HOH A 6 407 407 HOH HOH . G 7 HOH A 7 408 408 HOH HOH . G 7 HOH A 8 409 409 HOH HOH . G 7 HOH A 9 410 410 HOH HOH . G 7 HOH A 10 411 411 HOH HOH . G 7 HOH A 11 412 412 HOH HOH . G 7 HOH A 12 413 413 HOH HOH . G 7 HOH A 13 414 414 HOH HOH . G 7 HOH A 14 415 415 HOH HOH . G 7 HOH A 15 416 416 HOH HOH . G 7 HOH A 16 417 417 HOH HOH . G 7 HOH A 17 418 418 HOH HOH . G 7 HOH A 18 419 419 HOH HOH . G 7 HOH A 19 420 420 HOH HOH . G 7 HOH A 20 421 421 HOH HOH . G 7 HOH A 21 422 422 HOH HOH . G 7 HOH A 22 423 423 HOH HOH . G 7 HOH A 23 424 424 HOH HOH . G 7 HOH A 24 425 425 HOH HOH . G 7 HOH A 25 426 426 HOH HOH . G 7 HOH A 26 427 427 HOH HOH . G 7 HOH A 27 428 428 HOH HOH . G 7 HOH A 28 429 429 HOH HOH . G 7 HOH A 29 430 430 HOH HOH . G 7 HOH A 30 431 431 HOH HOH . G 7 HOH A 31 432 432 HOH HOH . G 7 HOH A 32 433 433 HOH HOH . G 7 HOH A 33 434 434 HOH HOH . G 7 HOH A 34 435 435 HOH HOH . G 7 HOH A 35 436 436 HOH HOH . G 7 HOH A 36 437 437 HOH HOH . G 7 HOH A 37 438 438 HOH HOH . G 7 HOH A 38 439 439 HOH HOH . G 7 HOH A 39 440 440 HOH HOH . G 7 HOH A 40 441 441 HOH HOH . G 7 HOH A 41 442 442 HOH HOH . G 7 HOH A 42 443 443 HOH HOH . G 7 HOH A 43 444 444 HOH HOH . G 7 HOH A 44 445 445 HOH HOH . G 7 HOH A 45 446 446 HOH HOH . G 7 HOH A 46 447 447 HOH HOH . G 7 HOH A 47 448 448 HOH HOH . G 7 HOH A 48 449 449 HOH HOH . G 7 HOH A 49 450 450 HOH HOH . G 7 HOH A 50 451 451 HOH HOH . G 7 HOH A 51 452 452 HOH HOH . G 7 HOH A 52 453 453 HOH HOH . G 7 HOH A 53 454 454 HOH HOH . G 7 HOH A 54 455 455 HOH HOH . G 7 HOH A 55 456 456 HOH HOH . G 7 HOH A 56 457 457 HOH HOH . G 7 HOH A 57 458 458 HOH HOH . G 7 HOH A 58 459 459 HOH HOH . G 7 HOH A 59 460 460 HOH HOH . G 7 HOH A 60 461 461 HOH HOH . G 7 HOH A 61 462 462 HOH HOH . G 7 HOH A 62 463 463 HOH HOH . G 7 HOH A 63 464 464 HOH HOH . G 7 HOH A 64 465 465 HOH HOH . G 7 HOH A 65 466 466 HOH HOH . G 7 HOH A 66 467 467 HOH HOH . G 7 HOH A 67 468 468 HOH HOH . G 7 HOH A 68 469 469 HOH HOH . G 7 HOH A 69 470 470 HOH HOH . G 7 HOH A 70 471 471 HOH HOH . G 7 HOH A 71 472 472 HOH HOH . G 7 HOH A 72 473 473 HOH HOH . G 7 HOH A 73 474 474 HOH HOH . G 7 HOH A 74 475 475 HOH HOH . G 7 HOH A 75 476 476 HOH HOH . G 7 HOH A 76 477 477 HOH HOH . G 7 HOH A 77 478 478 HOH HOH . G 7 HOH A 78 479 479 HOH HOH . G 7 HOH A 79 480 480 HOH HOH . G 7 HOH A 80 481 481 HOH HOH . G 7 HOH A 81 482 482 HOH HOH . G 7 HOH A 82 483 483 HOH HOH . G 7 HOH A 83 484 484 HOH HOH . G 7 HOH A 84 485 485 HOH HOH . G 7 HOH A 85 486 486 HOH HOH . G 7 HOH A 86 487 487 HOH HOH . G 7 HOH A 87 488 488 HOH HOH . G 7 HOH A 88 489 489 HOH HOH . G 7 HOH A 89 490 490 HOH HOH . G 7 HOH A 90 491 491 HOH HOH . G 7 HOH A 91 492 492 HOH HOH . G 7 HOH A 92 493 493 HOH HOH . G 7 HOH A 93 494 494 HOH HOH . G 7 HOH A 94 495 495 HOH HOH . G 7 HOH A 95 496 496 HOH HOH . G 7 HOH A 96 497 497 HOH HOH . G 7 HOH A 97 498 498 HOH HOH . G 7 HOH A 98 499 499 HOH HOH . G 7 HOH A 99 500 500 HOH HOH . G 7 HOH A 100 501 501 HOH HOH . G 7 HOH A 101 502 502 HOH HOH . G 7 HOH A 102 503 503 HOH HOH . G 7 HOH A 103 504 504 HOH HOH . G 7 HOH A 104 505 505 HOH HOH . G 7 HOH A 105 506 506 HOH HOH . G 7 HOH A 106 507 507 HOH HOH . G 7 HOH A 107 508 508 HOH HOH . G 7 HOH A 108 509 509 HOH HOH . G 7 HOH A 109 510 510 HOH HOH . G 7 HOH A 110 511 511 HOH HOH . G 7 HOH A 111 512 512 HOH HOH . G 7 HOH A 112 513 513 HOH HOH . G 7 HOH A 113 514 514 HOH HOH . G 7 HOH A 114 515 515 HOH HOH . G 7 HOH A 115 516 516 HOH HOH . G 7 HOH A 116 517 517 HOH HOH . G 7 HOH A 117 518 518 HOH HOH . G 7 HOH A 118 519 519 HOH HOH . G 7 HOH A 119 520 520 HOH HOH . G 7 HOH A 120 521 521 HOH HOH . G 7 HOH A 121 522 522 HOH HOH . G 7 HOH A 122 523 523 HOH HOH . G 7 HOH A 123 524 524 HOH HOH . G 7 HOH A 124 525 525 HOH HOH . G 7 HOH A 125 526 526 HOH HOH . G 7 HOH A 126 527 527 HOH HOH . G 7 HOH A 127 528 528 HOH HOH . G 7 HOH A 128 529 529 HOH HOH . G 7 HOH A 129 530 530 HOH HOH . G 7 HOH A 130 531 531 HOH HOH . G 7 HOH A 131 532 532 HOH HOH . G 7 HOH A 132 533 533 HOH HOH . G 7 HOH A 133 534 534 HOH HOH . G 7 HOH A 134 535 535 HOH HOH . G 7 HOH A 135 536 536 HOH HOH . G 7 HOH A 136 537 537 HOH HOH . G 7 HOH A 137 538 538 HOH HOH . G 7 HOH A 138 539 539 HOH HOH . G 7 HOH A 139 540 540 HOH HOH . G 7 HOH A 140 541 541 HOH HOH . G 7 HOH A 141 542 542 HOH HOH . G 7 HOH A 142 543 543 HOH HOH . G 7 HOH A 143 544 544 HOH HOH . G 7 HOH A 144 545 545 HOH HOH . G 7 HOH A 145 546 546 HOH HOH . G 7 HOH A 146 547 547 HOH HOH . G 7 HOH A 147 548 548 HOH HOH . G 7 HOH A 148 549 549 HOH HOH . G 7 HOH A 149 550 550 HOH HOH . G 7 HOH A 150 551 551 HOH HOH . G 7 HOH A 151 552 552 HOH HOH . G 7 HOH A 152 553 553 HOH HOH . G 7 HOH A 153 554 554 HOH HOH . G 7 HOH A 154 555 555 HOH HOH . G 7 HOH A 155 556 556 HOH HOH . G 7 HOH A 156 557 557 HOH HOH . G 7 HOH A 157 558 558 HOH HOH . G 7 HOH A 158 559 559 HOH HOH . G 7 HOH A 159 560 560 HOH HOH . G 7 HOH A 160 561 561 HOH HOH . G 7 HOH A 161 562 562 HOH HOH . G 7 HOH A 162 563 563 HOH HOH . G 7 HOH A 163 564 564 HOH HOH . G 7 HOH A 164 565 565 HOH HOH . G 7 HOH A 165 566 566 HOH HOH . G 7 HOH A 166 567 567 HOH HOH . G 7 HOH A 167 568 568 HOH HOH . G 7 HOH A 168 569 569 HOH HOH . G 7 HOH A 169 570 570 HOH HOH . G 7 HOH A 170 571 571 HOH HOH . G 7 HOH A 171 572 572 HOH HOH . G 7 HOH A 172 573 573 HOH HOH . G 7 HOH A 173 574 574 HOH HOH . G 7 HOH A 174 575 575 HOH HOH . G 7 HOH A 175 576 576 HOH HOH . G 7 HOH A 176 577 577 HOH HOH . G 7 HOH A 177 578 578 HOH HOH . G 7 HOH A 178 579 579 HOH HOH . G 7 HOH A 179 580 580 HOH HOH . G 7 HOH A 180 581 581 HOH HOH . G 7 HOH A 181 582 582 HOH HOH . G 7 HOH A 182 583 583 HOH HOH . G 7 HOH A 183 584 584 HOH HOH . G 7 HOH A 184 585 585 HOH HOH . G 7 HOH A 185 586 586 HOH HOH . G 7 HOH A 186 587 587 HOH HOH . G 7 HOH A 187 588 588 HOH HOH . G 7 HOH A 188 589 589 HOH HOH . G 7 HOH A 189 590 590 HOH HOH . G 7 HOH A 190 591 591 HOH HOH . G 7 HOH A 191 592 592 HOH HOH . G 7 HOH A 192 593 593 HOH HOH . G 7 HOH A 193 594 594 HOH HOH . G 7 HOH A 194 595 595 HOH HOH . G 7 HOH A 195 596 596 HOH HOH . G 7 HOH A 196 597 597 HOH HOH . G 7 HOH A 197 598 598 HOH HOH . G 7 HOH A 198 599 599 HOH HOH . G 7 HOH A 199 600 600 HOH HOH . G 7 HOH A 200 601 601 HOH HOH . G 7 HOH A 201 602 602 HOH HOH . G 7 HOH A 202 603 603 HOH HOH . G 7 HOH A 203 604 604 HOH HOH . G 7 HOH A 204 605 605 HOH HOH . G 7 HOH A 205 606 606 HOH HOH . G 7 HOH A 206 607 607 HOH HOH . G 7 HOH A 207 608 608 HOH HOH . G 7 HOH A 208 609 609 HOH HOH . G 7 HOH A 209 610 610 HOH HOH . G 7 HOH A 210 611 611 HOH HOH . G 7 HOH A 211 612 612 HOH HOH . G 7 HOH A 212 613 613 HOH HOH . G 7 HOH A 213 614 614 HOH HOH . G 7 HOH A 214 615 615 HOH HOH . G 7 HOH A 215 616 616 HOH HOH . G 7 HOH A 216 617 617 HOH HOH . G 7 HOH A 217 618 618 HOH HOH . G 7 HOH A 218 619 619 HOH HOH . G 7 HOH A 219 620 620 HOH HOH . G 7 HOH A 220 621 621 HOH HOH . G 7 HOH A 221 622 622 HOH HOH . G 7 HOH A 222 623 623 HOH HOH . G 7 HOH A 223 624 624 HOH HOH . G 7 HOH A 224 625 625 HOH HOH . G 7 HOH A 225 626 626 HOH HOH . G 7 HOH A 226 627 627 HOH HOH . G 7 HOH A 227 628 628 HOH HOH . G 7 HOH A 228 629 629 HOH HOH . G 7 HOH A 229 630 630 HOH HOH . G 7 HOH A 230 631 631 HOH HOH . G 7 HOH A 231 632 632 HOH HOH . G 7 HOH A 232 633 633 HOH HOH . G 7 HOH A 233 634 634 HOH HOH . G 7 HOH A 234 635 635 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 O O2 DOR . . . D 4 5.067 44.559 4.299 1 20.08 ? O2 DOR 399 A 1 HETATM 2 C C2 DOR . . . D 4 4.474 45.18 5.18 1 20.4 ? C2 DOR 399 A 1 HETATM 3 N N1 DOR . . . D 4 3.514 46.144 4.844 1 19.84 ? N1 DOR 399 A 1 HETATM 4 N N3 DOR . . . D 4 4.781 44.963 6.529 1 16.97 ? N3 DOR 399 A 1 HETATM 5 C C4 DOR . . . D 4 4.151 45.707 7.535 1 17.4 ? C4 DOR 399 A 1 HETATM 6 O O4 DOR . . . D 4 4.454 45.523 8.713 1 17.31 ? O4 DOR 399 A 1 HETATM 7 C C5 DOR . . . D 4 3.117 46.778 7.18 1 19.64 ? C5 DOR 399 A 1 HETATM 8 C C6 DOR . . . D 4 2.472 46.487 5.823 1 20.51 ? C6 DOR 399 A 1 HETATM 9 C C7 DOR . . . D 4 1.695 47.721 5.36 1 21.37 ? C7 DOR 399 A 1 HETATM 10 O O72 DOR . . . D 4 2.284 48.507 4.586 1 22.84 ? O72 DOR 399 A 1 HETATM 11 O O71 DOR . . . D 4 0.533 47.855 5.799 1 22.49 ? O71 DOR 399 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 11 #