data_3KVM
#
_model_server_result.job_id            4TH6fGQLpBQzJtdc2jnH3A 
_model_server_result.datetime_utc      '2024-11-27 07:57:38' 
_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          3kvm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":399}' 
#
_entry.id    3KVM 
#
_exptl.entry_id    3KVM 
_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            3KVM 
_cell.length_a            90.783 
_cell.length_b            90.783 
_cell.length_c            122.988 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KVM 
_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,H 
_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 158 n n 
C2 N1 DOR sing 159 n n 
C2 N3 DOR sing 160 n n 
N1 C6 DOR sing 161 n n 
N1 HN1 DOR sing 162 n n 
N3 C4 DOR sing 163 n n 
N3 HN3 DOR sing 164 n n 
C4 O4 DOR doub 165 n n 
C4 C5 DOR sing 166 n n 
C5 C6 DOR sing 167 n n 
C5 H51 DOR sing 168 n n 
C5 H52 DOR sing 169 n n 
C6 C7 DOR sing 170 n n 
C6 H6 DOR sing 171 n n 
C7 O72 DOR sing 172 n n 
C7 O71 DOR doub 173 n n 
O72 H72 DOR sing 174 n n 
#
_atom_sites.entry_id                     3KVM 
_atom_sites.fract_transf_matrix[1][1]    0.011015 
_atom_sites.fract_transf_matrix[1][2]    0.00636 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012719 
_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]    0.008131 
_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 ACT A 1 401 401 ACT ACT . 
G 7 951 A 1 402 402 951 951 . 
H 8 HOH A 1 403 403 HOH HOH . 
H 8 HOH A 2 404 404 HOH HOH . 
H 8 HOH A 3 405 405 HOH HOH . 
H 8 HOH A 4 406 406 HOH HOH . 
H 8 HOH A 5 407 407 HOH HOH . 
H 8 HOH A 6 408 408 HOH HOH . 
H 8 HOH A 7 409 409 HOH HOH . 
H 8 HOH A 8 410 410 HOH HOH . 
H 8 HOH A 9 411 411 HOH HOH . 
H 8 HOH A 10 412 412 HOH HOH . 
H 8 HOH A 11 413 413 HOH HOH . 
H 8 HOH A 12 414 414 HOH HOH . 
H 8 HOH A 13 415 415 HOH HOH . 
H 8 HOH A 14 416 416 HOH HOH . 
H 8 HOH A 15 417 417 HOH HOH . 
H 8 HOH A 16 418 418 HOH HOH . 
H 8 HOH A 17 419 419 HOH HOH . 
H 8 HOH A 18 420 420 HOH HOH . 
H 8 HOH A 19 421 421 HOH HOH . 
H 8 HOH A 20 422 422 HOH HOH . 
H 8 HOH A 21 423 423 HOH HOH . 
H 8 HOH A 22 424 424 HOH HOH . 
H 8 HOH A 23 425 425 HOH HOH . 
H 8 HOH A 24 426 426 HOH HOH . 
H 8 HOH A 25 427 427 HOH HOH . 
H 8 HOH A 26 428 428 HOH HOH . 
H 8 HOH A 27 429 429 HOH HOH . 
H 8 HOH A 28 430 430 HOH HOH . 
H 8 HOH A 29 431 431 HOH HOH . 
H 8 HOH A 30 432 432 HOH HOH . 
H 8 HOH A 31 433 433 HOH HOH . 
H 8 HOH A 32 434 434 HOH HOH . 
H 8 HOH A 33 435 435 HOH HOH . 
H 8 HOH A 34 436 436 HOH HOH . 
H 8 HOH A 35 437 437 HOH HOH . 
H 8 HOH A 36 438 438 HOH HOH . 
H 8 HOH A 37 439 439 HOH HOH . 
H 8 HOH A 38 440 440 HOH HOH . 
H 8 HOH A 39 441 441 HOH HOH . 
H 8 HOH A 40 442 442 HOH HOH . 
H 8 HOH A 41 443 443 HOH HOH . 
H 8 HOH A 42 444 444 HOH HOH . 
H 8 HOH A 43 445 445 HOH HOH . 
H 8 HOH A 44 446 446 HOH HOH . 
H 8 HOH A 45 447 447 HOH HOH . 
H 8 HOH A 46 448 448 HOH HOH . 
H 8 HOH A 47 449 449 HOH HOH . 
H 8 HOH A 48 450 450 HOH HOH . 
H 8 HOH A 49 451 451 HOH HOH . 
H 8 HOH A 50 452 452 HOH HOH . 
H 8 HOH A 51 453 453 HOH HOH . 
H 8 HOH A 52 454 454 HOH HOH . 
H 8 HOH A 53 455 455 HOH HOH . 
H 8 HOH A 54 456 456 HOH HOH . 
H 8 HOH A 55 457 457 HOH HOH . 
H 8 HOH A 56 458 458 HOH HOH . 
H 8 HOH A 57 459 459 HOH HOH . 
H 8 HOH A 58 460 460 HOH HOH . 
H 8 HOH A 59 461 461 HOH HOH . 
H 8 HOH A 60 462 462 HOH HOH . 
H 8 HOH A 61 463 463 HOH HOH . 
H 8 HOH A 62 464 464 HOH HOH . 
H 8 HOH A 63 465 465 HOH HOH . 
H 8 HOH A 64 466 466 HOH HOH . 
H 8 HOH A 65 467 467 HOH HOH . 
H 8 HOH A 66 468 468 HOH HOH . 
H 8 HOH A 67 469 469 HOH HOH . 
H 8 HOH A 68 470 470 HOH HOH . 
H 8 HOH A 69 471 471 HOH HOH . 
H 8 HOH A 70 472 472 HOH HOH . 
H 8 HOH A 71 473 473 HOH HOH . 
H 8 HOH A 72 474 474 HOH HOH . 
H 8 HOH A 73 475 475 HOH HOH . 
H 8 HOH A 74 476 476 HOH HOH . 
H 8 HOH A 75 477 477 HOH HOH . 
H 8 HOH A 76 478 478 HOH HOH . 
H 8 HOH A 77 479 479 HOH HOH . 
H 8 HOH A 78 480 480 HOH HOH . 
H 8 HOH A 79 481 481 HOH HOH . 
H 8 HOH A 80 482 482 HOH HOH . 
H 8 HOH A 81 483 483 HOH HOH . 
H 8 HOH A 82 484 484 HOH HOH . 
H 8 HOH A 83 485 485 HOH HOH . 
H 8 HOH A 84 486 486 HOH HOH . 
H 8 HOH A 85 487 487 HOH HOH . 
H 8 HOH A 86 488 488 HOH HOH . 
H 8 HOH A 87 489 489 HOH HOH . 
H 8 HOH A 88 490 490 HOH HOH . 
H 8 HOH A 89 491 491 HOH HOH . 
H 8 HOH A 90 492 492 HOH HOH . 
H 8 HOH A 91 493 493 HOH HOH . 
H 8 HOH A 92 494 494 HOH HOH . 
H 8 HOH A 93 495 495 HOH HOH . 
H 8 HOH A 94 496 496 HOH HOH . 
H 8 HOH A 95 497 497 HOH HOH . 
H 8 HOH A 96 498 498 HOH HOH . 
H 8 HOH A 97 499 499 HOH HOH . 
H 8 HOH A 98 500 500 HOH HOH . 
H 8 HOH A 99 501 501 HOH HOH . 
H 8 HOH A 100 502 502 HOH HOH . 
H 8 HOH A 101 503 503 HOH HOH . 
H 8 HOH A 102 504 504 HOH HOH . 
H 8 HOH A 103 505 505 HOH HOH . 
H 8 HOH A 104 506 506 HOH HOH . 
H 8 HOH A 105 507 507 HOH HOH . 
H 8 HOH A 106 508 508 HOH HOH . 
H 8 HOH A 107 509 509 HOH HOH . 
H 8 HOH A 108 510 510 HOH HOH . 
H 8 HOH A 109 511 511 HOH HOH . 
H 8 HOH A 110 512 512 HOH HOH . 
H 8 HOH A 111 513 513 HOH HOH . 
H 8 HOH A 112 514 514 HOH HOH . 
H 8 HOH A 113 515 515 HOH HOH . 
H 8 HOH A 114 516 516 HOH HOH . 
H 8 HOH A 115 517 517 HOH HOH . 
H 8 HOH A 116 518 518 HOH HOH . 
H 8 HOH A 117 519 519 HOH HOH . 
H 8 HOH A 118 520 520 HOH HOH . 
H 8 HOH A 119 521 521 HOH HOH . 
H 8 HOH A 120 522 522 HOH HOH . 
H 8 HOH A 121 523 523 HOH HOH . 
H 8 HOH A 122 524 524 HOH HOH . 
H 8 HOH A 123 525 525 HOH HOH . 
H 8 HOH A 124 526 526 HOH HOH . 
H 8 HOH A 125 527 527 HOH HOH . 
H 8 HOH A 126 528 528 HOH HOH . 
H 8 HOH A 127 529 529 HOH HOH . 
H 8 HOH A 128 530 530 HOH HOH . 
H 8 HOH A 129 531 531 HOH HOH . 
H 8 HOH A 130 532 532 HOH HOH . 
H 8 HOH A 131 533 533 HOH HOH . 
H 8 HOH A 132 534 534 HOH HOH . 
H 8 HOH A 133 535 535 HOH HOH . 
H 8 HOH A 134 536 536 HOH HOH . 
H 8 HOH A 135 537 537 HOH HOH . 
H 8 HOH A 136 538 538 HOH HOH . 
H 8 HOH A 137 539 539 HOH HOH . 
H 8 HOH A 138 540 540 HOH HOH . 
H 8 HOH A 139 541 541 HOH HOH . 
H 8 HOH A 140 542 542 HOH HOH . 
H 8 HOH A 141 543 543 HOH HOH . 
H 8 HOH A 142 544 544 HOH HOH . 
H 8 HOH A 143 545 545 HOH HOH . 
H 8 HOH A 144 546 546 HOH HOH . 
H 8 HOH A 145 547 547 HOH HOH . 
H 8 HOH A 146 548 548 HOH HOH . 
H 8 HOH A 147 549 549 HOH HOH . 
H 8 HOH A 148 550 550 HOH HOH . 
H 8 HOH A 149 551 551 HOH HOH . 
H 8 HOH A 150 552 552 HOH HOH . 
H 8 HOH A 151 553 553 HOH HOH . 
H 8 HOH A 152 554 554 HOH HOH . 
H 8 HOH A 153 555 555 HOH HOH . 
H 8 HOH A 154 556 556 HOH HOH . 
H 8 HOH A 155 557 557 HOH HOH . 
H 8 HOH A 156 558 558 HOH HOH . 
H 8 HOH A 157 559 559 HOH HOH . 
H 8 HOH A 158 560 560 HOH HOH . 
H 8 HOH A 159 561 561 HOH HOH . 
H 8 HOH A 160 562 562 HOH HOH . 
H 8 HOH A 161 563 563 HOH HOH . 
H 8 HOH A 162 564 564 HOH HOH . 
H 8 HOH A 163 565 565 HOH HOH . 
H 8 HOH A 164 566 566 HOH HOH . 
H 8 HOH A 165 567 567 HOH HOH . 
H 8 HOH A 166 568 568 HOH HOH . 
H 8 HOH A 167 569 569 HOH HOH . 
H 8 HOH A 168 570 570 HOH HOH . 
H 8 HOH A 169 571 571 HOH HOH . 
H 8 HOH A 170 572 572 HOH HOH . 
H 8 HOH A 171 573 573 HOH HOH . 
H 8 HOH A 172 574 574 HOH HOH . 
H 8 HOH A 173 575 575 HOH HOH . 
H 8 HOH A 174 576 576 HOH HOH . 
H 8 HOH A 175 577 577 HOH HOH . 
H 8 HOH A 176 578 578 HOH HOH . 
H 8 HOH A 177 579 579 HOH HOH . 
H 8 HOH A 178 580 580 HOH HOH . 
H 8 HOH A 179 581 581 HOH HOH . 
H 8 HOH A 180 582 582 HOH HOH . 
H 8 HOH A 181 583 583 HOH HOH . 
H 8 HOH A 182 584 584 HOH HOH . 
H 8 HOH A 183 585 585 HOH HOH . 
H 8 HOH A 184 586 586 HOH HOH . 
H 8 HOH A 185 587 587 HOH HOH . 
H 8 HOH A 186 588 588 HOH HOH . 
H 8 HOH A 187 589 589 HOH HOH . 
H 8 HOH A 188 590 590 HOH HOH . 
H 8 HOH A 189 591 591 HOH HOH . 
H 8 HOH A 190 592 592 HOH HOH . 
H 8 HOH A 191 593 593 HOH HOH . 
H 8 HOH A 192 594 594 HOH HOH . 
H 8 HOH A 193 595 595 HOH HOH . 
H 8 HOH A 194 596 596 HOH HOH . 
H 8 HOH A 195 597 597 HOH HOH . 
H 8 HOH A 196 598 598 HOH HOH . 
H 8 HOH A 197 599 599 HOH HOH . 
H 8 HOH A 198 600 600 HOH HOH . 
H 8 HOH A 199 601 601 HOH HOH . 
H 8 HOH A 200 602 602 HOH HOH . 
H 8 HOH A 201 603 603 HOH HOH . 
H 8 HOH A 202 604 604 HOH HOH . 
H 8 HOH A 203 605 605 HOH HOH . 
H 8 HOH A 204 606 606 HOH HOH . 
H 8 HOH A 205 607 607 HOH HOH . 
H 8 HOH A 206 608 608 HOH HOH . 
H 8 HOH A 207 609 609 HOH HOH . 
H 8 HOH A 208 610 610 HOH HOH . 
H 8 HOH A 209 611 611 HOH HOH . 
H 8 HOH A 210 612 612 HOH HOH . 
H 8 HOH A 211 613 613 HOH HOH . 
H 8 HOH A 212 614 614 HOH HOH . 
H 8 HOH A 213 615 615 HOH HOH . 
H 8 HOH A 214 616 616 HOH HOH . 
H 8 HOH A 215 617 617 HOH HOH . 
H 8 HOH A 216 618 618 HOH HOH . 
H 8 HOH A 217 619 619 HOH HOH . 
H 8 HOH A 218 620 620 HOH HOH . 
H 8 HOH A 219 621 621 HOH HOH . 
H 8 HOH A 220 622 622 HOH HOH . 
H 8 HOH A 221 623 623 HOH HOH . 
H 8 HOH A 222 624 624 HOH HOH . 
H 8 HOH A 223 625 625 HOH HOH . 
H 8 HOH A 224 626 626 HOH HOH . 
H 8 HOH A 225 627 627 HOH HOH . 
H 8 HOH A 226 628 628 HOH HOH . 
H 8 HOH A 227 629 629 HOH HOH . 
H 8 HOH A 228 630 630 HOH HOH . 
H 8 HOH A 229 631 631 HOH HOH . 
H 8 HOH A 230 632 632 HOH HOH . 
H 8 HOH A 231 633 633 HOH HOH . 
H 8 HOH A 232 634 634 HOH HOH . 
H 8 HOH A 233 635 635 HOH HOH . 
H 8 HOH A 234 636 636 HOH HOH . 
H 8 HOH A 235 637 637 HOH HOH . 
H 8 HOH A 236 638 638 HOH HOH . 
H 8 HOH A 237 639 639 HOH HOH . 
H 8 HOH A 238 640 640 HOH HOH . 
H 8 HOH A 239 641 641 HOH HOH . 
H 8 HOH A 240 642 642 HOH HOH . 
H 8 HOH A 241 643 643 HOH HOH . 
H 8 HOH A 242 644 644 HOH HOH . 
H 8 HOH A 243 645 645 HOH HOH . 
H 8 HOH A 244 646 646 HOH HOH . 
H 8 HOH A 245 647 647 HOH HOH . 
H 8 HOH A 246 648 648 HOH HOH . 
H 8 HOH A 247 649 649 HOH HOH . 
H 8 HOH A 248 650 650 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 36.003 -26.66 -16.186 1 21.52 ? O2 DOR 399 A 1 
HETATM 2 C C2 DOR . . . D 4 36.849 -26.461 -15.316 1 22.23 ? C2 DOR 399 A 1 
HETATM 3 N N1 DOR . . . D 4 38.155 -26.102 -15.669 1 22.2 ? N1 DOR 399 A 1 
HETATM 4 N N3 DOR . . . D 4 36.524 -26.616 -13.961 1 18.94 ? N3 DOR 399 A 1 
HETATM 5 C C4 DOR . . . D 4 37.495 -26.431 -12.968 1 20.35 ? C4 DOR 399 A 1 
HETATM 6 O O4 DOR . . . D 4 37.195 -26.58 -11.784 1 18.35 ? O4 DOR 399 A 1 
HETATM 7 C C5 DOR . . . D 4 38.934 -26.066 -13.344 1 21.76 ? C5 DOR 399 A 1 
HETATM 8 C C6 DOR . . . D 4 38.98 -25.362 -14.703 1 22.65 ? C6 DOR 399 A 1 
HETATM 9 C C7 DOR . . . D 4 40.427 -25.284 -15.191 1 23.85 ? C7 DOR 399 A 1 
HETATM 10 O O72 DOR . . . D 4 41.137 -24.374 -14.709 1 24.03 ? O72 DOR 399 A 1 
HETATM 11 O O71 DOR . . . D 4 40.796 -26.138 -16.026 1 25.18 ? O71 DOR 399 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           330 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           11 
#