data_6I25 # _model_server_result.job_id 5lw4xCaBxfLITUnuhyLAAQ _model_server_result.datetime_utc '2024-11-06 14:35:01' _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 6i25 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 6I25 # _exptl.entry_id 6I25 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 457.372 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R},3~{S},4~{S})-5-[(4~{a}~{R})-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a},5-dihydropyrimido[4,5-b]quinolin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate' _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 6I25 _cell.length_a 106.287 _cell.length_b 106.287 _cell.length_c 67.859 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6I25 _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _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 _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 # 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 covale ? covale1 A SG CYS 53 A CYS 230 1_555 D C4A 5DD . A 5DD 403 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.837 ? metalc ? metalc1 A O SER 46 A SER 223 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc2 A O SER 46 A SER 223 1_555 C MG MG . A MG 402 12_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc3 A O LEU 49 A LEU 226 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc4 A O LEU 49 A LEU 226 1_555 C MG MG . A MG 402 12_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc5 C MG MG . A MG 402 1_555 F O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc6 C MG MG . A MG 402 1_555 F O HOH . A HOH 511 12_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? # _chem_comp.formula 'C18 H24 N3 O9 P' _chem_comp.formula_weight 457.372 _chem_comp.id 5DD _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R},3~{S},4~{S})-5-[(4~{a}~{R})-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a},5-dihydropyrimido[4,5-b]quinolin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate' _chem_comp.type non-polymer _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 O2P P 5DD doub 1 n n C5' O5' 5DD sing 2 n n C5' C4' 5DD sing 3 n n P O5' 5DD sing 4 n n P O1P 5DD sing 5 n n P O3P 5DD sing 6 n n O4' C4' 5DD sing 7 n n C4' C3' 5DD sing 8 n n O2 C2 5DD doub 9 n n O3' C3' 5DD sing 10 n n C3' C2' 5DD sing 11 n n C2 N1 5DD sing 12 n n C2 N3 5DD sing 13 n n C1' C2' 5DD sing 14 n n C1' N10 5DD sing 15 n n N1 C10 5DD doub 16 n n N3 C4 5DD sing 17 n n C2' O2' 5DD sing 18 n n C10 N10 5DD sing 19 n n C10 C4A 5DD sing 20 n n N10 C9A 5DD sing 21 n n C4 C4A 5DD sing 22 n n C4 O4 5DD doub 23 n n C9A C9 5DD doub 24 n y C9A C5A 5DD sing 25 n y C4A C1 5DD sing 26 n n C1 C5A 5DD sing 27 n n C9 C8 5DD sing 28 n y C5A C6 5DD doub 29 n y C8 C8M 5DD sing 30 n n C8 C7 5DD doub 31 n y C6 C7 5DD sing 32 n y C7 C7M 5DD sing 33 n n O3P H1 5DD sing 34 n n O1P H2 5DD sing 35 n n C5' H3 5DD sing 36 n n C5' H4 5DD sing 37 n n C4' H5 5DD sing 38 n n O4' H6 5DD sing 39 n n C3' H7 5DD sing 40 n n O3' H8 5DD sing 41 n n C2' H9 5DD sing 42 n n O2' H10 5DD sing 43 n n C1' H11 5DD sing 44 n n C1' H12 5DD sing 45 n n C9 H13 5DD sing 46 n n C8M H14 5DD sing 47 n n C8M H15 5DD sing 48 n n C8M H16 5DD sing 49 n n C7M H17 5DD sing 50 n n C7M H18 5DD sing 51 n n C7M H19 5DD sing 52 n n C6 H20 5DD sing 53 n n C4A H21 5DD sing 54 n n N3 H22 5DD sing 55 n n C1 H23 5DD sing 56 n n C1 H24 5DD sing 57 n n # _atom_sites.entry_id 6I25 _atom_sites.fract_transf_matrix[1][1] 0.009408 _atom_sites.fract_transf_matrix[1][2] 0.005432 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010864 _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] 0.014736 _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 CL A 1 401 354 CL CL . C 3 MG A 1 402 358 MG MG . D 4 5DD A 1 403 361 5DD 5DD . E 5 9O9 A 1 404 365 9O9 5DF . F 6 HOH A 1 501 515 HOH HOH . F 6 HOH A 2 502 438 HOH HOH . F 6 HOH A 3 503 447 HOH HOH . F 6 HOH A 4 504 419 HOH HOH . F 6 HOH A 5 505 458 HOH HOH . F 6 HOH A 6 506 476 HOH HOH . F 6 HOH A 7 507 544 HOH HOH . F 6 HOH A 8 508 473 HOH HOH . F 6 HOH A 9 509 404 HOH HOH . F 6 HOH A 10 510 453 HOH HOH . F 6 HOH A 11 511 407 HOH HOH . F 6 HOH A 12 512 434 HOH HOH . F 6 HOH A 13 513 412 HOH HOH . F 6 HOH A 14 514 449 HOH HOH . F 6 HOH A 15 515 457 HOH HOH . F 6 HOH A 16 516 432 HOH HOH . F 6 HOH A 17 517 547 HOH HOH . F 6 HOH A 18 518 491 HOH HOH . F 6 HOH A 19 519 527 HOH HOH . F 6 HOH A 20 520 456 HOH HOH . F 6 HOH A 21 521 531 HOH HOH . F 6 HOH A 22 522 462 HOH HOH . F 6 HOH A 23 523 425 HOH HOH . F 6 HOH A 24 524 439 HOH HOH . F 6 HOH A 25 525 431 HOH HOH . F 6 HOH A 26 526 465 HOH HOH . F 6 HOH A 27 527 423 HOH HOH . F 6 HOH A 28 528 450 HOH HOH . F 6 HOH A 29 529 495 HOH HOH . F 6 HOH A 30 530 435 HOH HOH . F 6 HOH A 31 531 548 HOH HOH . F 6 HOH A 32 532 414 HOH HOH . F 6 HOH A 33 533 463 HOH HOH . F 6 HOH A 34 534 489 HOH HOH . F 6 HOH A 35 535 409 HOH HOH . F 6 HOH A 36 536 496 HOH HOH . F 6 HOH A 37 537 459 HOH HOH . F 6 HOH A 38 538 436 HOH HOH . F 6 HOH A 39 539 403 HOH HOH . F 6 HOH A 40 540 445 HOH HOH . F 6 HOH A 41 541 430 HOH HOH . F 6 HOH A 42 542 535 HOH HOH . F 6 HOH A 43 543 510 HOH HOH . F 6 HOH A 44 544 442 HOH HOH . F 6 HOH A 45 545 418 HOH HOH . F 6 HOH A 46 546 498 HOH HOH . F 6 HOH A 47 547 429 HOH HOH . F 6 HOH A 48 548 461 HOH HOH . F 6 HOH A 49 549 413 HOH HOH . F 6 HOH A 50 550 446 HOH HOH . F 6 HOH A 51 551 444 HOH HOH . F 6 HOH A 52 552 477 HOH HOH . F 6 HOH A 53 553 485 HOH HOH . F 6 HOH A 54 554 538 HOH HOH . F 6 HOH A 55 555 487 HOH HOH . F 6 HOH A 56 556 484 HOH HOH . F 6 HOH A 57 557 428 HOH HOH . F 6 HOH A 58 558 468 HOH HOH . F 6 HOH A 59 559 405 HOH HOH . F 6 HOH A 60 560 452 HOH HOH . F 6 HOH A 61 561 437 HOH HOH . F 6 HOH A 62 562 426 HOH HOH . F 6 HOH A 63 563 533 HOH HOH . F 6 HOH A 64 564 528 HOH HOH . F 6 HOH A 65 565 480 HOH HOH . F 6 HOH A 66 566 472 HOH HOH . F 6 HOH A 67 567 464 HOH HOH . F 6 HOH A 68 568 427 HOH HOH . F 6 HOH A 69 569 540 HOH HOH . F 6 HOH A 70 570 420 HOH HOH . F 6 HOH A 71 571 441 HOH HOH . F 6 HOH A 72 572 415 HOH HOH . F 6 HOH A 73 573 406 HOH HOH . F 6 HOH A 74 574 536 HOH HOH . F 6 HOH A 75 575 424 HOH HOH . F 6 HOH A 76 576 408 HOH HOH . F 6 HOH A 77 577 475 HOH HOH . F 6 HOH A 78 578 433 HOH HOH . F 6 HOH A 79 579 455 HOH HOH . F 6 HOH A 80 580 537 HOH HOH . F 6 HOH A 81 581 482 HOH HOH . F 6 HOH A 82 582 479 HOH HOH . F 6 HOH A 83 583 451 HOH HOH . F 6 HOH A 84 584 509 HOH HOH . F 6 HOH A 85 585 471 HOH HOH . F 6 HOH A 86 586 402 HOH HOH . F 6 HOH A 87 587 519 HOH HOH . F 6 HOH A 88 588 546 HOH HOH . F 6 HOH A 89 589 526 HOH HOH . F 6 HOH A 90 590 532 HOH HOH . F 6 HOH A 91 591 488 HOH HOH . F 6 HOH A 92 592 530 HOH HOH . F 6 HOH A 93 593 514 HOH HOH . F 6 HOH A 94 594 503 HOH HOH . F 6 HOH A 95 595 460 HOH HOH . F 6 HOH A 96 596 469 HOH HOH . F 6 HOH A 97 597 421 HOH HOH . F 6 HOH A 98 598 416 HOH HOH . F 6 HOH A 99 599 529 HOH HOH . F 6 HOH A 100 600 448 HOH HOH . F 6 HOH A 101 601 467 HOH HOH . F 6 HOH A 102 602 511 HOH HOH . F 6 HOH A 103 603 513 HOH HOH . F 6 HOH A 104 604 494 HOH HOH . F 6 HOH A 105 605 411 HOH HOH . F 6 HOH A 106 606 534 HOH HOH . F 6 HOH A 107 607 422 HOH HOH . F 6 HOH A 108 608 443 HOH HOH . F 6 HOH A 109 609 466 HOH HOH . F 6 HOH A 110 610 499 HOH HOH . F 6 HOH A 111 611 541 HOH HOH . F 6 HOH A 112 612 490 HOH HOH . F 6 HOH A 113 613 523 HOH HOH . F 6 HOH A 114 614 524 HOH HOH . F 6 HOH A 115 615 507 HOH HOH . F 6 HOH A 116 616 470 HOH HOH . F 6 HOH A 117 617 481 HOH HOH . F 6 HOH A 118 618 551 HOH HOH . F 6 HOH A 119 619 410 HOH HOH . F 6 HOH A 120 620 497 HOH HOH . F 6 HOH A 121 621 401 HOH HOH . F 6 HOH A 122 622 517 HOH HOH . F 6 HOH A 123 623 500 HOH HOH . F 6 HOH A 124 624 417 HOH HOH . F 6 HOH A 125 625 542 HOH HOH . F 6 HOH A 126 626 520 HOH HOH . F 6 HOH A 127 627 493 HOH HOH . F 6 HOH A 128 628 549 HOH HOH . F 6 HOH A 129 629 518 HOH HOH . F 6 HOH A 130 630 505 HOH HOH . F 6 HOH A 131 631 550 HOH HOH . F 6 HOH A 132 632 486 HOH HOH . F 6 HOH A 133 633 504 HOH HOH . F 6 HOH A 134 634 492 HOH HOH . F 6 HOH A 135 635 502 HOH HOH . F 6 HOH A 136 636 521 HOH HOH . F 6 HOH A 137 637 543 HOH HOH . F 6 HOH A 138 638 539 HOH HOH . F 6 HOH A 139 639 501 HOH HOH . F 6 HOH A 140 640 522 HOH HOH . F 6 HOH A 141 641 474 HOH HOH . F 6 HOH A 142 642 440 HOH HOH . F 6 HOH A 143 643 483 HOH HOH . F 6 HOH A 144 644 545 HOH HOH . F 6 HOH A 145 645 525 HOH HOH . F 6 HOH A 146 646 478 HOH HOH . F 6 HOH A 147 647 512 HOH HOH . F 6 HOH A 148 648 506 HOH HOH . F 6 HOH A 149 649 508 HOH HOH . F 6 HOH A 150 650 454 HOH HOH . F 6 HOH A 151 651 516 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 O3P 5DD . B . D 4 -37.754 46.138 5.33 0.3 17.29 ? O3P 5DD 403 A 1 HETATM 2 P P 5DD . B . D 4 -37.105 45.034 4.53 0.3 19.83 ? P 5DD 403 A 1 HETATM 3 O O1P 5DD . B . D 4 -35.646 44.869 4.93 0.3 19.83 ? O1P 5DD 403 A 1 HETATM 4 O O2P 5DD . B . D 4 -37.196 45.363 3.051 0.3 15.52 ? O2P 5DD 403 A 1 HETATM 5 O O5' 5DD . B . D 4 -37.915 43.666 4.825 0.3 20.45 ? O5' 5DD 403 A 1 HETATM 6 C C5' 5DD . B . D 4 -37.504 42.399 4.328 0.3 21.96 ? C5' 5DD 403 A 1 HETATM 7 C C4' 5DD . B . D 4 -36.389 41.825 5.197 0.3 22.2 ? C4' 5DD 403 A 1 HETATM 8 O O4' 5DD . B . D 4 -35.224 42.662 5.122 0.3 21.39 ? O4' 5DD 403 A 1 HETATM 9 C C3' 5DD . B . D 4 -36.867 41.692 6.643 0.3 21.7 ? C3' 5DD 403 A 1 HETATM 10 O O3' 5DD . B . D 4 -38.124 41.002 6.625 0.3 18.72 ? O3' 5DD 403 A 1 HETATM 11 C C2' 5DD . B . D 4 -35.859 40.942 7.528 0.3 21.67 ? C2' 5DD 403 A 1 HETATM 12 O O2' 5DD . B . D 4 -36.354 40.772 8.855 0.3 20.34 ? O2' 5DD 403 A 1 HETATM 13 C C1' 5DD . B . D 4 -35.566 39.582 6.918 0.3 21.62 ? C1' 5DD 403 A 1 HETATM 14 N N10 5DD . B . D 4 -35.118 38.62 7.912 0.3 21.51 ? N10 5DD 403 A 1 HETATM 15 C C9A 5DD . B . D 4 -36.048 37.928 8.677 0.3 21.19 ? C9A 5DD 403 A 1 HETATM 16 C C9 5DD . B . D 4 -37.314 38.451 8.912 0.3 21.12 ? C9 5DD 403 A 1 HETATM 17 C C8 5DD . B . D 4 -38.22 37.713 9.663 0.3 21.75 ? C8 5DD 403 A 1 HETATM 18 C C8M 5DD . B . D 4 -39.586 38.25 9.959 0.3 21.77 ? C8M 5DD 403 A 1 HETATM 19 C C7 5DD . B . D 4 -37.847 36.376 10.184 0.3 21.47 ? C7 5DD 403 A 1 HETATM 20 C C7M 5DD . B . D 4 -38.834 35.584 10.993 0.3 21.76 ? C7M 5DD 403 A 1 HETATM 21 C C6 5DD . B . D 4 -36.592 35.857 9.924 0.3 21.13 ? C6 5DD 403 A 1 HETATM 22 C C5A 5DD . B . D 4 -35.677 36.577 9.175 0.3 21.52 ? C5A 5DD 403 A 1 HETATM 23 C C10 5DD . B . D 4 -33.802 38.179 7.888 0.3 21.16 ? C10 5DD 403 A 1 HETATM 24 N N1 5DD . B . D 4 -33.037 38.732 6.928 0.3 19.9 ? N1 5DD 403 A 1 HETATM 25 C C4A 5DD . B . D 4 -33.289 37.119 8.846 0.3 21.66 ? C4A 5DD 403 A 1 HETATM 26 C C4 5DD . B . D 4 -31.919 36.714 8.439 0.3 22.24 ? C4 5DD 403 A 1 HETATM 27 O O4 5DD . B . D 4 -31.379 35.828 9.132 0.3 22.07 ? O4 5DD 403 A 1 HETATM 28 N N3 5DD . B . D 4 -31.229 37.371 7.49 0.3 22.11 ? N3 5DD 403 A 1 HETATM 29 C C2 5DD . B . D 4 -31.773 38.34 6.743 0.3 20.87 ? C2 5DD 403 A 1 HETATM 30 O O2 5DD . B . D 4 -31.106 38.905 5.855 0.3 19.81 ? O2 5DD 403 A 1 HETATM 31 C C1 5DD . B . D 4 -34.305 35.985 8.907 0.3 22.29 ? C1 5DD 403 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #