data_6I24 # _model_server_result.job_id w6Ku1GE2OZ3MIQEAYqiIvw _model_server_result.datetime_utc '2024-11-13 10:54:03' _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 6i24 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":419}' # _entry.id 6I24 # _exptl.entry_id 6I24 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 455.356 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol _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 6I24 _cell.length_a 106.314 _cell.length_b 106.314 _cell.length_c 67.541 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6I24 _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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _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 8 _struct_asym.id T _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 S C4A 5DD . A 5DD 418 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.804 ? covale ? covale2 E C2 EDO . A EDO 404 1_555 F C2 EDO . A EDO 405 12_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.189 ? covale ? covale3 E O2 EDO . A EDO 404 1_555 F C1 EDO . A EDO 405 12_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.364 ? metalc ? metalc1 A O SER 46 A SER 223 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc2 A O SER 46 A SER 223 1_555 D MG MG . A MG 403 11_656 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc3 A O LEU 49 A LEU 226 1_555 D MG MG . A MG 403 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc4 A O LEU 49 A LEU 226 1_555 D MG MG . A MG 403 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc5 A O LEU 49 A LEU 226 1_555 D MG MG . A MG 403 11_656 ? A ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc6 A O LEU 49 A LEU 226 1_555 D MG MG . A MG 403 11_656 ? B ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc7 D MG MG . A MG 403 1_555 U O HOH . A HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc8 D MG MG . A MG 403 1_555 U O HOH . A HOH 546 11_656 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? # _chem_comp.formula 'C18 H22 N3 O9 P' _chem_comp.formula_weight 455.356 _chem_comp.id 9O9 _chem_comp.mon_nstd_flag . _chem_comp.name 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol _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 O2 C2 9O9 doub 58 n n OBA CAU 9O9 sing 59 n n C2 N1 9O9 sing 60 n n C2 N3 9O9 sing 61 n n N1 C6 9O9 doub 62 n n N3 C4 9O9 sing 63 n n OAY CAT 9O9 sing 64 n n CAU CAT 9O9 sing 65 n n CAU CAV 9O9 sing 66 n n CAW CAV 9O9 sing 67 n n CAW OAX 9O9 sing 68 n n CAT CAS 9O9 sing 69 n n CAS NAG 9O9 sing 70 n n CAV OAZ 9O9 sing 71 n n OAX PBB 9O9 sing 72 n n C6 NAG 9O9 sing 73 n n C6 C5 9O9 sing 74 n n C4 O4 9O9 doub 75 n n C4 C5 9O9 sing 76 n n NAG CAD 9O9 sing 77 n n C5 CAJ 9O9 doub 78 n n OBE PBB 9O9 doub 79 n n PBB OBD 9O9 sing 80 n n PBB OBC 9O9 sing 81 n n CAD CAC 9O9 doub 82 n y CAD CAE 9O9 sing 83 n y CAJ CAE 9O9 sing 84 n n CAC CAB 9O9 sing 85 n y CAE CAF 9O9 doub 86 n y CAB CAP 9O9 sing 87 n n CAB CAA 9O9 doub 88 n y CAF CAA 9O9 sing 89 n y CAA CAO 9O9 sing 90 n n N3 H2 9O9 sing 91 n n CAC H3 9O9 sing 92 n n CAF H4 9O9 sing 93 n n CAJ H5 9O9 sing 94 n n CAO H6 9O9 sing 95 n n CAO H7 9O9 sing 96 n n CAO H8 9O9 sing 97 n n CAP H9 9O9 sing 98 n n CAP H10 9O9 sing 99 n n CAP H11 9O9 sing 100 n n CAS H12 9O9 sing 101 n n CAS H13 9O9 sing 102 n n CAT H14 9O9 sing 103 n n CAU H15 9O9 sing 104 n n CAV H16 9O9 sing 105 n n CAW H17 9O9 sing 106 n n CAW H18 9O9 sing 107 n n OAY H19 9O9 sing 108 n n OAZ H20 9O9 sing 109 n n OBA H21 9O9 sing 110 n n OBC H22 9O9 sing 111 n n OBD H23 9O9 sing 112 n n # _atom_sites.entry_id 6I24 _atom_sites.fract_transf_matrix[1][1] 0.009406 _atom_sites.fract_transf_matrix[1][2] 0.005431 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010861 _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] 0.014806 _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 ACT A 1 401 315 ACT ACT . C 3 CL A 1 402 317 CL CL . D 4 MG A 1 403 319 MG MG . E 5 EDO A 1 404 321 EDO EDO . F 5 EDO A 1 405 322 EDO EDO . G 5 EDO A 1 406 323 EDO EDO . H 5 EDO A 1 407 324 EDO EDO . I 5 EDO A 1 408 325 EDO EDO . J 5 EDO A 1 409 326 EDO EDO . K 5 EDO A 1 410 327 EDO EDO . L 5 EDO A 1 411 328 EDO EDO . M 5 EDO A 1 412 329 EDO EDO . N 5 EDO A 1 413 330 EDO EDO . O 5 EDO A 1 414 331 EDO EDO . P 5 EDO A 1 415 332 EDO EDO . Q 5 EDO A 1 416 333 EDO EDO . R 6 PEG A 1 417 341 PEG PEG . S 7 5DD A 1 418 351 5DD 5DD . T 8 9O9 A 1 419 353 9O9 5DF . U 9 HOH A 1 501 525 HOH HOH . U 9 HOH A 2 502 425 HOH HOH . U 9 HOH A 3 503 453 HOH HOH . U 9 HOH A 4 504 452 HOH HOH . U 9 HOH A 5 505 430 HOH HOH . U 9 HOH A 6 506 461 HOH HOH . U 9 HOH A 7 507 483 HOH HOH . U 9 HOH A 8 508 531 HOH HOH . U 9 HOH A 9 509 517 HOH HOH . U 9 HOH A 10 510 422 HOH HOH . U 9 HOH A 11 511 515 HOH HOH . U 9 HOH A 12 512 433 HOH HOH . U 9 HOH A 13 513 507 HOH HOH . U 9 HOH A 14 514 486 HOH HOH . U 9 HOH A 15 515 449 HOH HOH . U 9 HOH A 16 516 487 HOH HOH . U 9 HOH A 17 517 479 HOH HOH . U 9 HOH A 18 518 489 HOH HOH . U 9 HOH A 19 519 518 HOH HOH . U 9 HOH A 20 520 491 HOH HOH . U 9 HOH A 21 521 466 HOH HOH . U 9 HOH A 22 522 472 HOH HOH . U 9 HOH A 23 523 436 HOH HOH . U 9 HOH A 24 524 500 HOH HOH . U 9 HOH A 25 525 508 HOH HOH . U 9 HOH A 26 526 497 HOH HOH . U 9 HOH A 27 527 413 HOH HOH . U 9 HOH A 28 528 460 HOH HOH . U 9 HOH A 29 529 424 HOH HOH . U 9 HOH A 30 530 434 HOH HOH . U 9 HOH A 31 531 458 HOH HOH . U 9 HOH A 32 532 509 HOH HOH . U 9 HOH A 33 533 527 HOH HOH . U 9 HOH A 34 534 406 HOH HOH . U 9 HOH A 35 535 417 HOH HOH . U 9 HOH A 36 536 403 HOH HOH . U 9 HOH A 37 537 488 HOH HOH . U 9 HOH A 38 538 427 HOH HOH . U 9 HOH A 39 539 519 HOH HOH . U 9 HOH A 40 540 426 HOH HOH . U 9 HOH A 41 541 468 HOH HOH . U 9 HOH A 42 542 504 HOH HOH . U 9 HOH A 43 543 505 HOH HOH . U 9 HOH A 44 544 514 HOH HOH . U 9 HOH A 45 545 494 HOH HOH . U 9 HOH A 46 546 404 HOH HOH . U 9 HOH A 47 547 533 HOH HOH . U 9 HOH A 48 548 502 HOH HOH . U 9 HOH A 49 549 465 HOH HOH . U 9 HOH A 50 550 411 HOH HOH . U 9 HOH A 51 551 415 HOH HOH . U 9 HOH A 52 552 478 HOH HOH . U 9 HOH A 53 553 405 HOH HOH . U 9 HOH A 54 554 490 HOH HOH . U 9 HOH A 55 555 469 HOH HOH . U 9 HOH A 56 556 485 HOH HOH . U 9 HOH A 57 557 441 HOH HOH . U 9 HOH A 58 558 414 HOH HOH . U 9 HOH A 59 559 522 HOH HOH . U 9 HOH A 60 560 475 HOH HOH . U 9 HOH A 61 561 496 HOH HOH . U 9 HOH A 62 562 409 HOH HOH . U 9 HOH A 63 563 446 HOH HOH . U 9 HOH A 64 564 416 HOH HOH . U 9 HOH A 65 565 438 HOH HOH . U 9 HOH A 66 566 477 HOH HOH . U 9 HOH A 67 567 410 HOH HOH . U 9 HOH A 68 568 442 HOH HOH . U 9 HOH A 69 569 445 HOH HOH . U 9 HOH A 70 570 463 HOH HOH . U 9 HOH A 71 571 435 HOH HOH . U 9 HOH A 72 572 462 HOH HOH . U 9 HOH A 73 573 412 HOH HOH . U 9 HOH A 74 574 464 HOH HOH . U 9 HOH A 75 575 484 HOH HOH . U 9 HOH A 76 576 428 HOH HOH . U 9 HOH A 77 577 451 HOH HOH . U 9 HOH A 78 578 473 HOH HOH . U 9 HOH A 79 579 439 HOH HOH . U 9 HOH A 80 580 418 HOH HOH . U 9 HOH A 81 581 429 HOH HOH . U 9 HOH A 82 582 437 HOH HOH . U 9 HOH A 83 583 506 HOH HOH . U 9 HOH A 84 584 493 HOH HOH . U 9 HOH A 85 585 419 HOH HOH . U 9 HOH A 86 586 402 HOH HOH . U 9 HOH A 87 587 467 HOH HOH . U 9 HOH A 88 588 407 HOH HOH . U 9 HOH A 89 589 480 HOH HOH . U 9 HOH A 90 590 498 HOH HOH . U 9 HOH A 91 591 482 HOH HOH . U 9 HOH A 92 592 444 HOH HOH . U 9 HOH A 93 593 423 HOH HOH . U 9 HOH A 94 594 476 HOH HOH . U 9 HOH A 95 595 456 HOH HOH . U 9 HOH A 96 596 523 HOH HOH . U 9 HOH A 97 597 408 HOH HOH . U 9 HOH A 98 598 499 HOH HOH . U 9 HOH A 99 599 447 HOH HOH . U 9 HOH A 100 600 448 HOH HOH . U 9 HOH A 101 601 516 HOH HOH . U 9 HOH A 102 602 420 HOH HOH . U 9 HOH A 103 603 450 HOH HOH . U 9 HOH A 104 604 455 HOH HOH . U 9 HOH A 105 605 492 HOH HOH . U 9 HOH A 106 606 443 HOH HOH . U 9 HOH A 107 607 431 HOH HOH . U 9 HOH A 108 608 501 HOH HOH . U 9 HOH A 109 609 526 HOH HOH . U 9 HOH A 110 610 512 HOH HOH . U 9 HOH A 111 611 521 HOH HOH . U 9 HOH A 112 612 532 HOH HOH . U 9 HOH A 113 613 471 HOH HOH . U 9 HOH A 114 614 459 HOH HOH . U 9 HOH A 115 615 530 HOH HOH . U 9 HOH A 116 616 503 HOH HOH . U 9 HOH A 117 617 481 HOH HOH . U 9 HOH A 118 618 495 HOH HOH . U 9 HOH A 119 619 474 HOH HOH . U 9 HOH A 120 620 528 HOH HOH . U 9 HOH A 121 621 520 HOH HOH . U 9 HOH A 122 622 457 HOH HOH . U 9 HOH A 123 623 440 HOH HOH . U 9 HOH A 124 624 510 HOH HOH . U 9 HOH A 125 625 470 HOH HOH . U 9 HOH A 126 626 513 HOH HOH . U 9 HOH A 127 627 529 HOH HOH . U 9 HOH A 128 628 401 HOH HOH . U 9 HOH A 129 629 454 HOH HOH . U 9 HOH A 130 630 534 HOH HOH . U 9 HOH A 131 631 421 HOH HOH . U 9 HOH A 132 632 511 HOH HOH . U 9 HOH A 133 633 432 HOH HOH . U 9 HOH A 134 634 524 HOH HOH . U 9 HOH A 135 635 535 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 C C4 9O9 . A . T 8 47.576 9.79 18.907 0.7 14.61 ? C4 9O9 419 A 1 HETATM 2 C C5 9O9 . A . T 8 48.637 10.785 19.167 0.7 15.61 ? C5 9O9 419 A 1 HETATM 3 C C6 9O9 . A . T 8 49.927 10.64 18.462 0.7 15.76 ? C6 9O9 419 A 1 HETATM 4 N N1 9O9 . A . T 8 50.109 9.582 17.621 0.7 16.2 ? N1 9O9 419 A 1 HETATM 5 N N3 9O9 . A . T 8 47.902 8.796 18.045 0.7 15.28 ? N3 9O9 419 A 1 HETATM 6 C C2 9O9 . A . T 8 49.09 8.723 17.432 0.7 16.2 ? C2 9O9 419 A 1 HETATM 7 C CAA 9O9 . A . T 8 50.263 14.785 21.347 0.7 14.43 ? CAA 9O9 419 A 1 HETATM 8 C CAB 9O9 . A . T 8 51.561 14.671 20.666 0.7 14.12 ? CAB 9O9 419 A 1 HETATM 9 C CAC 9O9 . A . T 8 51.752 13.602 19.785 0.7 14.45 ? CAC 9O9 419 A 1 HETATM 10 C CAD 9O9 . A . T 8 50.751 12.671 19.56 0.7 14.41 ? CAD 9O9 419 A 1 HETATM 11 C CAE 9O9 . A . T 8 49.457 12.784 20.246 0.7 14.51 ? CAE 9O9 419 A 1 HETATM 12 C CAF 9O9 . A . T 8 49.256 13.852 21.13 0.7 14.28 ? CAF 9O9 419 A 1 HETATM 13 C CAJ 9O9 . A . T 8 48.443 11.867 20.042 0.7 15.67 ? CAJ 9O9 419 A 1 HETATM 14 C CAO 9O9 . A . T 8 50.011 15.929 22.313 0.7 14.5 ? CAO 9O9 419 A 1 HETATM 15 C CAP 9O9 . A . T 8 52.688 15.64 20.829 0.7 14.28 ? CAP 9O9 419 A 1 HETATM 16 C CAS 9O9 . A . T 8 52.178 11.408 17.88 0.7 15.25 ? CAS 9O9 419 A 1 HETATM 17 C CAT 9O9 . A . T 8 53.409 10.724 18.434 0.7 15.32 ? CAT 9O9 419 A 1 HETATM 18 C CAU 9O9 . A . T 8 54.677 11.172 17.683 0.7 16.23 ? CAU 9O9 419 A 1 HETATM 19 C CAV 9O9 . A . T 8 54.65 10.822 16.186 0.7 16.63 ? CAV 9O9 419 A 1 HETATM 20 C CAW 9O9 . A . T 8 55.838 11.39 15.403 0.7 17.17 ? CAW 9O9 419 A 1 HETATM 21 N NAG 9O9 . A . T 8 50.954 11.553 18.666 0.7 15.49 ? NAG 9O9 419 A 1 HETATM 22 O O2 9O9 . A . T 8 49.316 7.762 16.638 0.7 17.78 ? O2 9O9 419 A 1 HETATM 23 O O4 9O9 . A . T 8 46.468 9.813 19.452 0.7 14.71 ? O4 9O9 419 A 1 HETATM 24 O OAX 9O9 . A . T 8 57.088 11.247 16.077 0.7 17.8 ? OAX 9O9 419 A 1 HETATM 25 O OAY 9O9 . A . T 8 53.573 10.998 19.83 0.7 15.05 ? OAY 9O9 419 A 1 HETATM 26 O OAZ 9O9 . A . T 8 54.607 9.399 16.093 0.7 16.8 ? OAZ 9O9 419 A 1 HETATM 27 O OBA 9O9 . A . T 8 54.868 12.587 17.816 0.7 15.98 ? OBA 9O9 419 A 1 HETATM 28 O OBC 9O9 . A . T 8 57.154 8.71 16.057 0.7 20.07 ? OBC 9O9 419 A 1 HETATM 29 O OBD 9O9 . A . T 8 59.172 10.02 16.784 0.7 19 ? OBD 9O9 419 A 1 HETATM 30 O OBE 9O9 . A . T 8 58.399 10.038 14.373 0.7 18.94 ? OBE 9O9 419 A 1 HETATM 31 P PBB 9O9 . A . T 8 57.999 9.933 15.861 0.7 19.32 ? PBB 9O9 419 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #