data_6I25 # _model_server_result.job_id fB2yhQhJO1JwEp3Nz2zbSQ _model_server_result.datetime_utc '2024-11-06 14:23:22' _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":"E","auth_seq_id":404}' # _entry.id 6I25 # _exptl.entry_id 6I25 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 455.356 _entity.id 5 _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 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 5 _struct_asym.id E _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 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 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 C C4 9O9 . A . E 5 -32.367 36.457 7.612 0.7 17.62 ? C4 9O9 404 A 1 HETATM 2 C C5 9O9 . A . E 5 -33.768 36.862 7.914 0.7 16.86 ? C5 9O9 404 A 1 HETATM 3 C C6 9O9 . A . E 5 -34.272 38.079 7.239 0.7 17.89 ? C6 9O9 404 A 1 HETATM 4 N N1 9O9 . A . E 5 -33.45 38.756 6.399 0.7 16.81 ? N1 9O9 404 A 1 HETATM 5 N N3 9O9 . A . E 5 -31.664 37.23 6.748 0.7 17.2 ? N3 9O9 404 A 1 HETATM 6 C C2 9O9 . A . E 5 -32.195 38.348 6.172 0.7 17.49 ? C2 9O9 404 A 1 HETATM 7 C CAA 9O9 . A . E 5 -37.977 36.243 10.181 0.7 18.27 ? CAA 9O9 404 A 1 HETATM 8 C CAB 9O9 . A . E 5 -38.532 37.452 9.515 0.7 18.52 ? CAB 9O9 404 A 1 HETATM 9 C CAC 9O9 . A . E 5 -37.746 38.19 8.633 0.7 17.59 ? CAC 9O9 404 A 1 HETATM 10 C CAD 9O9 . A . E 5 -36.432 37.798 8.353 0.7 16.91 ? CAD 9O9 404 A 1 HETATM 11 C CAE 9O9 . A . E 5 -35.891 36.587 9.025 0.7 16.87 ? CAE 9O9 404 A 1 HETATM 12 C CAF 9O9 . A . E 5 -36.678 35.863 9.911 0.7 16.89 ? CAF 9O9 404 A 1 HETATM 13 C CAJ 9O9 . A . E 5 -34.595 36.15 8.775 0.7 17.96 ? CAJ 9O9 404 A 1 HETATM 14 C CAO 9O9 . A . E 5 -38.811 35.44 11.131 0.7 18.88 ? CAO 9O9 404 A 1 HETATM 15 C CAP 9O9 . A . E 5 -39.927 37.887 9.799 0.7 18.66 ? CAP 9O9 404 A 1 HETATM 16 C CAS 9O9 . A . E 5 -36.052 39.679 6.731 0.7 19.04 ? CAS 9O9 404 A 1 HETATM 17 C CAT 9O9 . A . E 5 -36.02 41.071 7.338 0.7 19.81 ? CAT 9O9 404 A 1 HETATM 18 C CAU 9O9 . A . E 5 -37.037 41.95 6.559 0.7 20.62 ? CAU 9O9 404 A 1 HETATM 19 C CAV 9O9 . A . E 5 -36.666 42.098 5.066 0.7 20.93 ? CAV 9O9 404 A 1 HETATM 20 C CAW 9O9 . A . E 5 -37.704 42.861 4.243 0.7 21.15 ? CAW 9O9 404 A 1 HETATM 21 N NAG 9O9 . A . E 5 -35.579 38.524 7.477 0.7 17.56 ? NAG 9O9 404 A 1 HETATM 22 O O2 9O9 . A . E 5 -31.548 39.06 5.379 0.7 17.74 ? O2 9O9 404 A 1 HETATM 23 O O4 9O9 . A . E 5 -31.871 35.444 8.179 0.7 14.8 ? O4 9O9 404 A 1 HETATM 24 O OAX 9O9 . A . E 5 -38.167 44.007 4.949 0.7 20.08 ? OAX 9O9 404 A 1 HETATM 25 O OAY 9O9 . A . E 5 -36.232 40.995 8.748 0.7 16.3 ? OAY 9O9 404 A 1 HETATM 26 O OAZ 9O9 . A . E 5 -35.389 42.75 4.945 0.7 20.4 ? OAZ 9O9 404 A 1 HETATM 27 O OBA 9O9 . A . E 5 -38.367 41.403 6.64 0.7 14.53 ? OBA 9O9 404 A 1 HETATM 28 O OBC 9O9 . A . E 5 -37.736 45.884 3.343 0.7 19.78 ? OBC 9O9 404 A 1 HETATM 29 O OBD 9O9 . A . E 5 -35.971 45.397 5.035 0.7 21.8 ? OBD 9O9 404 A 1 HETATM 30 O OBE 9O9 . A . E 5 -38.098 46.381 5.746 0.7 19.45 ? OBE 9O9 404 A 1 HETATM 31 P PBB 9O9 . A . E 5 -37.476 45.457 4.777 0.7 20.38 ? PBB 9O9 404 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #