data_6A3D # _model_server_result.job_id 6pfqleFcsyyAYzxCLjdtIw _model_server_result.datetime_utc '2024-11-08 06:45:37' _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 6a3d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":402}' # _entry.id 6A3D # _exptl.entry_id 6A3D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 548.395 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-deoxy-1-[(4aS)-4a-[(methoxycarbonyl)peroxy]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-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 90 _cell.entry_id 6A3D _cell.length_a 138.546 _cell.length_b 138.546 _cell.length_c 108.501 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6A3D _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C19 H25 N4 O13 P' _chem_comp.formula_weight 548.395 _chem_comp.id 9PX _chem_comp.mon_nstd_flag . _chem_comp.name 1-deoxy-1-[(4aS)-4a-[(methoxycarbonyl)peroxy]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-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 OAM CAL 9PX doub 1 n n OBD CAU 9PX sing 2 n n CAL NAK 9PX sing 3 n n CAL NAN 9PX sing 4 n n NAK CAJ 9PX doub 5 n n OBE CAT 9PX sing 6 n n CAU CAT 9PX sing 7 n n CAU CAV 9PX sing 8 n n NAN CAO 9PX sing 9 n n CAW CAV 9PX sing 10 n n CAW OAX 9PX sing 11 n n CAT CAS 9PX sing 12 n n CAV OBC 9PX sing 13 n n CAS NAI 9PX sing 14 n n OAX PAY 9PX sing 15 n n CAJ NAI 9PX sing 16 n n CAJ CAQ 9PX sing 17 n n CAO CAQ 9PX sing 18 n n CAO OAP 9PX doub 19 n n NAI CAE 9PX sing 20 n n OBJ CAQ 9PX sing 21 n n OBJ OBI 9PX sing 22 n n CAQ NAR 9PX sing 23 n n OBI CBF 9PX sing 24 n n OBA PAY 9PX doub 25 n n PAY OAZ 9PX sing 26 n n PAY OBB 9PX sing 27 n n CAE CAF 9PX doub 28 n y CAE CAD 9PX sing 29 n y NAR CAD 9PX sing 30 n n CBF OBH 9PX doub 31 n n CBF OBG 9PX sing 32 n n CAF CAG 9PX sing 33 n y CAD CAC 9PX doub 34 n y OBG CBK 9PX sing 35 n n CAG CAH 9PX sing 36 n n CAG CAB 9PX doub 37 n y CAC CAB 9PX sing 38 n y CAB CAA 9PX sing 39 n n CAA H1 9PX sing 40 n n CAA H2 9PX sing 41 n n CAA H3 9PX sing 42 n n CAC H4 9PX sing 43 n n CAF H5 9PX sing 44 n n CAH H6 9PX sing 45 n n CAH H7 9PX sing 46 n n CAH H8 9PX sing 47 n n CAS H9 9PX sing 48 n n CAS H10 9PX sing 49 n n CAT H11 9PX sing 50 n n CAU H12 9PX sing 51 n n CAV H13 9PX sing 52 n n CAW H14 9PX sing 53 n n CAW H15 9PX sing 54 n n CBK H16 9PX sing 55 n n CBK H17 9PX sing 56 n n CBK H18 9PX sing 57 n n NAN H19 9PX sing 58 n n NAR H20 9PX sing 59 n n OAZ H21 9PX sing 60 n n OBB H22 9PX sing 61 n n OBC H23 9PX sing 62 n n OBD H24 9PX sing 63 n n OBE H25 9PX sing 64 n n # _atom_sites.entry_id 6A3D _atom_sites.fract_transf_matrix[1][1] 0.007218 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007218 _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] 0.009217 _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 9PX A 1 402 1 9PX DRG . C 3 HOH A 1 501 184 HOH HOH . C 3 HOH A 2 502 177 HOH HOH . C 3 HOH A 3 503 119 HOH HOH . C 3 HOH A 4 504 65 HOH HOH . C 3 HOH A 5 505 138 HOH HOH . C 3 HOH A 6 506 36 HOH HOH . C 3 HOH A 7 507 150 HOH HOH . C 3 HOH A 8 508 87 HOH HOH . C 3 HOH A 9 509 115 HOH HOH . C 3 HOH A 10 510 20 HOH HOH . C 3 HOH A 11 511 84 HOH HOH . C 3 HOH A 12 512 51 HOH HOH . C 3 HOH A 13 513 190 HOH HOH . C 3 HOH A 14 514 131 HOH HOH . C 3 HOH A 15 515 72 HOH HOH . C 3 HOH A 16 516 120 HOH HOH . C 3 HOH A 17 517 8 HOH HOH . C 3 HOH A 18 518 95 HOH HOH . C 3 HOH A 19 519 45 HOH HOH . C 3 HOH A 20 520 128 HOH HOH . C 3 HOH A 21 521 93 HOH HOH . C 3 HOH A 22 522 17 HOH HOH . C 3 HOH A 23 523 103 HOH HOH . C 3 HOH A 24 524 99 HOH HOH . C 3 HOH A 25 525 126 HOH HOH . C 3 HOH A 26 526 78 HOH HOH . C 3 HOH A 27 527 35 HOH HOH . C 3 HOH A 28 528 113 HOH HOH . C 3 HOH A 29 529 16 HOH HOH . C 3 HOH A 30 530 79 HOH HOH . C 3 HOH A 31 531 48 HOH HOH . C 3 HOH A 32 532 11 HOH HOH . C 3 HOH A 33 533 42 HOH HOH . C 3 HOH A 34 534 83 HOH HOH . C 3 HOH A 35 535 5 HOH HOH . C 3 HOH A 36 536 192 HOH HOH . C 3 HOH A 37 537 2 HOH HOH . C 3 HOH A 38 538 165 HOH HOH . C 3 HOH A 39 539 38 HOH HOH . C 3 HOH A 40 540 180 HOH HOH . C 3 HOH A 41 541 68 HOH HOH . C 3 HOH A 42 542 26 HOH HOH . C 3 HOH A 43 543 34 HOH HOH . C 3 HOH A 44 544 62 HOH HOH . C 3 HOH A 45 545 96 HOH HOH . C 3 HOH A 46 546 40 HOH HOH . C 3 HOH A 47 547 29 HOH HOH . C 3 HOH A 48 548 114 HOH HOH . C 3 HOH A 49 549 188 HOH HOH . C 3 HOH A 50 550 121 HOH HOH . C 3 HOH A 51 551 28 HOH HOH . C 3 HOH A 52 552 4 HOH HOH . C 3 HOH A 53 553 100 HOH HOH . C 3 HOH A 54 554 32 HOH HOH . C 3 HOH A 55 555 47 HOH HOH . C 3 HOH A 56 556 74 HOH HOH . C 3 HOH A 57 557 12 HOH HOH . C 3 HOH A 58 558 179 HOH HOH . C 3 HOH A 59 559 14 HOH HOH . C 3 HOH A 60 560 90 HOH HOH . C 3 HOH A 61 561 127 HOH HOH . C 3 HOH A 62 562 75 HOH HOH . C 3 HOH A 63 563 89 HOH HOH . C 3 HOH A 64 564 135 HOH HOH . C 3 HOH A 65 565 98 HOH HOH . C 3 HOH A 66 566 129 HOH HOH . C 3 HOH A 67 567 64 HOH HOH . C 3 HOH A 68 568 22 HOH HOH . C 3 HOH A 69 569 30 HOH HOH . C 3 HOH A 70 570 159 HOH HOH . C 3 HOH A 71 571 134 HOH HOH . C 3 HOH A 72 572 23 HOH HOH . C 3 HOH A 73 573 7 HOH HOH . C 3 HOH A 74 574 108 HOH HOH . C 3 HOH A 75 575 185 HOH HOH . C 3 HOH A 76 576 164 HOH HOH . C 3 HOH A 77 577 106 HOH HOH . C 3 HOH A 78 578 31 HOH HOH . C 3 HOH A 79 579 21 HOH HOH . C 3 HOH A 80 580 56 HOH HOH . C 3 HOH A 81 581 148 HOH HOH . C 3 HOH A 82 582 97 HOH HOH . C 3 HOH A 83 583 81 HOH HOH . C 3 HOH A 84 584 24 HOH HOH . C 3 HOH A 85 585 147 HOH HOH . C 3 HOH A 86 586 27 HOH HOH . C 3 HOH A 87 587 204 HOH HOH . C 3 HOH A 88 588 130 HOH HOH . C 3 HOH A 89 589 116 HOH HOH . C 3 HOH A 90 590 91 HOH HOH . C 3 HOH A 91 591 132 HOH HOH . C 3 HOH A 92 592 25 HOH HOH . C 3 HOH A 93 593 19 HOH HOH . C 3 HOH A 94 594 69 HOH HOH . C 3 HOH A 95 595 193 HOH HOH . C 3 HOH A 96 596 6 HOH HOH . C 3 HOH A 97 597 107 HOH HOH . C 3 HOH A 98 598 160 HOH HOH . C 3 HOH A 99 599 10 HOH HOH . C 3 HOH A 100 600 80 HOH HOH . C 3 HOH A 101 601 67 HOH HOH . C 3 HOH A 102 602 143 HOH HOH . C 3 HOH A 103 603 194 HOH HOH . C 3 HOH A 104 604 41 HOH HOH . C 3 HOH A 105 605 82 HOH HOH . C 3 HOH A 106 606 123 HOH HOH . C 3 HOH A 107 607 13 HOH HOH . C 3 HOH A 108 608 66 HOH HOH . C 3 HOH A 109 609 9 HOH HOH . C 3 HOH A 110 610 86 HOH HOH . C 3 HOH A 111 611 109 HOH HOH . C 3 HOH A 112 612 3 HOH HOH . C 3 HOH A 113 613 170 HOH HOH . C 3 HOH A 114 614 49 HOH HOH . C 3 HOH A 115 615 52 HOH HOH . C 3 HOH A 116 616 144 HOH HOH . C 3 HOH A 117 617 178 HOH HOH . C 3 HOH A 118 618 200 HOH HOH . C 3 HOH A 119 619 158 HOH HOH . C 3 HOH A 120 620 145 HOH HOH . C 3 HOH A 121 621 53 HOH HOH . C 3 HOH A 122 622 146 HOH HOH . C 3 HOH A 123 623 118 HOH HOH . C 3 HOH A 124 624 152 HOH HOH . C 3 HOH A 125 625 18 HOH HOH . C 3 HOH A 126 626 162 HOH HOH . C 3 HOH A 127 627 59 HOH HOH . C 3 HOH A 128 628 88 HOH HOH . C 3 HOH A 129 629 136 HOH HOH . C 3 HOH A 130 630 44 HOH HOH . C 3 HOH A 131 631 33 HOH HOH . C 3 HOH A 132 632 61 HOH HOH . C 3 HOH A 133 633 58 HOH HOH . C 3 HOH A 134 634 163 HOH HOH . C 3 HOH A 135 635 198 HOH HOH . C 3 HOH A 136 636 15 HOH HOH . C 3 HOH A 137 637 117 HOH HOH . C 3 HOH A 138 638 133 HOH HOH . C 3 HOH A 139 639 205 HOH HOH . C 3 HOH A 140 640 54 HOH HOH . C 3 HOH A 141 641 174 HOH HOH . C 3 HOH A 142 642 156 HOH HOH . C 3 HOH A 143 643 71 HOH HOH . C 3 HOH A 144 644 141 HOH HOH . C 3 HOH A 145 645 189 HOH HOH . C 3 HOH A 146 646 105 HOH HOH . C 3 HOH A 147 647 39 HOH HOH . C 3 HOH A 148 648 76 HOH HOH . C 3 HOH A 149 649 155 HOH HOH . C 3 HOH A 150 650 175 HOH HOH . C 3 HOH A 151 651 173 HOH HOH . C 3 HOH A 152 652 169 HOH HOH . C 3 HOH A 153 653 124 HOH HOH . C 3 HOH A 154 654 197 HOH HOH . C 3 HOH A 155 655 92 HOH HOH . C 3 HOH A 156 656 186 HOH HOH . C 3 HOH A 157 657 55 HOH HOH . C 3 HOH A 158 658 202 HOH HOH . C 3 HOH A 159 659 43 HOH HOH . C 3 HOH A 160 660 94 HOH HOH . C 3 HOH A 161 661 181 HOH HOH . C 3 HOH A 162 662 77 HOH HOH . C 3 HOH A 163 663 153 HOH HOH . C 3 HOH A 164 664 102 HOH HOH . C 3 HOH A 165 665 73 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 CAA 9PX . . . B 2 28.056 -8.861 29.561 1 37.57 ? CAA 9PX 402 A 1 HETATM 2 C CAB 9PX . . . B 2 28.092 -8.887 28.163 1 37.57 ? CAB 9PX 402 A 1 HETATM 3 C CAC 9PX . . . B 2 29.318 -8.869 27.507 1 33.81 ? CAC 9PX 402 A 1 HETATM 4 C CAD 9PX . . . B 2 29.362 -8.898 26.115 1 38.14 ? CAD 9PX 402 A 1 HETATM 5 C CAE 9PX . . . B 2 28.183 -8.9 25.354 1 27.8 ? CAE 9PX 402 A 1 HETATM 6 C CAF 9PX . . . B 2 26.968 -8.954 26.025 1 29.91 ? CAF 9PX 402 A 1 HETATM 7 C CAG 9PX . . . B 2 26.918 -8.932 27.416 1 28.41 ? CAG 9PX 402 A 1 HETATM 8 C CAH 9PX . . . B 2 25.677 -8.94 28.042 1 41.28 ? CAH 9PX 402 A 1 HETATM 9 C CAJ 9PX . . . B 2 29.417 -8.98 23.38 1 33.66 ? CAJ 9PX 402 A 1 HETATM 10 C CAL 9PX . . . B 2 30.662 -9.049 21.412 1 37.96 ? CAL 9PX 402 A 1 HETATM 11 C CAO 9PX . . . B 2 31.661 -8.842 23.582 1 40.94 ? CAO 9PX 402 A 1 HETATM 12 C CAQ 9PX . . . B 2 30.409 -8.58 24.151 1 44.59 ? CAQ 9PX 402 A 1 HETATM 13 C CAS 9PX . . . B 2 26.967 -9.087 23.195 1 19.82 ? CAS 9PX 402 A 1 HETATM 14 C CAT 9PX . . . B 2 26.602 -10.54 22.913 1 15.55 ? CAT 9PX 402 A 1 HETATM 15 C CAU 9PX . . . B 2 25.243 -10.638 22.191 1 19.61 ? CAU 9PX 402 A 1 HETATM 16 C CAV 9PX . . . B 2 24.09 -10.229 23.069 1 29.44 ? CAV 9PX 402 A 1 HETATM 17 C CAW 9PX . . . B 2 22.96 -11.154 22.625 1 23.65 ? CAW 9PX 402 A 1 HETATM 18 C CBF 9PX . . . B 2 31.802 -5.892 25.517 1 67.43 ? CBF 9PX 402 A 1 HETATM 19 C CBK 9PX . . . B 2 30.984 -5.287 27.538 1 39.47 ? CBK 9PX 402 A 1 HETATM 20 N NAI 9PX . . . B 2 28.222 -8.965 23.997 1 30.62 ? NAI 9PX 402 A 1 HETATM 21 N NAK 9PX . . . B 2 29.483 -9.075 22.04 1 26.95 ? NAK 9PX 402 A 1 HETATM 22 N NAN 9PX . . . B 2 31.808 -8.945 22.193 1 37.09 ? NAN 9PX 402 A 1 HETATM 23 N NAR 9PX . . . B 2 30.544 -8.895 25.485 1 26.59 ? NAR 9PX 402 A 1 HETATM 24 O OAM 9PX . . . B 2 30.739 -9.166 20.185 1 34.37 ? OAM 9PX 402 A 1 HETATM 25 O OAP 9PX . . . B 2 32.682 -8.706 24.263 1 45.19 ? OAP 9PX 402 A 1 HETATM 26 O OAX 9PX . . . B 2 21.799 -10.719 23.263 1 25.49 ? OAX 9PX 402 A 1 HETATM 27 O OAZ 9PX . . . B 2 19.886 -10.921 24.806 1 21.25 ? OAZ 9PX 402 A 1 HETATM 28 O OBA 9PX . . . B 2 21.135 -13.042 24.287 1 17.11 ? OBA 9PX 402 A 1 HETATM 29 O OBB 9PX . . . B 2 22.285 -11.319 25.766 1 23.6 ? OBB 9PX 402 A 1 HETATM 30 O OBC 9PX . . . B 2 24.375 -10.428 24.458 1 29.32 ? OBC 9PX 402 A 1 HETATM 31 O OBD 9PX . . . B 2 25.165 -9.801 21.029 1 20 ? OBD 9PX 402 A 1 HETATM 32 O OBE 9PX . . . B 2 27.598 -11.107 22.063 1 15.41 ? OBE 9PX 402 A 1 HETATM 33 O OBG 9PX . . . B 2 30.646 -5.747 26.225 1 66.25 ? OBG 9PX 402 A 1 HETATM 34 O OBH 9PX . . . B 2 32.907 -5.639 26 1 58.67 ? OBH 9PX 402 A 1 HETATM 35 O OBI 9PX . . . B 2 31.641 -6.315 24.224 1 51.08 ? OBI 9PX 402 A 1 HETATM 36 O OBJ 9PX . . . B 2 30.451 -7.194 24.019 1 61.99 ? OBJ 9PX 402 A 1 HETATM 37 P PAY 9PX . . . B 2 21.228 -11.473 24.55 1 21.99 ? PAY 9PX 402 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 37 #