data_5OM3 # _model_server_result.job_id adqjHUKiyT-V4WLZpWRECg _model_server_result.datetime_utc '2024-11-05 06:58:20' _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 5om3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 5OM3 # _exptl.entry_id 5OM3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 444.435 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE _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 5OM3 _cell.length_a 84.321 _cell.length_b 84.321 _cell.length_c 98.156 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OM3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _chem_comp.formula 'C22 H24 N2 O8' _chem_comp.formula_weight 444.435 _chem_comp.id DXT _chem_comp.mon_nstd_flag . _chem_comp.name (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DOXYTETRACYCLINE;DOXYCYCLINE # 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 C1 C4B DXT sing 83 n n C1 O1 DXT doub 84 n n C1 C2 DXT sing 85 n n C2 C21 DXT sing 86 n n C2 C3 DXT doub 87 n n O21 C21 DXT doub 88 n n C21 N21 DXT sing 89 n n N21 H211 DXT sing 90 n n N21 H212 DXT sing 91 n n C3 O3 DXT sing 92 n n C3 C4 DXT sing 93 n n O3 HO3 DXT sing 94 n n C4 H4 DXT sing 95 n n C4 N4 DXT sing 96 n n C4 C4A DXT sing 97 n n N4 C41 DXT sing 98 n n N4 C42 DXT sing 99 n n C41 H411 DXT sing 100 n n C41 H412 DXT sing 101 n n C41 H413 DXT sing 102 n n C42 H421 DXT sing 103 n n C42 H422 DXT sing 104 n n C42 H423 DXT sing 105 n n C4A C4B DXT sing 106 n n C4A H4A DXT sing 107 n n C4A C5 DXT sing 108 n n C5 H5 DXT sing 109 n n C5 O5 DXT sing 110 n n C5 C5A DXT sing 111 n n O5 HO5 DXT sing 112 n n C5A C5B DXT sing 113 n n C5A H5A DXT sing 114 n n C5A C6 DXT sing 115 n n C6 H6 DXT sing 116 n n C6 C6A DXT sing 117 n n C6 C61 DXT sing 118 n n C61 H611 DXT sing 119 n n C61 H612 DXT sing 120 n n C61 H613 DXT sing 121 n n C6A C6B DXT sing 122 n y C6A C7 DXT doub 123 n y C7 H7 DXT sing 124 n n C7 C8 DXT sing 125 n y C8 H8 DXT sing 126 n n C8 C9 DXT doub 127 n y C9 C10 DXT sing 128 n y C9 H9 DXT sing 129 n n C10 O10 DXT sing 130 n n C10 C6B DXT doub 131 n y O10 H10 DXT sing 132 n n C6B C11 DXT sing 133 n n C11 O11 DXT doub 134 n n C11 C5B DXT sing 135 n n C5B C12 DXT doub 136 n n C12 O12 DXT sing 137 n n C12 C4B DXT sing 138 n n O12 H12 DXT sing 139 n n C4B O13 DXT sing 140 n n O13 H13 DXT sing 141 n n # _atom_sites.entry_id 5OM3 _atom_sites.fract_transf_matrix[1][1] 0.011859 _atom_sites.fract_transf_matrix[1][2] 0.006847 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013694 _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] 0.010188 _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 C 3 PEG A 1 401 1 PEG PEG . D 4 DXT B 1 501 1 DXT DXT . E 5 HOH A 1 601 164 HOH HOH . E 5 HOH A 2 602 106 HOH HOH . E 5 HOH A 3 603 82 HOH HOH . E 5 HOH A 4 604 190 HOH HOH . E 5 HOH A 5 605 51 HOH HOH . E 5 HOH A 6 606 60 HOH HOH . E 5 HOH A 7 607 135 HOH HOH . E 5 HOH A 8 608 25 HOH HOH . E 5 HOH A 9 609 49 HOH HOH . E 5 HOH A 10 610 88 HOH HOH . E 5 HOH A 11 611 192 HOH HOH . E 5 HOH A 12 612 80 HOH HOH . E 5 HOH A 13 613 110 HOH HOH . E 5 HOH A 14 614 64 HOH HOH . E 5 HOH A 15 615 145 HOH HOH . E 5 HOH A 16 616 45 HOH HOH . E 5 HOH A 17 617 91 HOH HOH . E 5 HOH A 18 618 79 HOH HOH . E 5 HOH A 19 619 166 HOH HOH . E 5 HOH A 20 620 59 HOH HOH . E 5 HOH A 21 621 85 HOH HOH . E 5 HOH A 22 622 121 HOH HOH . E 5 HOH A 23 623 71 HOH HOH . E 5 HOH A 24 624 125 HOH HOH . E 5 HOH A 25 625 55 HOH HOH . E 5 HOH A 26 626 70 HOH HOH . E 5 HOH A 27 627 92 HOH HOH . E 5 HOH A 28 628 151 HOH HOH . E 5 HOH A 29 629 12 HOH HOH . E 5 HOH A 30 630 31 HOH HOH . E 5 HOH A 31 631 28 HOH HOH . E 5 HOH A 32 632 83 HOH HOH . E 5 HOH A 33 633 160 HOH HOH . E 5 HOH A 34 634 77 HOH HOH . E 5 HOH A 35 635 78 HOH HOH . E 5 HOH A 36 636 202 HOH HOH . E 5 HOH A 37 637 2 HOH HOH . E 5 HOH A 38 638 39 HOH HOH . E 5 HOH A 39 639 20 HOH HOH . E 5 HOH A 40 640 13 HOH HOH . E 5 HOH A 41 641 15 HOH HOH . E 5 HOH A 42 642 113 HOH HOH . E 5 HOH A 43 643 167 HOH HOH . E 5 HOH A 44 644 3 HOH HOH . E 5 HOH A 45 645 146 HOH HOH . E 5 HOH A 46 646 205 HOH HOH . E 5 HOH A 47 647 87 HOH HOH . E 5 HOH A 48 648 42 HOH HOH . E 5 HOH A 49 649 8 HOH HOH . E 5 HOH A 50 650 94 HOH HOH . E 5 HOH A 51 651 58 HOH HOH . E 5 HOH A 52 652 9 HOH HOH . E 5 HOH A 53 653 48 HOH HOH . E 5 HOH A 54 654 68 HOH HOH . E 5 HOH A 55 655 173 HOH HOH . E 5 HOH A 56 656 4 HOH HOH . E 5 HOH A 57 657 129 HOH HOH . E 5 HOH A 58 658 204 HOH HOH . E 5 HOH A 59 659 17 HOH HOH . E 5 HOH A 60 660 67 HOH HOH . E 5 HOH A 61 661 134 HOH HOH . E 5 HOH A 62 662 1 HOH HOH . E 5 HOH A 63 663 57 HOH HOH . E 5 HOH A 64 664 16 HOH HOH . E 5 HOH A 65 665 37 HOH HOH . E 5 HOH A 66 666 44 HOH HOH . E 5 HOH A 67 667 193 HOH HOH . E 5 HOH A 68 668 154 HOH HOH . E 5 HOH A 69 669 115 HOH HOH . E 5 HOH A 70 670 21 HOH HOH . E 5 HOH A 71 671 40 HOH HOH . E 5 HOH A 72 672 43 HOH HOH . E 5 HOH A 73 673 187 HOH HOH . E 5 HOH A 74 674 213 HOH HOH . E 5 HOH A 75 675 194 HOH HOH . E 5 HOH A 76 676 102 HOH HOH . E 5 HOH A 77 677 23 HOH HOH . E 5 HOH A 78 678 84 HOH HOH . E 5 HOH A 79 679 96 HOH HOH . E 5 HOH A 80 680 27 HOH HOH . E 5 HOH A 81 681 34 HOH HOH . E 5 HOH A 82 682 14 HOH HOH . E 5 HOH A 83 683 81 HOH HOH . E 5 HOH A 84 684 112 HOH HOH . E 5 HOH A 85 685 26 HOH HOH . E 5 HOH A 86 686 74 HOH HOH . E 5 HOH A 87 687 107 HOH HOH . E 5 HOH A 88 688 89 HOH HOH . E 5 HOH A 89 689 116 HOH HOH . E 5 HOH A 90 690 29 HOH HOH . E 5 HOH A 91 691 149 HOH HOH . E 5 HOH A 92 692 143 HOH HOH . E 5 HOH A 93 693 86 HOH HOH . E 5 HOH A 94 694 156 HOH HOH . E 5 HOH A 95 695 177 HOH HOH . E 5 HOH A 96 696 35 HOH HOH . E 5 HOH A 97 697 214 HOH HOH . E 5 HOH A 98 698 120 HOH HOH . E 5 HOH A 99 699 178 HOH HOH . E 5 HOH A 100 700 66 HOH HOH . E 5 HOH A 101 701 152 HOH HOH . E 5 HOH A 102 702 41 HOH HOH . E 5 HOH A 103 703 93 HOH HOH . E 5 HOH A 104 704 65 HOH HOH . E 5 HOH A 105 705 169 HOH HOH . E 5 HOH A 106 706 50 HOH HOH . E 5 HOH A 107 707 209 HOH HOH . E 5 HOH A 108 708 148 HOH HOH . E 5 HOH A 109 709 18 HOH HOH . E 5 HOH A 110 710 73 HOH HOH . E 5 HOH A 111 711 61 HOH HOH . E 5 HOH A 112 712 99 HOH HOH . E 5 HOH A 113 713 95 HOH HOH . E 5 HOH A 114 714 114 HOH HOH . E 5 HOH A 115 715 53 HOH HOH . E 5 HOH A 116 716 159 HOH HOH . E 5 HOH A 117 717 144 HOH HOH . E 5 HOH A 118 718 170 HOH HOH . E 5 HOH A 119 719 54 HOH HOH . E 5 HOH A 120 720 172 HOH HOH . E 5 HOH A 121 721 47 HOH HOH . E 5 HOH A 122 722 133 HOH HOH . E 5 HOH A 123 723 30 HOH HOH . E 5 HOH A 124 724 104 HOH HOH . E 5 HOH A 125 725 210 HOH HOH . E 5 HOH A 126 726 132 HOH HOH . E 5 HOH A 127 727 188 HOH HOH . E 5 HOH A 128 728 141 HOH HOH . E 5 HOH A 129 729 127 HOH HOH . E 5 HOH A 130 730 105 HOH HOH . E 5 HOH A 131 731 186 HOH HOH . E 5 HOH A 132 732 176 HOH HOH . E 5 HOH A 133 733 181 HOH HOH . E 5 HOH A 134 734 200 HOH HOH . E 5 HOH A 135 735 153 HOH HOH . E 5 HOH A 136 736 126 HOH HOH . E 5 HOH A 137 737 179 HOH HOH . E 5 HOH A 138 738 165 HOH HOH . E 5 HOH A 139 739 130 HOH HOH . E 5 HOH A 140 740 189 HOH HOH . E 5 HOH A 141 741 191 HOH HOH . E 5 HOH A 142 742 131 HOH HOH . E 5 HOH A 143 743 72 HOH HOH . E 5 HOH A 144 744 140 HOH HOH . E 5 HOH A 145 745 128 HOH HOH . E 5 HOH A 146 746 184 HOH HOH . E 5 HOH A 147 747 150 HOH HOH . E 5 HOH A 148 748 211 HOH HOH . E 5 HOH A 149 749 109 HOH HOH . E 5 HOH A 150 750 163 HOH HOH . E 5 HOH A 151 751 119 HOH HOH . E 5 HOH A 152 752 203 HOH HOH . E 5 HOH A 153 753 69 HOH HOH . E 5 HOH A 154 754 199 HOH HOH . E 5 HOH A 155 755 90 HOH HOH . E 5 HOH A 156 756 75 HOH HOH . E 5 HOH A 157 757 108 HOH HOH . E 5 HOH A 158 758 185 HOH HOH . F 5 HOH B 1 601 198 HOH HOH . F 5 HOH B 2 602 206 HOH HOH . F 5 HOH B 3 603 38 HOH HOH . F 5 HOH B 4 604 22 HOH HOH . F 5 HOH B 5 605 62 HOH HOH . F 5 HOH B 6 606 10 HOH HOH . F 5 HOH B 7 607 7 HOH HOH . F 5 HOH B 8 608 24 HOH HOH . F 5 HOH B 9 609 97 HOH HOH . F 5 HOH B 10 610 212 HOH HOH . F 5 HOH B 11 611 137 HOH HOH . F 5 HOH B 12 612 196 HOH HOH . F 5 HOH B 13 613 32 HOH HOH . F 5 HOH B 14 614 56 HOH HOH . F 5 HOH B 15 615 33 HOH HOH . F 5 HOH B 16 616 208 HOH HOH . F 5 HOH B 17 617 182 HOH HOH . F 5 HOH B 18 618 46 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 C1 DXT . . . D 4 -2.235 16.296 -15.905 1 66.13 ? C1 DXT 501 B 1 HETATM 2 O O1 DXT . . . D 4 -1.154 16.863 -15.897 1 63.49 ? O1 DXT 501 B 1 HETATM 3 C C2 DXT . . . D 4 -2.635 15.323 -16.91 1 69.52 ? C2 DXT 501 B 1 HETATM 4 O O21 DXT . . . D 4 -0.696 15.814 -18.302 1 69.47 ? O21 DXT 501 B 1 HETATM 5 C C21 DXT . . . D 4 -1.77 15.233 -18.141 1 69.59 ? C21 DXT 501 B 1 HETATM 6 N N21 DXT . . . D 4 -2.313 14.409 -19.121 1 69.28 ? N21 DXT 501 B 1 HETATM 7 C C3 DXT . . . D 4 -3.836 14.71 -16.971 1 69.61 ? C3 DXT 501 B 1 HETATM 8 O O3 DXT . . . D 4 -4.471 14.466 -18.138 1 72.68 ? O3 DXT 501 B 1 HETATM 9 C C4 DXT . . . D 4 -4.851 14.792 -15.849 1 69.21 ? C4 DXT 501 B 1 HETATM 10 N N4 DXT . . . D 4 -4.897 13.456 -14.991 1 71.13 ? N4 DXT 501 B 1 HETATM 11 C C41 DXT . . . D 4 -3.667 13.249 -14.158 1 63.87 ? C41 DXT 501 B 1 HETATM 12 C C42 DXT . . . D 4 -5.007 12.264 -15.906 1 62.97 ? C42 DXT 501 B 1 HETATM 13 C C4A DXT . . . D 4 -4.709 16.144 -15.038 1 59.19 ? C4A DXT 501 B 1 HETATM 14 C C5 DXT . . . D 4 -5.623 17.197 -15.758 1 62.62 ? C5 DXT 501 B 1 HETATM 15 O O5 DXT . . . D 4 -6.924 16.682 -15.871 1 61.2 ? O5 DXT 501 B 1 HETATM 16 C C5A DXT . . . D 4 -5.615 18.622 -15.11 1 54.95 ? C5A DXT 501 B 1 HETATM 17 C C6 DXT . . . D 4 -6.168 19.776 -16.029 1 53.7 ? C6 DXT 501 B 1 HETATM 18 C C61 DXT . . . D 4 -7.555 19.512 -16.563 1 54.54 ? C61 DXT 501 B 1 HETATM 19 C C6A DXT . . . D 4 -6.138 21.1 -15.324 1 47.66 ? C6A DXT 501 B 1 HETATM 20 C C7 DXT . . . D 4 -7.095 22.074 -15.577 1 40.03 ? C7 DXT 501 B 1 HETATM 21 C C8 DXT . . . D 4 -7.068 23.311 -14.928 1 37.86 ? C8 DXT 501 B 1 HETATM 22 C C9 DXT . . . D 4 -6.088 23.606 -14.004 1 42.13 ? C9 DXT 501 B 1 HETATM 23 C C10 DXT . . . D 4 -5.115 22.622 -13.741 1 48.79 ? C10 DXT 501 B 1 HETATM 24 O O10 DXT . . . D 4 -4.178 22.976 -12.819 1 49.72 ? O10 DXT 501 B 1 HETATM 25 C C6B DXT . . . D 4 -5.134 21.376 -14.395 1 51.07 ? C6B DXT 501 B 1 HETATM 26 C C11 DXT . . . D 4 -4.108 20.377 -14.096 1 54.11 ? C11 DXT 501 B 1 HETATM 27 O O11 DXT . . . D 4 -3.13 20.644 -13.373 1 52.17 ? O11 DXT 501 B 1 HETATM 28 C C5B DXT . . . D 4 -4.239 19.023 -14.662 1 56.12 ? C5B DXT 501 B 1 HETATM 29 C C12 DXT . . . D 4 -3.207 18.162 -14.476 1 55.82 ? C12 DXT 501 B 1 HETATM 30 O O12 DXT . . . D 4 -2.111 18.415 -13.753 1 53 ? O12 DXT 501 B 1 HETATM 31 C C4B DXT . . . D 4 -3.219 16.637 -14.76 1 61.53 ? C4B DXT 501 B 1 HETATM 32 O O13 DXT . . . D 4 -2.76 16.04 -13.591 1 60.19 ? O13 DXT 501 B 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 361 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #