data_9DQI # _model_server_result.job_id UaipURHnLT5HdurF1t-cKw _model_server_result.datetime_utc '2025-06-24 03:15:59' _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 9dqi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":602}' # _entry.id 9DQI # _exptl.entry_id 9DQI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 204.179 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '1,4-dihydroxy-2-naphthoic acid' _entity.pdbx_number_of_molecules 2 _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 9DQI _cell.length_a 101.565 _cell.length_b 139.978 _cell.length_c 183.859 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DQI _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 J N N ? 5 R N 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 metalc ? metalc1 B OD1 ASP 460 D ASP 440 1_555 L MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc2 B OD1 ASP 489 D ASP 469 1_555 L MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc3 B O GLY 491 D GLY 471 1_555 L MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc4 I O2A TPP . D TPP 601 1_555 L MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc5 I O1B TPP . D TPP 601 1_555 L MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc6 L MG MG . D MG 604 1_555 U O HOH . D HOH 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc7 D OD1 ASP 460 C ASP 440 1_555 S MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc8 D OD1 ASP 489 C ASP 469 1_555 S MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc9 D O GLY 491 C GLY 471 1_555 S MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc10 Q O2A TPP . C TPP 601 1_555 S MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc11 Q O1B TPP . C TPP 601 1_555 S MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc12 S MG MG . C MG 603 1_555 W O HOH . C HOH 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? # _chem_comp.formula 'C11 H8 O4' _chem_comp.formula_weight 204.179 _chem_comp.id DNA _chem_comp.mon_nstd_flag . _chem_comp.name '1,4-dihydroxy-2-naphthoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '1,4-dihydroxynaphthalene-2-carboxylic acid' # 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 O1A C1J DNA doub 83 n n C1J O1B DNA sing 84 n n O1B HO1B DNA sing 85 n n C1K O1C DNA sing 86 n n O1C HO1C DNA sing 87 n n O1D C1M DNA sing 88 n n O1D HO1D DNA sing 89 n n C1F C1E DNA doub 90 n y C1E C1G DNA sing 91 n y C1E H1E DNA sing 92 n n C1F C1H DNA sing 93 n y C1F H1F DNA sing 94 n n C1G C1N DNA doub 95 n y C1G H1G DNA sing 96 n n C1H C1O DNA doub 97 n y C1H H1H DNA sing 98 n n C1L C1I DNA sing 99 n y C1K C1I DNA doub 100 n y C1I H1I DNA sing 101 n n C1L C1J DNA sing 102 n n C1N C1K DNA sing 103 n y C1M C1L DNA doub 104 n y C1O C1M DNA sing 105 n y C1O C1N DNA sing 106 n y # _atom_sites.entry_id 9DQI _atom_sites.fract_transf_matrix[1][1] 0.009846 _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] 0.007144 _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] 0.005439 _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 E 2 EDO A 1 601 601 EDO EDO . F 2 EDO A 1 602 604 EDO EDO . G 3 CL A 1 603 2 CL CL . H 3 CL A 1 604 4 CL CL . I 4 TPP D 1 601 601 TPP TPP . J 5 DNA D 1 602 602 DNA DNA . K 2 EDO D 1 603 603 EDO EDO . L 6 MG D 1 604 1 MG MG . M 3 CL D 1 605 5 CL CL . N 2 EDO B 1 601 601 EDO EDO . O 3 CL B 1 602 1 CL CL . P 3 CL B 1 603 3 CL CL . Q 4 TPP C 1 601 601 TPP TPP . R 5 DNA C 1 602 602 DNA DNA . S 6 MG C 1 603 2 MG MG . T 7 HOH A 1 701 23 HOH HOH . T 7 HOH A 2 702 58 HOH HOH . T 7 HOH A 3 703 61 HOH HOH . T 7 HOH A 4 704 129 HOH HOH . T 7 HOH A 5 705 52 HOH HOH . T 7 HOH A 6 706 186 HOH HOH . T 7 HOH A 7 707 11 HOH HOH . T 7 HOH A 8 708 54 HOH HOH . T 7 HOH A 9 709 5 HOH HOH . T 7 HOH A 10 710 141 HOH HOH . T 7 HOH A 11 711 156 HOH HOH . T 7 HOH A 12 712 97 HOH HOH . T 7 HOH A 13 713 64 HOH HOH . T 7 HOH A 14 714 51 HOH HOH . T 7 HOH A 15 715 2 HOH HOH . T 7 HOH A 16 716 72 HOH HOH . T 7 HOH A 17 717 34 HOH HOH . T 7 HOH A 18 718 30 HOH HOH . T 7 HOH A 19 719 99 HOH HOH . T 7 HOH A 20 720 22 HOH HOH . T 7 HOH A 21 721 59 HOH HOH . T 7 HOH A 22 722 68 HOH HOH . T 7 HOH A 23 723 7 HOH HOH . T 7 HOH A 24 724 122 HOH HOH . T 7 HOH A 25 725 113 HOH HOH . T 7 HOH A 26 726 76 HOH HOH . T 7 HOH A 27 727 25 HOH HOH . T 7 HOH A 28 728 28 HOH HOH . T 7 HOH A 29 729 175 HOH HOH . T 7 HOH A 30 730 106 HOH HOH . T 7 HOH A 31 731 100 HOH HOH . T 7 HOH A 32 732 163 HOH HOH . T 7 HOH A 33 733 71 HOH HOH . T 7 HOH A 34 734 89 HOH HOH . T 7 HOH A 35 735 181 HOH HOH . T 7 HOH A 36 736 79 HOH HOH . T 7 HOH A 37 737 78 HOH HOH . T 7 HOH A 38 738 147 HOH HOH . T 7 HOH A 39 739 19 HOH HOH . T 7 HOH A 40 740 102 HOH HOH . T 7 HOH A 41 741 14 HOH HOH . T 7 HOH A 42 742 133 HOH HOH . T 7 HOH A 43 743 172 HOH HOH . T 7 HOH A 44 744 159 HOH HOH . T 7 HOH A 45 745 177 HOH HOH . T 7 HOH A 46 746 194 HOH HOH . T 7 HOH A 47 747 67 HOH HOH . T 7 HOH A 48 748 8 HOH HOH . T 7 HOH A 49 749 39 HOH HOH . T 7 HOH A 50 750 176 HOH HOH . T 7 HOH A 51 751 75 HOH HOH . T 7 HOH A 52 752 188 HOH HOH . T 7 HOH A 53 753 185 HOH HOH . U 7 HOH D 1 701 74 HOH HOH . U 7 HOH D 2 702 62 HOH HOH . U 7 HOH D 3 703 13 HOH HOH . U 7 HOH D 4 704 96 HOH HOH . U 7 HOH D 5 705 29 HOH HOH . U 7 HOH D 6 706 16 HOH HOH . U 7 HOH D 7 707 160 HOH HOH . U 7 HOH D 8 708 107 HOH HOH . U 7 HOH D 9 709 46 HOH HOH . U 7 HOH D 10 710 116 HOH HOH . U 7 HOH D 11 711 82 HOH HOH . U 7 HOH D 12 712 165 HOH HOH . U 7 HOH D 13 713 41 HOH HOH . U 7 HOH D 14 714 31 HOH HOH . U 7 HOH D 15 715 135 HOH HOH . U 7 HOH D 16 716 169 HOH HOH . U 7 HOH D 17 717 43 HOH HOH . U 7 HOH D 18 718 114 HOH HOH . U 7 HOH D 19 719 45 HOH HOH . U 7 HOH D 20 720 70 HOH HOH . U 7 HOH D 21 721 50 HOH HOH . U 7 HOH D 22 722 35 HOH HOH . U 7 HOH D 23 723 18 HOH HOH . U 7 HOH D 24 724 56 HOH HOH . U 7 HOH D 25 725 32 HOH HOH . U 7 HOH D 26 726 170 HOH HOH . U 7 HOH D 27 727 4 HOH HOH . U 7 HOH D 28 728 139 HOH HOH . U 7 HOH D 29 729 85 HOH HOH . U 7 HOH D 30 730 167 HOH HOH . U 7 HOH D 31 731 6 HOH HOH . U 7 HOH D 32 732 192 HOH HOH . U 7 HOH D 33 733 161 HOH HOH . U 7 HOH D 34 734 1 HOH HOH . U 7 HOH D 35 735 138 HOH HOH . U 7 HOH D 36 736 49 HOH HOH . U 7 HOH D 37 737 66 HOH HOH . U 7 HOH D 38 738 77 HOH HOH . U 7 HOH D 39 739 91 HOH HOH . U 7 HOH D 40 740 88 HOH HOH . U 7 HOH D 41 741 158 HOH HOH . U 7 HOH D 42 742 24 HOH HOH . U 7 HOH D 43 743 26 HOH HOH . U 7 HOH D 44 744 142 HOH HOH . U 7 HOH D 45 745 80 HOH HOH . U 7 HOH D 46 746 117 HOH HOH . U 7 HOH D 47 747 145 HOH HOH . U 7 HOH D 48 748 143 HOH HOH . U 7 HOH D 49 749 38 HOH HOH . U 7 HOH D 50 750 73 HOH HOH . U 7 HOH D 51 751 60 HOH HOH . U 7 HOH D 52 752 27 HOH HOH . U 7 HOH D 53 753 124 HOH HOH . U 7 HOH D 54 754 90 HOH HOH . U 7 HOH D 55 755 55 HOH HOH . U 7 HOH D 56 756 112 HOH HOH . U 7 HOH D 57 757 98 HOH HOH . U 7 HOH D 58 758 191 HOH HOH . U 7 HOH D 59 759 20 HOH HOH . U 7 HOH D 60 760 132 HOH HOH . U 7 HOH D 61 761 83 HOH HOH . U 7 HOH D 62 762 119 HOH HOH . U 7 HOH D 63 763 84 HOH HOH . U 7 HOH D 64 764 63 HOH HOH . U 7 HOH D 65 765 127 HOH HOH . U 7 HOH D 66 766 164 HOH HOH . U 7 HOH D 67 767 9 HOH HOH . U 7 HOH D 68 768 125 HOH HOH . U 7 HOH D 69 769 126 HOH HOH . U 7 HOH D 70 770 144 HOH HOH . U 7 HOH D 71 771 182 HOH HOH . U 7 HOH D 72 772 154 HOH HOH . U 7 HOH D 73 773 157 HOH HOH . U 7 HOH D 74 774 110 HOH HOH . U 7 HOH D 75 775 103 HOH HOH . U 7 HOH D 76 776 95 HOH HOH . U 7 HOH D 77 777 140 HOH HOH . U 7 HOH D 78 778 47 HOH HOH . U 7 HOH D 79 779 183 HOH HOH . U 7 HOH D 80 780 168 HOH HOH . U 7 HOH D 81 781 151 HOH HOH . U 7 HOH D 82 782 189 HOH HOH . U 7 HOH D 83 783 42 HOH HOH . U 7 HOH D 84 784 148 HOH HOH . U 7 HOH D 85 785 81 HOH HOH . U 7 HOH D 86 786 152 HOH HOH . U 7 HOH D 87 787 92 HOH HOH . U 7 HOH D 88 788 69 HOH HOH . U 7 HOH D 89 789 162 HOH HOH . U 7 HOH D 90 790 94 HOH HOH . U 7 HOH D 91 791 150 HOH HOH . V 7 HOH B 1 701 10 HOH HOH . V 7 HOH B 2 702 109 HOH HOH . V 7 HOH B 3 703 37 HOH HOH . V 7 HOH B 4 704 36 HOH HOH . V 7 HOH B 5 705 65 HOH HOH . V 7 HOH B 6 706 87 HOH HOH . V 7 HOH B 7 707 134 HOH HOH . V 7 HOH B 8 708 12 HOH HOH . V 7 HOH B 9 709 136 HOH HOH . V 7 HOH B 10 710 44 HOH HOH . V 7 HOH B 11 711 21 HOH HOH . V 7 HOH B 12 712 40 HOH HOH . V 7 HOH B 13 713 111 HOH HOH . V 7 HOH B 14 714 115 HOH HOH . V 7 HOH B 15 715 57 HOH HOH . V 7 HOH B 16 716 184 HOH HOH . V 7 HOH B 17 717 174 HOH HOH . V 7 HOH B 18 718 3 HOH HOH . V 7 HOH B 19 719 15 HOH HOH . V 7 HOH B 20 720 48 HOH HOH . V 7 HOH B 21 721 128 HOH HOH . V 7 HOH B 22 722 118 HOH HOH . V 7 HOH B 23 723 146 HOH HOH . V 7 HOH B 24 724 137 HOH HOH . V 7 HOH B 25 725 190 HOH HOH . W 7 HOH C 1 701 193 HOH HOH . W 7 HOH C 2 702 166 HOH HOH . W 7 HOH C 3 703 180 HOH HOH . W 7 HOH C 4 704 33 HOH HOH . W 7 HOH C 5 705 108 HOH HOH . W 7 HOH C 6 706 149 HOH HOH . W 7 HOH C 7 707 195 HOH HOH . W 7 HOH C 8 708 86 HOH HOH . W 7 HOH C 9 709 17 HOH HOH . W 7 HOH C 10 710 105 HOH HOH . W 7 HOH C 11 711 53 HOH HOH . W 7 HOH C 12 712 131 HOH HOH . W 7 HOH C 13 713 101 HOH HOH . W 7 HOH C 14 714 155 HOH HOH . W 7 HOH C 15 715 178 HOH HOH . W 7 HOH C 16 716 179 HOH HOH . W 7 HOH C 17 717 153 HOH HOH . W 7 HOH C 18 718 171 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 O1A DNA . . . R 5 66.915 9.771 -3.353 1 61.78 ? O1A DNA 602 C 1 HETATM 2 O O1B DNA . . . R 5 68.33 8.237 -2.672 1 70.64 ? O1B DNA 602 C 1 HETATM 3 O O1C DNA . . . R 5 66.511 6.562 1.669 1 73.75 ? O1C DNA 602 C 1 HETATM 4 O O1D DNA . . . R 5 65.321 10.925 -1.704 1 67.98 ? O1D DNA 602 C 1 HETATM 5 C C1E DNA . . . R 5 63.525 9.403 2.877 1 70.57 ? C1E DNA 602 C 1 HETATM 6 C C1F DNA . . . R 5 63.22 10.484 2.046 1 71.84 ? C1F DNA 602 C 1 HETATM 7 C C1G DNA . . . R 5 64.487 8.46 2.521 1 69.34 ? C1G DNA 602 C 1 HETATM 8 C C1H DNA . . . R 5 63.872 10.672 0.83 1 66.19 ? C1H DNA 602 C 1 HETATM 9 C C1I DNA . . . R 5 66.861 7.795 -0.339 1 68.02 ? C1I DNA 602 C 1 HETATM 10 C C1J DNA . . . R 5 67.333 8.971 -2.489 1 58.29 ? C1J DNA 602 C 1 HETATM 11 C C1K DNA . . . R 5 66.201 7.626 0.877 1 70.65 ? C1K DNA 602 C 1 HETATM 12 C C1L DNA . . . R 5 66.592 8.865 -1.195 1 60.16 ? C1L DNA 602 C 1 HETATM 13 C C1M DNA . . . R 5 65.571 9.89 -0.853 1 70.48 ? C1M DNA 602 C 1 HETATM 14 C C1N DNA . . . R 5 65.16 8.603 1.313 1 75.25 ? C1N DNA 602 C 1 HETATM 15 C C1O DNA . . . R 5 64.839 9.758 0.435 1 66.37 ? C1O DNA 602 C 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 15 #