data_6DQD # _model_server_result.job_id chPUeMpFQX4fDamysMYGDg _model_server_result.datetime_utc '2025-07-03 20:44:30' _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 6dqd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":603}' # _entry.id 6DQD # _exptl.entry_id 6DQD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 92.17 _cell.angle_gamma 90 _cell.entry_id 6DQD _cell.length_a 116.61 _cell.length_b 61.899 _cell.length_c 46.649 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DQD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 A,B,C,D,E,F,G,H 2 1,2 # 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E 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 A NE2 HIS 225 A HIS 483 1_555 C MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc2 A OE1 GLU 227 A GLU 485 1_555 C MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc3 A NE2 HIS 313 A HIS 571 1_555 C MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc4 B N06 H67 . A H67 601 1_555 C MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc5 C MN MN . A MN 602 1_555 H O HOH . A HOH 748 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 O1 GOL sing 138 n n C1 C2 GOL sing 139 n n C1 H11 GOL sing 140 n n C1 H12 GOL sing 141 n n O1 HO1 GOL sing 142 n n C2 O2 GOL sing 143 n n C2 C3 GOL sing 144 n n C2 H2 GOL sing 145 n n O2 HO2 GOL sing 146 n n C3 O3 GOL sing 147 n n C3 H31 GOL sing 148 n n C3 H32 GOL sing 149 n n O3 HO3 GOL sing 150 n n # _atom_sites.entry_id 6DQD _atom_sites.fract_transf_matrix[1][1] 0.008576 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000325 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016155 _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] 0.021452 _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 H67 A 1 601 1 H67 LIG . C 3 MN A 1 602 1 MN MN . D 4 GOL A 1 603 501 GOL GOL . E 4 GOL A 1 604 502 GOL GOL . F 5 DMS A 1 605 601 DMS DMS . G 5 DMS A 1 606 602 DMS DMS . H 6 HOH A 1 701 85 HOH HOH . H 6 HOH A 2 702 24 HOH HOH . H 6 HOH A 3 703 33 HOH HOH . H 6 HOH A 4 704 26 HOH HOH . H 6 HOH A 5 705 119 HOH HOH . H 6 HOH A 6 706 78 HOH HOH . H 6 HOH A 7 707 58 HOH HOH . H 6 HOH A 8 708 55 HOH HOH . H 6 HOH A 9 709 3 HOH HOH . H 6 HOH A 10 710 80 HOH HOH . H 6 HOH A 11 711 19 HOH HOH . H 6 HOH A 12 712 150 HOH HOH . H 6 HOH A 13 713 138 HOH HOH . H 6 HOH A 14 714 27 HOH HOH . H 6 HOH A 15 715 23 HOH HOH . H 6 HOH A 16 716 36 HOH HOH . H 6 HOH A 17 717 16 HOH HOH . H 6 HOH A 18 718 2 HOH HOH . H 6 HOH A 19 719 132 HOH HOH . H 6 HOH A 20 720 8 HOH HOH . H 6 HOH A 21 721 7 HOH HOH . H 6 HOH A 22 722 22 HOH HOH . H 6 HOH A 23 723 137 HOH HOH . H 6 HOH A 24 724 72 HOH HOH . H 6 HOH A 25 725 71 HOH HOH . H 6 HOH A 26 726 41 HOH HOH . H 6 HOH A 27 727 134 HOH HOH . H 6 HOH A 28 728 5 HOH HOH . H 6 HOH A 29 729 101 HOH HOH . H 6 HOH A 30 730 99 HOH HOH . H 6 HOH A 31 731 1 HOH HOH . H 6 HOH A 32 732 28 HOH HOH . H 6 HOH A 33 733 34 HOH HOH . H 6 HOH A 34 734 12 HOH HOH . H 6 HOH A 35 735 17 HOH HOH . H 6 HOH A 36 736 81 HOH HOH . H 6 HOH A 37 737 122 HOH HOH . H 6 HOH A 38 738 32 HOH HOH . H 6 HOH A 39 739 75 HOH HOH . H 6 HOH A 40 740 20 HOH HOH . H 6 HOH A 41 741 10 HOH HOH . H 6 HOH A 42 742 9 HOH HOH . H 6 HOH A 43 743 13 HOH HOH . H 6 HOH A 44 744 31 HOH HOH . H 6 HOH A 45 745 46 HOH HOH . H 6 HOH A 46 746 62 HOH HOH . H 6 HOH A 47 747 102 HOH HOH . H 6 HOH A 48 748 183 HOH HOH . H 6 HOH A 49 749 56 HOH HOH . H 6 HOH A 50 750 171 HOH HOH . H 6 HOH A 51 751 48 HOH HOH . H 6 HOH A 52 752 129 HOH HOH . H 6 HOH A 53 753 158 HOH HOH . H 6 HOH A 54 754 44 HOH HOH . H 6 HOH A 55 755 115 HOH HOH . H 6 HOH A 56 756 42 HOH HOH . H 6 HOH A 57 757 70 HOH HOH . H 6 HOH A 58 758 59 HOH HOH . H 6 HOH A 59 759 143 HOH HOH . H 6 HOH A 60 760 4 HOH HOH . H 6 HOH A 61 761 43 HOH HOH . H 6 HOH A 62 762 51 HOH HOH . H 6 HOH A 63 763 89 HOH HOH . H 6 HOH A 64 764 15 HOH HOH . H 6 HOH A 65 765 14 HOH HOH . H 6 HOH A 66 766 106 HOH HOH . H 6 HOH A 67 767 25 HOH HOH . H 6 HOH A 68 768 69 HOH HOH . H 6 HOH A 69 769 153 HOH HOH . H 6 HOH A 70 770 98 HOH HOH . H 6 HOH A 71 771 52 HOH HOH . H 6 HOH A 72 772 64 HOH HOH . H 6 HOH A 73 773 110 HOH HOH . H 6 HOH A 74 774 63 HOH HOH . H 6 HOH A 75 775 120 HOH HOH . H 6 HOH A 76 776 66 HOH HOH . H 6 HOH A 77 777 18 HOH HOH . H 6 HOH A 78 778 155 HOH HOH . H 6 HOH A 79 779 112 HOH HOH . H 6 HOH A 80 780 60 HOH HOH . H 6 HOH A 81 781 50 HOH HOH . H 6 HOH A 82 782 90 HOH HOH . H 6 HOH A 83 783 83 HOH HOH . H 6 HOH A 84 784 40 HOH HOH . H 6 HOH A 85 785 65 HOH HOH . H 6 HOH A 86 786 142 HOH HOH . H 6 HOH A 87 787 128 HOH HOH . H 6 HOH A 88 788 97 HOH HOH . H 6 HOH A 89 789 35 HOH HOH . H 6 HOH A 90 790 157 HOH HOH . H 6 HOH A 91 791 94 HOH HOH . H 6 HOH A 92 792 165 HOH HOH . H 6 HOH A 93 793 38 HOH HOH . H 6 HOH A 94 794 49 HOH HOH . H 6 HOH A 95 795 67 HOH HOH . H 6 HOH A 96 796 47 HOH HOH . H 6 HOH A 97 797 118 HOH HOH . H 6 HOH A 98 798 6 HOH HOH . H 6 HOH A 99 799 29 HOH HOH . H 6 HOH A 100 800 73 HOH HOH . H 6 HOH A 101 801 57 HOH HOH . H 6 HOH A 102 802 140 HOH HOH . H 6 HOH A 103 803 53 HOH HOH . H 6 HOH A 104 804 93 HOH HOH . H 6 HOH A 105 805 68 HOH HOH . H 6 HOH A 106 806 82 HOH HOH . H 6 HOH A 107 807 139 HOH HOH . H 6 HOH A 108 808 61 HOH HOH . H 6 HOH A 109 809 79 HOH HOH . H 6 HOH A 110 810 136 HOH HOH . H 6 HOH A 111 811 39 HOH HOH . H 6 HOH A 112 812 126 HOH HOH . H 6 HOH A 113 813 11 HOH HOH . H 6 HOH A 114 814 30 HOH HOH . H 6 HOH A 115 815 54 HOH HOH . H 6 HOH A 116 816 103 HOH HOH . H 6 HOH A 117 817 84 HOH HOH . H 6 HOH A 118 818 104 HOH HOH . H 6 HOH A 119 819 95 HOH HOH . H 6 HOH A 120 820 151 HOH HOH . H 6 HOH A 121 821 96 HOH HOH . H 6 HOH A 122 822 74 HOH HOH . H 6 HOH A 123 823 117 HOH HOH . H 6 HOH A 124 824 121 HOH HOH . H 6 HOH A 125 825 76 HOH HOH . H 6 HOH A 126 826 100 HOH HOH . H 6 HOH A 127 827 160 HOH HOH . H 6 HOH A 128 828 144 HOH HOH . H 6 HOH A 129 829 21 HOH HOH . H 6 HOH A 130 830 86 HOH HOH . H 6 HOH A 131 831 182 HOH HOH . H 6 HOH A 132 832 167 HOH HOH . H 6 HOH A 133 833 161 HOH HOH . H 6 HOH A 134 834 127 HOH HOH . H 6 HOH A 135 835 174 HOH HOH . H 6 HOH A 136 836 133 HOH HOH . H 6 HOH A 137 837 175 HOH HOH . H 6 HOH A 138 838 108 HOH HOH . H 6 HOH A 139 839 149 HOH HOH . H 6 HOH A 140 840 156 HOH HOH . H 6 HOH A 141 841 131 HOH HOH . H 6 HOH A 142 842 77 HOH HOH . H 6 HOH A 143 843 45 HOH HOH . H 6 HOH A 144 844 152 HOH HOH . H 6 HOH A 145 845 163 HOH HOH . H 6 HOH A 146 846 105 HOH HOH . H 6 HOH A 147 847 185 HOH HOH . H 6 HOH A 148 848 87 HOH HOH . H 6 HOH A 149 849 162 HOH HOH . H 6 HOH A 150 850 88 HOH HOH . H 6 HOH A 151 851 125 HOH HOH . H 6 HOH A 152 852 111 HOH HOH . H 6 HOH A 153 853 130 HOH HOH . H 6 HOH A 154 854 116 HOH HOH . H 6 HOH A 155 855 109 HOH HOH . H 6 HOH A 156 856 113 HOH HOH . H 6 HOH A 157 857 186 HOH HOH . H 6 HOH A 158 858 179 HOH HOH . H 6 HOH A 159 859 92 HOH HOH . H 6 HOH A 160 860 166 HOH HOH . H 6 HOH A 161 861 181 HOH HOH . H 6 HOH A 162 862 37 HOH HOH . H 6 HOH A 163 863 184 HOH HOH . H 6 HOH A 164 864 169 HOH HOH . H 6 HOH A 165 865 168 HOH HOH . H 6 HOH A 166 866 170 HOH HOH . H 6 HOH A 167 867 107 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 GOL . . . D 4 -27.81 19.726 -11.688 1 55.12 ? C1 GOL 603 A 1 HETATM 2 O O1 GOL . . . D 4 -28.258 19.571 -13.003 1 52.88 ? O1 GOL 603 A 1 HETATM 3 C C2 GOL . . . D 4 -26.838 18.552 -11.395 1 56.59 ? C2 GOL 603 A 1 HETATM 4 O O2 GOL . . . D 4 -25.828 18.47 -12.338 1 58.95 ? O2 GOL 603 A 1 HETATM 5 C C3 GOL . . . D 4 -26.287 18.827 -9.969 1 54.97 ? C3 GOL 603 A 1 HETATM 6 O O3 GOL . . . D 4 -25.27 19.775 -10.102 1 55.49 ? O3 GOL 603 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 6 #