data_3D40 # _model_server_result.job_id 3ML0Oh1QOZEoS4gw95obYg _model_server_result.datetime_utc '2025-02-27 06:18:04' _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 3d40 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2811}' # _entry.id 3D40 # _exptl.entry_id 3D40 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 173.943 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description DIPHOSPHATE _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 3D40 _cell.length_a 88.361 _cell.length_b 88.361 _cell.length_c 79.046 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D40 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 6_555 -x,-x+y,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 52.697333 # _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 'O7 P2 -4' _chem_comp.formula_weight 173.943 _chem_comp.id DPO _chem_comp.mon_nstd_flag . _chem_comp.name DIPHOSPHATE _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 P1 O1 DPO doub 83 n n P1 O2 DPO sing 84 n n P1 O3 DPO sing 85 n n P1 O4 DPO sing 86 n n O4 P2 DPO sing 87 n n P2 O5 DPO doub 88 n n P2 O6 DPO sing 89 n n P2 O7 DPO sing 90 n n # _atom_sites.entry_id 3D40 _atom_sites.fract_transf_matrix[1][1] 0.011317 _atom_sites.fract_transf_matrix[1][2] 0.006534 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013068 _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] 0.012651 _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 DPO A 1 2811 2811 DPO DPO . C 3 HOH A 1 2812 1 HOH HOH . C 3 HOH A 2 2813 2 HOH HOH . C 3 HOH A 3 2814 3 HOH HOH . C 3 HOH A 4 2815 4 HOH HOH . C 3 HOH A 5 2816 5 HOH HOH . C 3 HOH A 6 2817 6 HOH HOH . C 3 HOH A 7 2818 7 HOH HOH . C 3 HOH A 8 2819 8 HOH HOH . C 3 HOH A 9 2820 9 HOH HOH . C 3 HOH A 10 2821 10 HOH HOH . C 3 HOH A 11 2822 11 HOH HOH . C 3 HOH A 12 2823 12 HOH HOH . C 3 HOH A 13 2824 13 HOH HOH . C 3 HOH A 14 2825 14 HOH HOH . C 3 HOH A 15 2826 15 HOH HOH . C 3 HOH A 16 2827 16 HOH HOH . C 3 HOH A 17 2828 17 HOH HOH . C 3 HOH A 18 2829 18 HOH HOH . C 3 HOH A 19 2830 19 HOH HOH . C 3 HOH A 20 2831 20 HOH HOH . C 3 HOH A 21 2832 21 HOH HOH . C 3 HOH A 22 2833 22 HOH HOH . C 3 HOH A 23 2834 23 HOH HOH . C 3 HOH A 24 2835 24 HOH HOH . C 3 HOH A 25 2836 25 HOH HOH . C 3 HOH A 26 2837 26 HOH HOH . C 3 HOH A 27 2838 27 HOH HOH . C 3 HOH A 28 2839 28 HOH HOH . C 3 HOH A 29 2840 29 HOH HOH . C 3 HOH A 30 2841 30 HOH HOH . C 3 HOH A 31 2842 31 HOH HOH . C 3 HOH A 32 2843 32 HOH HOH . C 3 HOH A 33 2844 33 HOH HOH . C 3 HOH A 34 2845 34 HOH HOH . C 3 HOH A 35 2846 35 HOH HOH . C 3 HOH A 36 2847 36 HOH HOH . C 3 HOH A 37 2848 37 HOH HOH . C 3 HOH A 38 2849 38 HOH HOH . C 3 HOH A 39 2850 39 HOH HOH . C 3 HOH A 40 2851 40 HOH HOH . C 3 HOH A 41 2852 41 HOH HOH . C 3 HOH A 42 2853 42 HOH HOH . C 3 HOH A 43 2854 43 HOH HOH . C 3 HOH A 44 2855 44 HOH HOH . C 3 HOH A 45 2856 45 HOH HOH . C 3 HOH A 46 2857 46 HOH HOH . C 3 HOH A 47 2858 47 HOH HOH . C 3 HOH A 48 2859 48 HOH HOH . C 3 HOH A 49 2860 49 HOH HOH . C 3 HOH A 50 2861 50 HOH HOH . C 3 HOH A 51 2862 51 HOH HOH . C 3 HOH A 52 2863 52 HOH HOH . C 3 HOH A 53 2864 53 HOH HOH . C 3 HOH A 54 2865 54 HOH HOH . C 3 HOH A 55 2866 55 HOH HOH . C 3 HOH A 56 2867 56 HOH HOH . C 3 HOH A 57 2868 57 HOH HOH . C 3 HOH A 58 2869 58 HOH HOH . C 3 HOH A 59 2870 59 HOH HOH . C 3 HOH A 60 2871 60 HOH HOH . C 3 HOH A 61 2872 61 HOH HOH . C 3 HOH A 62 2873 62 HOH HOH . C 3 HOH A 63 2874 63 HOH HOH . C 3 HOH A 64 2875 64 HOH HOH . C 3 HOH A 65 2876 65 HOH HOH . C 3 HOH A 66 2877 66 HOH HOH . C 3 HOH A 67 2878 67 HOH HOH . C 3 HOH A 68 2879 68 HOH HOH . C 3 HOH A 69 2880 69 HOH HOH . C 3 HOH A 70 2881 70 HOH HOH . C 3 HOH A 71 2882 71 HOH HOH . C 3 HOH A 72 2883 72 HOH HOH . C 3 HOH A 73 2884 73 HOH HOH . C 3 HOH A 74 2885 74 HOH HOH . C 3 HOH A 75 2886 75 HOH HOH . C 3 HOH A 76 2887 76 HOH HOH . C 3 HOH A 77 2888 77 HOH HOH . C 3 HOH A 78 2889 78 HOH HOH . C 3 HOH A 79 2890 79 HOH HOH . C 3 HOH A 80 2891 80 HOH HOH . C 3 HOH A 81 2892 81 HOH HOH . C 3 HOH A 82 2893 82 HOH HOH . C 3 HOH A 83 2894 83 HOH HOH . C 3 HOH A 84 2895 84 HOH HOH . C 3 HOH A 85 2896 85 HOH HOH . C 3 HOH A 86 2897 86 HOH HOH . C 3 HOH A 87 2898 87 HOH HOH . C 3 HOH A 88 2899 88 HOH HOH . C 3 HOH A 89 2900 89 HOH HOH . C 3 HOH A 90 2901 90 HOH HOH . C 3 HOH A 91 2902 91 HOH HOH . C 3 HOH A 92 2903 92 HOH HOH . C 3 HOH A 93 2904 93 HOH HOH . C 3 HOH A 94 2905 94 HOH HOH . C 3 HOH A 95 2906 95 HOH HOH . C 3 HOH A 96 2907 96 HOH HOH . C 3 HOH A 97 2908 97 HOH HOH . C 3 HOH A 98 2909 98 HOH HOH . C 3 HOH A 99 2910 99 HOH HOH . C 3 HOH A 100 2911 100 HOH HOH . C 3 HOH A 101 2912 101 HOH HOH . C 3 HOH A 102 2913 102 HOH HOH . C 3 HOH A 103 2914 103 HOH HOH . C 3 HOH A 104 2915 104 HOH HOH . C 3 HOH A 105 2916 105 HOH HOH . C 3 HOH A 106 2917 106 HOH HOH . C 3 HOH A 107 2918 107 HOH HOH . C 3 HOH A 108 2919 108 HOH HOH . C 3 HOH A 109 2920 109 HOH HOH . C 3 HOH A 110 2921 110 HOH HOH . C 3 HOH A 111 2922 111 HOH HOH . C 3 HOH A 112 2923 112 HOH HOH . C 3 HOH A 113 2924 113 HOH HOH . C 3 HOH A 114 2925 114 HOH HOH . C 3 HOH A 115 2926 115 HOH HOH . C 3 HOH A 116 2927 116 HOH HOH . C 3 HOH A 117 2928 117 HOH HOH . C 3 HOH A 118 2929 118 HOH HOH . C 3 HOH A 119 2930 119 HOH HOH . C 3 HOH A 120 2931 120 HOH HOH . C 3 HOH A 121 2932 121 HOH HOH . C 3 HOH A 122 2933 122 HOH HOH . C 3 HOH A 123 2934 123 HOH HOH . C 3 HOH A 124 2935 124 HOH HOH . C 3 HOH A 125 2936 125 HOH HOH . C 3 HOH A 126 2937 126 HOH HOH . C 3 HOH A 127 2938 127 HOH HOH . C 3 HOH A 128 2939 128 HOH HOH . C 3 HOH A 129 2940 129 HOH HOH . C 3 HOH A 130 2941 130 HOH HOH . C 3 HOH A 131 2942 131 HOH HOH . C 3 HOH A 132 2943 132 HOH HOH . C 3 HOH A 133 2944 133 HOH HOH . C 3 HOH A 134 2945 134 HOH HOH . C 3 HOH A 135 2946 135 HOH HOH . C 3 HOH A 136 2947 136 HOH HOH . C 3 HOH A 137 2948 137 HOH HOH . C 3 HOH A 138 2949 138 HOH HOH . C 3 HOH A 139 2950 139 HOH HOH . C 3 HOH A 140 2951 140 HOH HOH . C 3 HOH A 141 2952 141 HOH HOH . C 3 HOH A 142 2953 142 HOH HOH . C 3 HOH A 143 2954 143 HOH HOH . C 3 HOH A 144 2955 144 HOH HOH . C 3 HOH A 145 2956 145 HOH HOH . C 3 HOH A 146 2957 146 HOH HOH . C 3 HOH A 147 2958 147 HOH HOH . C 3 HOH A 148 2959 148 HOH HOH . C 3 HOH A 149 2960 149 HOH HOH . C 3 HOH A 150 2961 150 HOH HOH . C 3 HOH A 151 2962 151 HOH HOH . C 3 HOH A 152 2963 152 HOH HOH . C 3 HOH A 153 2964 153 HOH HOH . C 3 HOH A 154 2965 154 HOH HOH . C 3 HOH A 155 2966 155 HOH HOH . C 3 HOH A 156 2967 156 HOH HOH . C 3 HOH A 157 2968 157 HOH HOH . C 3 HOH A 158 2969 158 HOH HOH . C 3 HOH A 159 2970 159 HOH HOH . C 3 HOH A 160 2971 160 HOH HOH . C 3 HOH A 161 2972 161 HOH HOH . C 3 HOH A 162 2973 162 HOH HOH . C 3 HOH A 163 2974 163 HOH HOH . C 3 HOH A 164 2975 164 HOH HOH . C 3 HOH A 165 2976 165 HOH HOH . C 3 HOH A 166 2977 166 HOH HOH . C 3 HOH A 167 2978 167 HOH HOH . C 3 HOH A 168 2979 168 HOH HOH . C 3 HOH A 169 2980 169 HOH HOH . C 3 HOH A 170 2981 170 HOH HOH . C 3 HOH A 171 2982 171 HOH HOH . C 3 HOH A 172 2983 172 HOH HOH . C 3 HOH A 173 2984 173 HOH HOH . C 3 HOH A 174 2985 174 HOH HOH . C 3 HOH A 175 2986 175 HOH HOH . C 3 HOH A 176 2987 176 HOH HOH . C 3 HOH A 177 2988 177 HOH HOH . C 3 HOH A 178 2989 178 HOH HOH . C 3 HOH A 179 2990 179 HOH HOH . C 3 HOH A 180 2991 180 HOH HOH . C 3 HOH A 181 2992 181 HOH HOH . C 3 HOH A 182 2993 182 HOH HOH . C 3 HOH A 183 2994 183 HOH HOH . C 3 HOH A 184 2995 184 HOH HOH . C 3 HOH A 185 2996 185 HOH HOH . C 3 HOH A 186 2997 186 HOH HOH . C 3 HOH A 187 2998 187 HOH HOH . C 3 HOH A 188 2999 188 HOH HOH . C 3 HOH A 189 3000 189 HOH HOH . C 3 HOH A 190 3001 190 HOH HOH . C 3 HOH A 191 3002 191 HOH HOH . C 3 HOH A 192 3003 192 HOH HOH . C 3 HOH A 193 3004 193 HOH HOH . C 3 HOH A 194 3005 194 HOH HOH . C 3 HOH A 195 3006 195 HOH HOH . C 3 HOH A 196 3007 196 HOH HOH . C 3 HOH A 197 3008 197 HOH HOH . C 3 HOH A 198 3009 198 HOH HOH . C 3 HOH A 199 3010 199 HOH HOH . C 3 HOH A 200 3011 200 HOH HOH . C 3 HOH A 201 3012 201 HOH HOH . C 3 HOH A 202 3013 202 HOH HOH . C 3 HOH A 203 3014 203 HOH HOH . C 3 HOH A 204 3015 204 HOH HOH . C 3 HOH A 205 3016 205 HOH HOH . C 3 HOH A 206 3017 206 HOH HOH . C 3 HOH A 207 3018 207 HOH HOH . C 3 HOH A 208 3019 208 HOH HOH . C 3 HOH A 209 3020 209 HOH HOH . C 3 HOH A 210 3021 210 HOH HOH . C 3 HOH A 211 3022 211 HOH HOH . C 3 HOH A 212 3023 212 HOH HOH . C 3 HOH A 213 3024 213 HOH HOH . C 3 HOH A 214 3025 214 HOH HOH . C 3 HOH A 215 3026 215 HOH HOH . C 3 HOH A 216 3027 216 HOH HOH . C 3 HOH A 217 3028 217 HOH HOH . C 3 HOH A 218 3029 218 HOH HOH . C 3 HOH A 219 3030 219 HOH HOH . C 3 HOH A 220 3031 220 HOH HOH . C 3 HOH A 221 3032 221 HOH HOH . C 3 HOH A 222 3033 222 HOH HOH . C 3 HOH A 223 3034 223 HOH HOH . C 3 HOH A 224 3035 224 HOH HOH . C 3 HOH A 225 3036 225 HOH HOH . C 3 HOH A 226 3037 226 HOH HOH . C 3 HOH A 227 3038 227 HOH HOH . C 3 HOH A 228 3039 228 HOH HOH . C 3 HOH A 229 3040 229 HOH HOH . C 3 HOH A 230 3041 230 HOH HOH . C 3 HOH A 231 3042 231 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 P P1 DPO . . . B 2 3.862 29.147 28.209 1 44.39 ? P1 DPO 2811 A 1 HETATM 2 O O1 DPO . . . B 2 3.907 30.263 27.11 1 41.82 ? O1 DPO 2811 A 1 HETATM 3 O O2 DPO . . . B 2 3.414 29.451 29.58 1 20.41 ? O2 DPO 2811 A 1 HETATM 4 O O3 DPO . . . B 2 3.368 27.825 27.725 1 35.74 ? O3 DPO 2811 A 1 HETATM 5 O O4 DPO . . . B 2 5.443 29.094 28.523 1 46.85 ? O4 DPO 2811 A 1 HETATM 6 P P2 DPO . . . B 2 6.068 30.56 28.768 1 51.29 ? P2 DPO 2811 A 1 HETATM 7 O O5 DPO . . . B 2 6.633 30.531 30.187 1 46.04 ? O5 DPO 2811 A 1 HETATM 8 O O6 DPO . . . B 2 6.973 30.764 27.564 1 49.25 ? O6 DPO 2811 A 1 HETATM 9 O O7 DPO . . . B 2 4.935 31.562 28.62 1 41.38 ? O7 DPO 2811 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 9 #