data_4DG8 # _model_server_result.job_id pbbK2meL6q9bg-6W2KYDZw _model_server_result.datetime_utc '2024-10-13 01:23:19' _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 4dg8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 4DG8 # _exptl.entry_id 4DG8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 4DG8 _cell.length_a 92.565 _cell.length_b 92.565 _cell.length_c 164.391 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DG8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 4DG8 _atom_sites.fract_transf_matrix[1][1] 0.010803 _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] 0.010803 _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] 0.006083 _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 AMP A 1 701 551 AMP AMP . C 3 BU3 A 1 702 1 BU3 BU3 . D 3 BU3 A 1 703 2 BU3 BU3 . E 4 HOH A 1 801 1 HOH HOH . E 4 HOH A 2 802 2 HOH HOH . E 4 HOH A 3 803 3 HOH HOH . E 4 HOH A 4 804 4 HOH HOH . E 4 HOH A 5 805 5 HOH HOH . E 4 HOH A 6 806 6 HOH HOH . E 4 HOH A 7 807 7 HOH HOH . E 4 HOH A 8 808 8 HOH HOH . E 4 HOH A 9 809 9 HOH HOH . E 4 HOH A 10 810 10 HOH HOH . E 4 HOH A 11 811 11 HOH HOH . E 4 HOH A 12 812 13 HOH HOH . E 4 HOH A 13 813 14 HOH HOH . E 4 HOH A 14 814 15 HOH HOH . E 4 HOH A 15 815 16 HOH HOH . E 4 HOH A 16 816 17 HOH HOH . E 4 HOH A 17 817 18 HOH HOH . E 4 HOH A 18 818 19 HOH HOH . E 4 HOH A 19 819 20 HOH HOH . E 4 HOH A 20 820 21 HOH HOH . E 4 HOH A 21 821 22 HOH HOH . E 4 HOH A 22 822 23 HOH HOH . E 4 HOH A 23 823 24 HOH HOH . E 4 HOH A 24 824 25 HOH HOH . E 4 HOH A 25 825 26 HOH HOH . E 4 HOH A 26 826 27 HOH HOH . E 4 HOH A 27 827 28 HOH HOH . E 4 HOH A 28 828 29 HOH HOH . E 4 HOH A 29 829 30 HOH HOH . E 4 HOH A 30 830 32 HOH HOH . E 4 HOH A 31 831 33 HOH HOH . E 4 HOH A 32 832 34 HOH HOH . E 4 HOH A 33 833 35 HOH HOH . E 4 HOH A 34 834 36 HOH HOH . E 4 HOH A 35 835 37 HOH HOH . E 4 HOH A 36 836 38 HOH HOH . E 4 HOH A 37 837 39 HOH HOH . E 4 HOH A 38 838 40 HOH HOH . E 4 HOH A 39 839 41 HOH HOH . E 4 HOH A 40 840 42 HOH HOH . E 4 HOH A 41 841 43 HOH HOH . E 4 HOH A 42 842 44 HOH HOH . E 4 HOH A 43 843 45 HOH HOH . E 4 HOH A 44 844 46 HOH HOH . E 4 HOH A 45 845 47 HOH HOH . E 4 HOH A 46 846 48 HOH HOH . E 4 HOH A 47 847 50 HOH HOH . E 4 HOH A 48 848 51 HOH HOH . E 4 HOH A 49 849 52 HOH HOH . E 4 HOH A 50 850 53 HOH HOH . E 4 HOH A 51 851 54 HOH HOH . E 4 HOH A 52 852 56 HOH HOH . E 4 HOH A 53 853 57 HOH HOH . E 4 HOH A 54 854 59 HOH HOH . E 4 HOH A 55 855 60 HOH HOH . E 4 HOH A 56 856 61 HOH HOH . E 4 HOH A 57 857 62 HOH HOH . E 4 HOH A 58 858 63 HOH HOH . E 4 HOH A 59 859 64 HOH HOH . E 4 HOH A 60 860 65 HOH HOH . E 4 HOH A 61 861 67 HOH HOH . E 4 HOH A 62 862 68 HOH HOH . E 4 HOH A 63 863 69 HOH HOH . E 4 HOH A 64 864 70 HOH HOH . E 4 HOH A 65 865 71 HOH HOH . E 4 HOH A 66 866 72 HOH HOH . E 4 HOH A 67 867 73 HOH HOH . E 4 HOH A 68 868 74 HOH HOH . E 4 HOH A 69 869 75 HOH HOH . E 4 HOH A 70 870 76 HOH HOH . E 4 HOH A 71 871 77 HOH HOH . E 4 HOH A 72 872 78 HOH HOH . E 4 HOH A 73 873 79 HOH HOH . E 4 HOH A 74 874 80 HOH HOH . E 4 HOH A 75 875 81 HOH HOH . E 4 HOH A 76 876 82 HOH HOH . E 4 HOH A 77 877 83 HOH HOH . E 4 HOH A 78 878 85 HOH HOH . E 4 HOH A 79 879 86 HOH HOH . E 4 HOH A 80 880 87 HOH HOH . E 4 HOH A 81 881 88 HOH HOH . E 4 HOH A 82 882 89 HOH HOH . E 4 HOH A 83 883 91 HOH HOH . E 4 HOH A 84 884 92 HOH HOH . E 4 HOH A 85 885 93 HOH HOH . E 4 HOH A 86 886 94 HOH HOH . E 4 HOH A 87 887 96 HOH HOH . E 4 HOH A 88 888 97 HOH HOH . E 4 HOH A 89 889 98 HOH HOH . E 4 HOH A 90 890 99 HOH HOH . E 4 HOH A 91 891 100 HOH HOH . E 4 HOH A 92 892 101 HOH HOH . E 4 HOH A 93 893 102 HOH HOH . E 4 HOH A 94 894 103 HOH HOH . E 4 HOH A 95 895 104 HOH HOH . E 4 HOH A 96 896 105 HOH HOH . E 4 HOH A 97 897 106 HOH HOH . E 4 HOH A 98 898 107 HOH HOH . E 4 HOH A 99 899 108 HOH HOH . E 4 HOH A 100 900 109 HOH HOH . E 4 HOH A 101 901 110 HOH HOH . E 4 HOH A 102 902 111 HOH HOH . E 4 HOH A 103 903 112 HOH HOH . E 4 HOH A 104 904 115 HOH HOH . E 4 HOH A 105 905 116 HOH HOH . E 4 HOH A 106 906 117 HOH HOH . E 4 HOH A 107 907 118 HOH HOH . E 4 HOH A 108 908 119 HOH HOH . E 4 HOH A 109 909 120 HOH HOH . E 4 HOH A 110 910 121 HOH HOH . E 4 HOH A 111 911 122 HOH HOH . E 4 HOH A 112 912 123 HOH HOH . E 4 HOH A 113 913 125 HOH HOH . E 4 HOH A 114 914 127 HOH HOH . E 4 HOH A 115 915 128 HOH HOH . E 4 HOH A 116 916 129 HOH HOH . E 4 HOH A 117 917 130 HOH HOH . E 4 HOH A 118 918 131 HOH HOH . E 4 HOH A 119 919 132 HOH HOH . E 4 HOH A 120 920 133 HOH HOH . E 4 HOH A 121 921 134 HOH HOH . E 4 HOH A 122 922 135 HOH HOH . E 4 HOH A 123 923 136 HOH HOH . E 4 HOH A 124 924 137 HOH HOH . E 4 HOH A 125 925 139 HOH HOH . E 4 HOH A 126 926 140 HOH HOH . E 4 HOH A 127 927 141 HOH HOH . E 4 HOH A 128 928 142 HOH HOH . E 4 HOH A 129 929 143 HOH HOH . E 4 HOH A 130 930 144 HOH HOH . E 4 HOH A 131 931 145 HOH HOH . E 4 HOH A 132 932 146 HOH HOH . E 4 HOH A 133 933 148 HOH HOH . E 4 HOH A 134 934 149 HOH HOH . E 4 HOH A 135 935 150 HOH HOH . E 4 HOH A 136 936 151 HOH HOH . E 4 HOH A 137 937 152 HOH HOH . E 4 HOH A 138 938 153 HOH HOH . E 4 HOH A 139 939 154 HOH HOH . E 4 HOH A 140 940 155 HOH HOH . E 4 HOH A 141 941 156 HOH HOH . E 4 HOH A 142 942 157 HOH HOH . E 4 HOH A 143 943 158 HOH HOH . E 4 HOH A 144 944 159 HOH HOH . E 4 HOH A 145 945 160 HOH HOH . E 4 HOH A 146 946 161 HOH HOH . E 4 HOH A 147 947 162 HOH HOH . E 4 HOH A 148 948 163 HOH HOH . E 4 HOH A 149 949 164 HOH HOH . E 4 HOH A 150 950 165 HOH HOH . E 4 HOH A 151 951 166 HOH HOH . E 4 HOH A 152 952 167 HOH HOH . E 4 HOH A 153 953 168 HOH HOH . E 4 HOH A 154 954 169 HOH HOH . E 4 HOH A 155 955 170 HOH HOH . E 4 HOH A 156 956 171 HOH HOH . E 4 HOH A 157 957 172 HOH HOH . E 4 HOH A 158 958 173 HOH HOH . E 4 HOH A 159 959 174 HOH HOH . E 4 HOH A 160 960 175 HOH HOH . E 4 HOH A 161 961 176 HOH HOH . E 4 HOH A 162 962 177 HOH HOH . E 4 HOH A 163 963 178 HOH HOH . E 4 HOH A 164 964 179 HOH HOH . E 4 HOH A 165 965 180 HOH HOH . E 4 HOH A 166 966 181 HOH HOH . E 4 HOH A 167 967 182 HOH HOH . E 4 HOH A 168 968 183 HOH HOH . E 4 HOH A 169 969 184 HOH HOH . E 4 HOH A 170 970 185 HOH HOH . E 4 HOH A 171 971 186 HOH HOH . E 4 HOH A 172 972 187 HOH HOH . E 4 HOH A 173 973 188 HOH HOH . E 4 HOH A 174 974 189 HOH HOH . E 4 HOH A 175 975 190 HOH HOH . E 4 HOH A 176 976 191 HOH HOH . E 4 HOH A 177 977 192 HOH HOH . E 4 HOH A 178 978 193 HOH HOH . E 4 HOH A 179 979 194 HOH HOH . E 4 HOH A 180 980 195 HOH HOH . E 4 HOH A 181 981 196 HOH HOH . E 4 HOH A 182 982 197 HOH HOH . E 4 HOH A 183 983 198 HOH HOH . E 4 HOH A 184 984 199 HOH HOH . E 4 HOH A 185 985 200 HOH HOH . E 4 HOH A 186 986 201 HOH HOH . E 4 HOH A 187 987 202 HOH HOH . E 4 HOH A 188 988 203 HOH HOH . E 4 HOH A 189 989 204 HOH HOH . E 4 HOH A 190 990 205 HOH HOH . E 4 HOH A 191 991 206 HOH HOH . E 4 HOH A 192 992 207 HOH HOH . E 4 HOH A 193 993 208 HOH HOH . E 4 HOH A 194 994 209 HOH HOH . E 4 HOH A 195 995 210 HOH HOH . E 4 HOH A 196 996 211 HOH HOH . E 4 HOH A 197 997 212 HOH HOH . E 4 HOH A 198 998 213 HOH HOH . E 4 HOH A 199 999 214 HOH HOH . E 4 HOH A 200 1000 215 HOH HOH . E 4 HOH A 201 1001 216 HOH HOH . E 4 HOH A 202 1002 217 HOH HOH . E 4 HOH A 203 1003 218 HOH HOH . E 4 HOH A 204 1004 219 HOH HOH . E 4 HOH A 205 1005 220 HOH HOH . E 4 HOH A 206 1006 221 HOH HOH . E 4 HOH A 207 1007 222 HOH HOH . E 4 HOH A 208 1008 224 HOH HOH . E 4 HOH A 209 1009 225 HOH HOH . E 4 HOH A 210 1010 227 HOH HOH . E 4 HOH A 211 1011 228 HOH HOH . E 4 HOH A 212 1012 229 HOH HOH . E 4 HOH A 213 1013 230 HOH HOH . E 4 HOH A 214 1014 231 HOH HOH . E 4 HOH A 215 1015 232 HOH HOH . E 4 HOH A 216 1016 233 HOH HOH . E 4 HOH A 217 1017 234 HOH HOH . E 4 HOH A 218 1018 235 HOH HOH . E 4 HOH A 219 1019 236 HOH HOH . E 4 HOH A 220 1020 237 HOH HOH . E 4 HOH A 221 1021 238 HOH HOH . E 4 HOH A 222 1022 239 HOH HOH . E 4 HOH A 223 1023 240 HOH HOH . E 4 HOH A 224 1024 241 HOH HOH . E 4 HOH A 225 1025 242 HOH HOH . E 4 HOH A 226 1026 243 HOH HOH . E 4 HOH A 227 1027 244 HOH HOH . E 4 HOH A 228 1028 245 HOH HOH . E 4 HOH A 229 1029 246 HOH HOH . E 4 HOH A 230 1030 247 HOH HOH . E 4 HOH A 231 1031 248 HOH HOH . E 4 HOH A 232 1032 249 HOH HOH . E 4 HOH A 233 1033 250 HOH HOH . E 4 HOH A 234 1034 251 HOH HOH . E 4 HOH A 235 1035 252 HOH HOH . E 4 HOH A 236 1036 253 HOH HOH . E 4 HOH A 237 1037 254 HOH HOH . E 4 HOH A 238 1038 255 HOH HOH . E 4 HOH A 239 1039 256 HOH HOH . E 4 HOH A 240 1040 257 HOH HOH . E 4 HOH A 241 1041 258 HOH HOH . E 4 HOH A 242 1042 259 HOH HOH . E 4 HOH A 243 1043 260 HOH HOH . E 4 HOH A 244 1044 261 HOH HOH . E 4 HOH A 245 1045 262 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 P AMP . . . B 2 0.749 26.559 18.314 1 26.02 ? P AMP 701 A 1 HETATM 2 O O1P AMP . . . B 2 0.391 25.519 17.274 1 21.91 ? O1P AMP 701 A 1 HETATM 3 O O2P AMP . . . B 2 0.623 26.189 19.786 1 21.46 ? O2P AMP 701 A 1 HETATM 4 O O3P AMP . . . B 2 2.162 27.015 18 1 18.74 ? O3P AMP 701 A 1 HETATM 5 O O5' AMP . . . B 2 -0.071 27.892 18.037 1 23.28 ? O5' AMP 701 A 1 HETATM 6 C C5' AMP . . . B 2 0.26 29.092 18.708 1 19.44 ? C5' AMP 701 A 1 HETATM 7 C C4' AMP . . . B 2 -0.678 30.209 18.342 1 26.58 ? C4' AMP 701 A 1 HETATM 8 O O4' AMP . . . B 2 -2.048 29.825 18.633 1 25.16 ? O4' AMP 701 A 1 HETATM 9 C C3' AMP . . . B 2 -0.484 31.506 19.106 1 27.62 ? C3' AMP 701 A 1 HETATM 10 O O3' AMP . . . B 2 0.583 32.294 18.59 1 25.55 ? O3' AMP 701 A 1 HETATM 11 C C2' AMP . . . B 2 -1.851 32.166 18.992 1 26.56 ? C2' AMP 701 A 1 HETATM 12 O O2' AMP . . . B 2 -2.007 32.768 17.712 1 24.71 ? O2' AMP 701 A 1 HETATM 13 C C1' AMP . . . B 2 -2.782 30.953 19.075 1 22.01 ? C1' AMP 701 A 1 HETATM 14 N N9 AMP . . . B 2 -3.243 30.7 20.46 1 25.49 ? N9 AMP 701 A 1 HETATM 15 C C8 AMP . . . B 2 -2.742 29.741 21.275 1 23.02 ? C8 AMP 701 A 1 HETATM 16 N N7 AMP . . . B 2 -3.355 29.742 22.484 1 22.04 ? N7 AMP 701 A 1 HETATM 17 C C5 AMP . . . B 2 -4.269 30.724 22.477 1 26.91 ? C5 AMP 701 A 1 HETATM 18 C C6 AMP . . . B 2 -5.263 31.267 23.443 1 23.79 ? C6 AMP 701 A 1 HETATM 19 N N6 AMP . . . B 2 -5.39 30.749 24.678 1 20.51 ? N6 AMP 701 A 1 HETATM 20 N N1 AMP . . . B 2 -6.044 32.3 23.043 1 28.59 ? N1 AMP 701 A 1 HETATM 21 C C2 AMP . . . B 2 -5.917 32.816 21.802 1 23.97 ? C2 AMP 701 A 1 HETATM 22 N N3 AMP . . . B 2 -5.04 32.371 20.879 1 22.74 ? N3 AMP 701 A 1 HETATM 23 C C4 AMP . . . B 2 -4.199 31.346 21.139 1 23.44 ? C4 AMP 701 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 23 #