data_1YVD # _model_server_result.job_id 3vSkcdx5Eu16MpAmv6wV_A _model_server_result.datetime_utc '2024-11-23 15:40:16' _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 1yvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":850}' # _entry.id 1YVD # _exptl.entry_id 1YVD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 24.305 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM ION' _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 1YVD _cell.length_a 45.536 _cell.length_b 45.536 _cell.length_c 150.338 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YVD _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 # 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 OG SER 19 A SER 19 1_555 B MG MG . A MG 850 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc2 A OG1 THR 37 A THR 37 1_555 B MG MG . A MG 850 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc3 B MG MG . A MG 850 1_555 C O2G GNP . A GNP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc4 B MG MG . A MG 850 1_555 C O2B GNP . A GNP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc5 B MG MG . A MG 850 1_555 D O HOH . A HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc6 B MG MG . A MG 850 1_555 D O HOH . A HOH 916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? # _chem_comp.formula 'Mg 2' _chem_comp.formula_weight 24.305 _chem_comp.id MG _chem_comp.mon_nstd_flag . _chem_comp.name 'MAGNESIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1YVD _atom_sites.fract_transf_matrix[1][1] 0.021961 _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] 0.021961 _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] 0.006652 _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 MG A 1 850 300 MG MG . C 3 GNP A 1 900 200 GNP GNP . D 4 HOH A 1 901 1 HOH HOH . D 4 HOH A 2 902 2 HOH HOH . D 4 HOH A 3 903 3 HOH HOH . D 4 HOH A 4 904 4 HOH HOH . D 4 HOH A 5 905 5 HOH HOH . D 4 HOH A 6 906 6 HOH HOH . D 4 HOH A 7 907 7 HOH HOH . D 4 HOH A 8 908 8 HOH HOH . D 4 HOH A 9 909 9 HOH HOH . D 4 HOH A 10 910 10 HOH HOH . D 4 HOH A 11 911 11 HOH HOH . D 4 HOH A 12 912 12 HOH HOH . D 4 HOH A 13 913 13 HOH HOH . D 4 HOH A 14 914 14 HOH HOH . D 4 HOH A 15 915 15 HOH HOH . D 4 HOH A 16 916 16 HOH HOH . D 4 HOH A 17 917 17 HOH HOH . D 4 HOH A 18 918 18 HOH HOH . D 4 HOH A 19 919 19 HOH HOH . D 4 HOH A 20 920 20 HOH HOH . D 4 HOH A 21 921 21 HOH HOH . D 4 HOH A 22 922 22 HOH HOH . D 4 HOH A 23 923 23 HOH HOH . D 4 HOH A 24 924 24 HOH HOH . D 4 HOH A 25 925 25 HOH HOH . D 4 HOH A 26 926 26 HOH HOH . D 4 HOH A 27 927 27 HOH HOH . D 4 HOH A 28 928 29 HOH HOH . D 4 HOH A 29 929 30 HOH HOH . D 4 HOH A 30 930 31 HOH HOH . D 4 HOH A 31 931 32 HOH HOH . D 4 HOH A 32 932 34 HOH HOH . D 4 HOH A 33 933 35 HOH HOH . D 4 HOH A 34 934 36 HOH HOH . D 4 HOH A 35 935 37 HOH HOH . D 4 HOH A 36 936 38 HOH HOH . D 4 HOH A 37 937 39 HOH HOH . D 4 HOH A 38 938 40 HOH HOH . D 4 HOH A 39 939 41 HOH HOH . D 4 HOH A 40 940 42 HOH HOH . D 4 HOH A 41 941 43 HOH HOH . D 4 HOH A 42 942 44 HOH HOH . D 4 HOH A 43 943 45 HOH HOH . D 4 HOH A 44 944 46 HOH HOH . D 4 HOH A 45 945 47 HOH HOH . D 4 HOH A 46 946 48 HOH HOH . D 4 HOH A 47 947 49 HOH HOH . D 4 HOH A 48 948 50 HOH HOH . D 4 HOH A 49 949 52 HOH HOH . D 4 HOH A 50 950 54 HOH HOH . D 4 HOH A 51 951 55 HOH HOH . D 4 HOH A 52 952 56 HOH HOH . D 4 HOH A 53 953 57 HOH HOH . D 4 HOH A 54 954 58 HOH HOH . D 4 HOH A 55 955 60 HOH HOH . D 4 HOH A 56 956 61 HOH HOH . D 4 HOH A 57 957 62 HOH HOH . D 4 HOH A 58 958 63 HOH HOH . D 4 HOH A 59 959 64 HOH HOH . D 4 HOH A 60 960 65 HOH HOH . D 4 HOH A 61 961 66 HOH HOH . D 4 HOH A 62 962 67 HOH HOH . D 4 HOH A 63 963 69 HOH HOH . D 4 HOH A 64 964 70 HOH HOH . D 4 HOH A 65 965 71 HOH HOH . D 4 HOH A 66 966 72 HOH HOH . D 4 HOH A 67 967 73 HOH HOH . D 4 HOH A 68 968 74 HOH HOH . D 4 HOH A 69 969 75 HOH HOH . D 4 HOH A 70 970 76 HOH HOH . D 4 HOH A 71 971 77 HOH HOH . D 4 HOH A 72 972 79 HOH HOH . D 4 HOH A 73 973 80 HOH HOH . D 4 HOH A 74 974 81 HOH HOH . D 4 HOH A 75 975 82 HOH HOH . D 4 HOH A 76 976 83 HOH HOH . D 4 HOH A 77 977 84 HOH HOH . D 4 HOH A 78 978 85 HOH HOH . D 4 HOH A 79 979 87 HOH HOH . D 4 HOH A 80 980 88 HOH HOH . D 4 HOH A 81 981 89 HOH HOH . D 4 HOH A 82 982 90 HOH HOH . D 4 HOH A 83 983 91 HOH HOH . D 4 HOH A 84 984 92 HOH HOH . D 4 HOH A 85 985 93 HOH HOH . D 4 HOH A 86 986 94 HOH HOH . D 4 HOH A 87 987 95 HOH HOH . D 4 HOH A 88 988 96 HOH HOH . D 4 HOH A 89 989 97 HOH HOH . D 4 HOH A 90 990 99 HOH HOH . D 4 HOH A 91 991 100 HOH HOH . D 4 HOH A 92 992 101 HOH HOH . D 4 HOH A 93 993 102 HOH HOH . D 4 HOH A 94 994 103 HOH HOH . D 4 HOH A 95 995 104 HOH HOH . D 4 HOH A 96 996 105 HOH HOH . D 4 HOH A 97 997 106 HOH HOH . D 4 HOH A 98 998 107 HOH HOH . D 4 HOH A 99 999 108 HOH HOH . D 4 HOH A 100 1000 109 HOH HOH . D 4 HOH A 101 1001 110 HOH HOH . D 4 HOH A 102 1002 111 HOH HOH . D 4 HOH A 103 1003 114 HOH HOH . D 4 HOH A 104 1004 115 HOH HOH . D 4 HOH A 105 1005 116 HOH HOH . D 4 HOH A 106 1006 117 HOH HOH . D 4 HOH A 107 1007 118 HOH HOH . D 4 HOH A 108 1008 119 HOH HOH . D 4 HOH A 109 1009 120 HOH HOH . D 4 HOH A 110 1010 121 HOH HOH . D 4 HOH A 111 1011 122 HOH HOH . D 4 HOH A 112 1012 123 HOH HOH . D 4 HOH A 113 1013 124 HOH HOH . D 4 HOH A 114 1014 126 HOH HOH . D 4 HOH A 115 1015 128 HOH HOH . D 4 HOH A 116 1016 130 HOH HOH . D 4 HOH A 117 1017 131 HOH HOH . D 4 HOH A 118 1018 132 HOH HOH . D 4 HOH A 119 1019 133 HOH HOH . D 4 HOH A 120 1020 135 HOH HOH . D 4 HOH A 121 1021 136 HOH HOH . D 4 HOH A 122 1022 138 HOH HOH . D 4 HOH A 123 1023 139 HOH HOH . D 4 HOH A 124 1024 140 HOH HOH . D 4 HOH A 125 1025 141 HOH HOH . D 4 HOH A 126 1026 142 HOH HOH . D 4 HOH A 127 1027 144 HOH HOH . D 4 HOH A 128 1028 145 HOH HOH . D 4 HOH A 129 1029 147 HOH HOH . D 4 HOH A 130 1030 149 HOH HOH . D 4 HOH A 131 1031 150 HOH HOH . D 4 HOH A 132 1032 153 HOH HOH . D 4 HOH A 133 1033 154 HOH HOH . D 4 HOH A 134 1034 155 HOH HOH . D 4 HOH A 135 1035 157 HOH HOH . D 4 HOH A 136 1036 158 HOH HOH . D 4 HOH A 137 1037 159 HOH HOH . D 4 HOH A 138 1038 160 HOH HOH . D 4 HOH A 139 1039 161 HOH HOH . D 4 HOH A 140 1040 162 HOH HOH . D 4 HOH A 141 1041 163 HOH HOH . D 4 HOH A 142 1042 164 HOH HOH . D 4 HOH A 143 1043 166 HOH HOH . D 4 HOH A 144 1044 167 HOH HOH . D 4 HOH A 145 1045 168 HOH HOH . D 4 HOH A 146 1046 169 HOH HOH . D 4 HOH A 147 1047 170 HOH HOH . D 4 HOH A 148 1048 171 HOH HOH . D 4 HOH A 149 1049 172 HOH HOH . D 4 HOH A 150 1050 173 HOH HOH . D 4 HOH A 151 1051 177 HOH HOH . D 4 HOH A 152 1052 178 HOH HOH . D 4 HOH A 153 1053 179 HOH HOH . D 4 HOH A 154 1054 181 HOH HOH . D 4 HOH A 155 1055 182 HOH HOH . D 4 HOH A 156 1056 183 HOH HOH . D 4 HOH A 157 1057 184 HOH HOH . D 4 HOH A 158 1058 186 HOH HOH . D 4 HOH A 159 1059 189 HOH HOH . D 4 HOH A 160 1060 190 HOH HOH . D 4 HOH A 161 1061 192 HOH HOH . D 4 HOH A 162 1062 193 HOH HOH . D 4 HOH A 163 1063 195 HOH HOH . D 4 HOH A 164 1064 197 HOH HOH . D 4 HOH A 165 1065 198 HOH HOH . D 4 HOH A 166 1066 199 HOH HOH . D 4 HOH A 167 1067 200 HOH HOH . D 4 HOH A 168 1068 201 HOH HOH . D 4 HOH A 169 1069 202 HOH HOH . D 4 HOH A 170 1070 203 HOH HOH . D 4 HOH A 171 1071 204 HOH HOH . D 4 HOH A 172 1072 205 HOH HOH . D 4 HOH A 173 1073 206 HOH HOH . D 4 HOH A 174 1074 208 HOH HOH . D 4 HOH A 175 1075 209 HOH HOH . D 4 HOH A 176 1076 210 HOH HOH . D 4 HOH A 177 1077 211 HOH HOH . D 4 HOH A 178 1078 215 HOH HOH . D 4 HOH A 179 1079 217 HOH HOH . D 4 HOH A 180 1080 219 HOH HOH . D 4 HOH A 181 1081 220 HOH HOH . D 4 HOH A 182 1082 221 HOH HOH . D 4 HOH A 183 1083 222 HOH HOH . D 4 HOH A 184 1084 223 HOH HOH . D 4 HOH A 185 1085 224 HOH HOH . D 4 HOH A 186 1086 225 HOH HOH . D 4 HOH A 187 1087 226 HOH HOH . D 4 HOH A 188 1088 228 HOH HOH . D 4 HOH A 189 1089 229 HOH HOH . D 4 HOH A 190 1090 230 HOH HOH . D 4 HOH A 191 1091 232 HOH HOH . D 4 HOH A 192 1092 233 HOH HOH . D 4 HOH A 193 1093 234 HOH HOH . D 4 HOH A 194 1094 235 HOH HOH . D 4 HOH A 195 1095 236 HOH HOH . D 4 HOH A 196 1096 237 HOH HOH . D 4 HOH A 197 1097 239 HOH HOH . D 4 HOH A 198 1098 240 HOH HOH . D 4 HOH A 199 1099 242 HOH HOH . D 4 HOH A 200 1100 246 HOH HOH . D 4 HOH A 201 1101 247 HOH HOH . D 4 HOH A 202 1102 248 HOH HOH . D 4 HOH A 203 1103 249 HOH HOH . D 4 HOH A 204 1104 252 HOH HOH . D 4 HOH A 205 1105 253 HOH HOH . D 4 HOH A 206 1106 255 HOH HOH . D 4 HOH A 207 1107 259 HOH HOH . D 4 HOH A 208 1108 260 HOH HOH . D 4 HOH A 209 1109 263 HOH HOH . D 4 HOH A 210 1110 264 HOH HOH . D 4 HOH A 211 1111 270 HOH HOH . D 4 HOH A 212 1112 272 HOH HOH . D 4 HOH A 213 1113 273 HOH HOH . D 4 HOH A 214 1114 274 HOH HOH . D 4 HOH A 215 1115 276 HOH HOH . D 4 HOH A 216 1116 281 HOH HOH . D 4 HOH A 217 1117 285 HOH HOH . D 4 HOH A 218 1118 289 HOH HOH . D 4 HOH A 219 1119 300 HOH HOH . D 4 HOH A 220 1120 301 HOH HOH . D 4 HOH A 221 1121 302 HOH HOH . D 4 HOH A 222 1122 308 HOH HOH . D 4 HOH A 223 1123 320 HOH HOH . D 4 HOH A 224 1124 321 HOH HOH . D 4 HOH A 225 1125 334 HOH HOH . D 4 HOH A 226 1126 339 HOH HOH . D 4 HOH A 227 1127 341 HOH HOH . D 4 HOH A 228 1128 343 HOH HOH . D 4 HOH A 229 1129 344 HOH HOH . D 4 HOH A 230 1130 357 HOH HOH . D 4 HOH A 231 1131 376 HOH HOH . D 4 HOH A 232 1132 377 HOH HOH . D 4 HOH A 233 1133 392 HOH HOH . D 4 HOH A 234 1134 395 HOH HOH . D 4 HOH A 235 1135 398 HOH HOH . D 4 HOH A 236 1136 408 HOH HOH . D 4 HOH A 237 1137 421 HOH HOH . D 4 HOH A 238 1138 425 HOH HOH . D 4 HOH A 239 1139 427 HOH HOH . D 4 HOH A 240 1140 429 HOH HOH . D 4 HOH A 241 1141 445 HOH HOH . D 4 HOH A 242 1142 567 HOH HOH . D 4 HOH A 243 1143 595 HOH HOH . D 4 HOH A 244 1144 633 HOH HOH . D 4 HOH A 245 1145 806 HOH HOH . D 4 HOH A 246 1146 811 HOH HOH . D 4 HOH A 247 1147 814 HOH HOH . D 4 HOH A 248 1148 815 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MG _atom_site.label_atom_id MG _atom_site.label_comp_id MG _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id B _atom_site.label_entity_id 2 _atom_site.Cartn_x 33.992 _atom_site.Cartn_y 22.796 _atom_site.Cartn_z 38.939 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 13.34 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 850 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #