data_3DKD # _model_server_result.job_id 80y2KgOivTR1sBRwquQOOA _model_server_result.datetime_utc '2024-11-16 21:41:24' _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 3dkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":142}' # _entry.id 3DKD # _exptl.entry_id 3DKD _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 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 120 _cell.entry_id 3DKD _cell.length_a 70.07 _cell.length_b 70.07 _cell.length_c 103.221 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 35.035 60.6824 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -35.035 60.6824 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 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 C MG MG . A MG 142 1_555 D O1B GDP . A GDP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc2 C MG MG . A MG 142 1_555 G O HOH . A HOH 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc3 E MG MG . B MG 142 1_555 F O1B GDP . B GDP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc4 E MG MG . B MG 142 1_555 F O1A GDP . B GDP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc5 E MG MG . B MG 142 1_555 H O HOH . B HOH 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? # _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 3DKD _atom_sites.fract_transf_matrix[1][1] 0.014271 _atom_sites.fract_transf_matrix[1][2] 0.00824 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016479 _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] 0.009688 _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 C 2 MG A 1 142 1 MG MG . D 3 GDP A 1 143 1 GDP GDP . E 2 MG B 1 142 1 MG MG . F 3 GDP B 1 143 1 GDP GDP . G 4 HOH A 1 144 1 HOH HOH . G 4 HOH A 2 145 2 HOH HOH . G 4 HOH A 3 146 4 HOH HOH . G 4 HOH A 4 147 5 HOH HOH . G 4 HOH A 5 148 8 HOH HOH . G 4 HOH A 6 149 9 HOH HOH . G 4 HOH A 7 150 10 HOH HOH . G 4 HOH A 8 151 11 HOH HOH . G 4 HOH A 9 152 14 HOH HOH . G 4 HOH A 10 153 17 HOH HOH . G 4 HOH A 11 154 18 HOH HOH . G 4 HOH A 12 155 19 HOH HOH . G 4 HOH A 13 156 21 HOH HOH . G 4 HOH A 14 157 22 HOH HOH . G 4 HOH A 15 158 23 HOH HOH . G 4 HOH A 16 159 24 HOH HOH . G 4 HOH A 17 160 25 HOH HOH . G 4 HOH A 18 161 26 HOH HOH . G 4 HOH A 19 162 29 HOH HOH . G 4 HOH A 20 163 30 HOH HOH . G 4 HOH A 21 164 33 HOH HOH . G 4 HOH A 22 165 34 HOH HOH . G 4 HOH A 23 166 37 HOH HOH . G 4 HOH A 24 167 39 HOH HOH . G 4 HOH A 25 168 40 HOH HOH . G 4 HOH A 26 169 41 HOH HOH . G 4 HOH A 27 170 44 HOH HOH . G 4 HOH A 28 171 46 HOH HOH . G 4 HOH A 29 172 51 HOH HOH . G 4 HOH A 30 173 53 HOH HOH . G 4 HOH A 31 174 54 HOH HOH . G 4 HOH A 32 175 58 HOH HOH . G 4 HOH A 33 176 61 HOH HOH . G 4 HOH A 34 177 62 HOH HOH . G 4 HOH A 35 178 63 HOH HOH . G 4 HOH A 36 179 65 HOH HOH . G 4 HOH A 37 180 67 HOH HOH . G 4 HOH A 38 181 68 HOH HOH . G 4 HOH A 39 182 71 HOH HOH . G 4 HOH A 40 183 76 HOH HOH . G 4 HOH A 41 184 78 HOH HOH . G 4 HOH A 42 185 81 HOH HOH . G 4 HOH A 43 186 84 HOH HOH . G 4 HOH A 44 187 85 HOH HOH . G 4 HOH A 45 188 86 HOH HOH . G 4 HOH A 46 189 88 HOH HOH . G 4 HOH A 47 190 89 HOH HOH . G 4 HOH A 48 191 91 HOH HOH . G 4 HOH A 49 192 94 HOH HOH . G 4 HOH A 50 193 96 HOH HOH . G 4 HOH A 51 194 98 HOH HOH . G 4 HOH A 52 195 101 HOH HOH . G 4 HOH A 53 196 102 HOH HOH . G 4 HOH A 54 197 103 HOH HOH . G 4 HOH A 55 198 104 HOH HOH . G 4 HOH A 56 199 108 HOH HOH . G 4 HOH A 57 200 109 HOH HOH . G 4 HOH A 58 201 113 HOH HOH . G 4 HOH A 59 202 116 HOH HOH . G 4 HOH A 60 203 117 HOH HOH . G 4 HOH A 61 204 119 HOH HOH . G 4 HOH A 62 205 121 HOH HOH . G 4 HOH A 63 206 124 HOH HOH . G 4 HOH A 64 207 130 HOH HOH . G 4 HOH A 65 208 131 HOH HOH . G 4 HOH A 66 209 134 HOH HOH . G 4 HOH A 67 210 139 HOH HOH . G 4 HOH A 68 211 141 HOH HOH . G 4 HOH A 69 212 142 HOH HOH . G 4 HOH A 70 213 143 HOH HOH . G 4 HOH A 71 214 144 HOH HOH . G 4 HOH A 72 215 146 HOH HOH . G 4 HOH A 73 216 147 HOH HOH . G 4 HOH A 74 217 151 HOH HOH . G 4 HOH A 75 218 154 HOH HOH . G 4 HOH A 76 219 157 HOH HOH . G 4 HOH A 77 220 158 HOH HOH . G 4 HOH A 78 221 162 HOH HOH . G 4 HOH A 79 222 165 HOH HOH . G 4 HOH A 80 223 166 HOH HOH . G 4 HOH A 81 224 168 HOH HOH . G 4 HOH A 82 225 170 HOH HOH . G 4 HOH A 83 226 171 HOH HOH . G 4 HOH A 84 227 173 HOH HOH . G 4 HOH A 85 228 176 HOH HOH . G 4 HOH A 86 229 177 HOH HOH . G 4 HOH A 87 230 182 HOH HOH . G 4 HOH A 88 231 183 HOH HOH . G 4 HOH A 89 232 186 HOH HOH . G 4 HOH A 90 233 187 HOH HOH . G 4 HOH A 91 234 191 HOH HOH . G 4 HOH A 92 235 193 HOH HOH . G 4 HOH A 93 236 194 HOH HOH . G 4 HOH A 94 237 201 HOH HOH . G 4 HOH A 95 238 202 HOH HOH . G 4 HOH A 96 239 204 HOH HOH . G 4 HOH A 97 240 208 HOH HOH . G 4 HOH A 98 241 210 HOH HOH . G 4 HOH A 99 242 211 HOH HOH . G 4 HOH A 100 243 213 HOH HOH . G 4 HOH A 101 244 214 HOH HOH . G 4 HOH A 102 245 217 HOH HOH . G 4 HOH A 103 246 220 HOH HOH . G 4 HOH A 104 247 221 HOH HOH . G 4 HOH A 105 248 225 HOH HOH . G 4 HOH A 106 249 230 HOH HOH . G 4 HOH A 107 250 232 HOH HOH . G 4 HOH A 108 251 234 HOH HOH . G 4 HOH A 109 252 241 HOH HOH . G 4 HOH A 110 253 244 HOH HOH . G 4 HOH A 111 254 245 HOH HOH . G 4 HOH A 112 255 246 HOH HOH . G 4 HOH A 113 256 248 HOH HOH . G 4 HOH A 114 257 135 HOH HOH . G 4 HOH A 115 258 203 HOH HOH . H 4 HOH B 1 183 73 HOH HOH . H 4 HOH B 2 184 205 HOH HOH . H 4 HOH B 3 185 206 HOH HOH . H 4 HOH B 4 186 219 HOH HOH . H 4 HOH B 5 187 3 HOH HOH . H 4 HOH B 6 188 6 HOH HOH . H 4 HOH B 7 189 7 HOH HOH . H 4 HOH B 8 190 12 HOH HOH . H 4 HOH B 9 191 13 HOH HOH . H 4 HOH B 10 192 15 HOH HOH . H 4 HOH B 11 193 16 HOH HOH . H 4 HOH B 12 194 20 HOH HOH . H 4 HOH B 13 195 27 HOH HOH . H 4 HOH B 14 196 28 HOH HOH . H 4 HOH B 15 197 31 HOH HOH . H 4 HOH B 16 198 32 HOH HOH . H 4 HOH B 17 199 35 HOH HOH . H 4 HOH B 18 200 36 HOH HOH . H 4 HOH B 19 201 38 HOH HOH . H 4 HOH B 20 202 42 HOH HOH . H 4 HOH B 21 203 43 HOH HOH . H 4 HOH B 22 204 45 HOH HOH . H 4 HOH B 23 205 47 HOH HOH . H 4 HOH B 24 206 48 HOH HOH . H 4 HOH B 25 207 49 HOH HOH . H 4 HOH B 26 208 50 HOH HOH . H 4 HOH B 27 209 52 HOH HOH . H 4 HOH B 28 210 55 HOH HOH . H 4 HOH B 29 211 56 HOH HOH . H 4 HOH B 30 212 57 HOH HOH . H 4 HOH B 31 213 59 HOH HOH . H 4 HOH B 32 214 60 HOH HOH . H 4 HOH B 33 215 64 HOH HOH . H 4 HOH B 34 216 66 HOH HOH . H 4 HOH B 35 217 69 HOH HOH . H 4 HOH B 36 218 70 HOH HOH . H 4 HOH B 37 219 72 HOH HOH . H 4 HOH B 38 220 74 HOH HOH . H 4 HOH B 39 221 75 HOH HOH . H 4 HOH B 40 222 77 HOH HOH . H 4 HOH B 41 223 79 HOH HOH . H 4 HOH B 42 224 80 HOH HOH . H 4 HOH B 43 225 82 HOH HOH . H 4 HOH B 44 226 83 HOH HOH . H 4 HOH B 45 227 87 HOH HOH . H 4 HOH B 46 228 90 HOH HOH . H 4 HOH B 47 229 92 HOH HOH . H 4 HOH B 48 230 93 HOH HOH . H 4 HOH B 49 231 95 HOH HOH . H 4 HOH B 50 232 97 HOH HOH . H 4 HOH B 51 233 99 HOH HOH . H 4 HOH B 52 234 100 HOH HOH . H 4 HOH B 53 235 105 HOH HOH . H 4 HOH B 54 236 106 HOH HOH . H 4 HOH B 55 237 107 HOH HOH . H 4 HOH B 56 238 110 HOH HOH . H 4 HOH B 57 239 111 HOH HOH . H 4 HOH B 58 240 112 HOH HOH . H 4 HOH B 59 241 114 HOH HOH . H 4 HOH B 60 242 115 HOH HOH . H 4 HOH B 61 243 118 HOH HOH . H 4 HOH B 62 244 120 HOH HOH . H 4 HOH B 63 245 122 HOH HOH . H 4 HOH B 64 246 123 HOH HOH . H 4 HOH B 65 247 125 HOH HOH . H 4 HOH B 66 248 126 HOH HOH . H 4 HOH B 67 249 127 HOH HOH . H 4 HOH B 68 250 128 HOH HOH . H 4 HOH B 69 251 129 HOH HOH . H 4 HOH B 70 252 132 HOH HOH . H 4 HOH B 71 253 133 HOH HOH . H 4 HOH B 72 254 136 HOH HOH . H 4 HOH B 73 255 137 HOH HOH . H 4 HOH B 74 256 138 HOH HOH . H 4 HOH B 75 257 140 HOH HOH . H 4 HOH B 76 258 145 HOH HOH . H 4 HOH B 77 259 148 HOH HOH . H 4 HOH B 78 260 149 HOH HOH . H 4 HOH B 79 261 150 HOH HOH . H 4 HOH B 80 262 152 HOH HOH . H 4 HOH B 81 263 153 HOH HOH . H 4 HOH B 82 264 155 HOH HOH . H 4 HOH B 83 265 156 HOH HOH . H 4 HOH B 84 266 159 HOH HOH . H 4 HOH B 85 267 160 HOH HOH . H 4 HOH B 86 268 161 HOH HOH . H 4 HOH B 87 269 163 HOH HOH . H 4 HOH B 88 270 164 HOH HOH . H 4 HOH B 89 271 167 HOH HOH . H 4 HOH B 90 272 169 HOH HOH . H 4 HOH B 91 273 172 HOH HOH . H 4 HOH B 92 274 174 HOH HOH . H 4 HOH B 93 275 175 HOH HOH . H 4 HOH B 94 276 178 HOH HOH . H 4 HOH B 95 277 179 HOH HOH . H 4 HOH B 96 278 180 HOH HOH . H 4 HOH B 97 279 181 HOH HOH . H 4 HOH B 98 280 184 HOH HOH . H 4 HOH B 99 281 185 HOH HOH . H 4 HOH B 100 282 188 HOH HOH . H 4 HOH B 101 283 189 HOH HOH . H 4 HOH B 102 284 190 HOH HOH . H 4 HOH B 103 285 192 HOH HOH . H 4 HOH B 104 286 195 HOH HOH . H 4 HOH B 105 287 196 HOH HOH . H 4 HOH B 106 288 197 HOH HOH . H 4 HOH B 107 289 198 HOH HOH . H 4 HOH B 108 290 199 HOH HOH . H 4 HOH B 109 291 200 HOH HOH . H 4 HOH B 110 292 207 HOH HOH . H 4 HOH B 111 293 209 HOH HOH . H 4 HOH B 112 294 212 HOH HOH . H 4 HOH B 113 295 215 HOH HOH . H 4 HOH B 114 296 216 HOH HOH . H 4 HOH B 115 297 218 HOH HOH . H 4 HOH B 116 298 222 HOH HOH . H 4 HOH B 117 299 223 HOH HOH . H 4 HOH B 118 300 224 HOH HOH . H 4 HOH B 119 301 226 HOH HOH . H 4 HOH B 120 302 227 HOH HOH . H 4 HOH B 121 303 228 HOH HOH . H 4 HOH B 122 304 229 HOH HOH . H 4 HOH B 123 305 231 HOH HOH . H 4 HOH B 124 306 233 HOH HOH . H 4 HOH B 125 307 235 HOH HOH . H 4 HOH B 126 308 236 HOH HOH . H 4 HOH B 127 309 237 HOH HOH . H 4 HOH B 128 310 238 HOH HOH . H 4 HOH B 129 311 239 HOH HOH . H 4 HOH B 130 312 240 HOH HOH . H 4 HOH B 131 313 242 HOH HOH . H 4 HOH B 132 314 243 HOH HOH . H 4 HOH B 133 315 247 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 C _atom_site.label_entity_id 2 _atom_site.Cartn_x -15.292 _atom_site.Cartn_y 53.991 _atom_site.Cartn_z 43.51 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 25.47 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 142 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 1 #