data_3MDI # _model_server_result.job_id U28W3PvQcJppqX0F5vnW1w _model_server_result.datetime_utc '2024-11-22 08:48:31' _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 3mdi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":228}' # _entry.id 3MDI # _exptl.entry_id 3MDI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _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 90 _cell.angle_gamma 90 _cell.entry_id 3MDI _cell.length_a 71.362 _cell.length_b 72.037 _cell.length_c 96.16 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3MDI _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,F,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 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 hydrog TYPE_10_PAIR hydrog1 C N2 G 2 C G 2 1_555 C N1 A 6 C A 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_10_PAIR hydrog2 C N3 G 2 C G 2 1_555 C N6 A 6 C A 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 208 n n C1 C2 GOL sing 209 n n C1 H11 GOL sing 210 n n C1 H12 GOL sing 211 n n O1 HO1 GOL sing 212 n n C2 O2 GOL sing 213 n n C2 C3 GOL sing 214 n n C2 H2 GOL sing 215 n n O2 HO2 GOL sing 216 n n C3 O3 GOL sing 217 n n C3 H31 GOL sing 218 n n C3 H32 GOL sing 219 n n O3 HO3 GOL sing 220 n n # _atom_sites.entry_id 3MDI _atom_sites.fract_transf_matrix[1][1] 0.014013 _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] 0.013882 _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] 0.010399 _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 D 3 GOL A 1 228 1 GOL GOL . E 3 GOL B 1 228 2 GOL GOL . F 4 HOH A 1 229 229 HOH HOH . F 4 HOH A 2 230 230 HOH HOH . F 4 HOH A 3 231 231 HOH HOH . F 4 HOH A 4 232 232 HOH HOH . F 4 HOH A 5 233 1 HOH HOH . F 4 HOH A 6 234 234 HOH HOH . F 4 HOH A 7 235 2 HOH HOH . F 4 HOH A 8 236 9 HOH HOH . F 4 HOH A 9 237 237 HOH HOH . F 4 HOH A 10 238 12 HOH HOH . F 4 HOH A 11 239 239 HOH HOH . F 4 HOH A 12 240 240 HOH HOH . F 4 HOH A 13 241 241 HOH HOH . F 4 HOH A 14 242 242 HOH HOH . F 4 HOH A 15 243 13 HOH HOH . F 4 HOH A 16 244 14 HOH HOH . F 4 HOH A 17 245 245 HOH HOH . F 4 HOH A 18 246 15 HOH HOH . F 4 HOH A 19 247 247 HOH HOH . F 4 HOH A 20 248 248 HOH HOH . F 4 HOH A 21 249 16 HOH HOH . F 4 HOH A 22 250 250 HOH HOH . F 4 HOH A 23 251 251 HOH HOH . F 4 HOH A 24 252 252 HOH HOH . F 4 HOH A 25 253 253 HOH HOH . F 4 HOH A 26 254 254 HOH HOH . F 4 HOH A 27 255 17 HOH HOH . F 4 HOH A 28 256 256 HOH HOH . F 4 HOH A 29 257 18 HOH HOH . F 4 HOH A 30 258 258 HOH HOH . F 4 HOH A 31 259 19 HOH HOH . F 4 HOH A 32 260 20 HOH HOH . F 4 HOH A 33 261 21 HOH HOH . F 4 HOH A 34 262 22 HOH HOH . F 4 HOH A 35 263 23 HOH HOH . F 4 HOH A 36 264 264 HOH HOH . F 4 HOH A 37 265 265 HOH HOH . F 4 HOH A 38 266 266 HOH HOH . F 4 HOH A 39 267 267 HOH HOH . F 4 HOH A 40 268 268 HOH HOH . F 4 HOH A 41 269 269 HOH HOH . F 4 HOH A 42 270 24 HOH HOH . F 4 HOH A 43 271 25 HOH HOH . F 4 HOH A 44 272 26 HOH HOH . F 4 HOH A 45 273 27 HOH HOH . F 4 HOH A 46 274 33 HOH HOH . F 4 HOH A 47 275 34 HOH HOH . F 4 HOH A 48 276 35 HOH HOH . F 4 HOH A 49 277 36 HOH HOH . F 4 HOH A 50 278 37 HOH HOH . F 4 HOH A 51 279 53 HOH HOH . F 4 HOH A 52 280 54 HOH HOH . F 4 HOH A 53 281 59 HOH HOH . F 4 HOH A 54 282 60 HOH HOH . F 4 HOH A 55 283 61 HOH HOH . F 4 HOH A 56 284 62 HOH HOH . F 4 HOH A 57 285 63 HOH HOH . F 4 HOH A 58 286 64 HOH HOH . F 4 HOH A 59 287 65 HOH HOH . F 4 HOH A 60 288 66 HOH HOH . F 4 HOH A 61 289 67 HOH HOH . F 4 HOH A 62 290 68 HOH HOH . F 4 HOH A 63 291 69 HOH HOH . F 4 HOH A 64 292 71 HOH HOH . F 4 HOH A 65 293 77 HOH HOH . F 4 HOH A 66 294 78 HOH HOH . F 4 HOH A 67 295 79 HOH HOH . F 4 HOH A 68 296 80 HOH HOH . F 4 HOH A 69 297 82 HOH HOH . F 4 HOH A 70 298 83 HOH HOH . F 4 HOH A 71 299 86 HOH HOH . F 4 HOH A 72 300 88 HOH HOH . F 4 HOH A 73 301 91 HOH HOH . F 4 HOH A 74 302 96 HOH HOH . F 4 HOH A 75 303 97 HOH HOH . F 4 HOH A 76 304 98 HOH HOH . F 4 HOH A 77 305 103 HOH HOH . F 4 HOH A 78 306 105 HOH HOH . F 4 HOH A 79 307 106 HOH HOH . F 4 HOH A 80 308 107 HOH HOH . F 4 HOH A 81 309 110 HOH HOH . F 4 HOH A 82 310 111 HOH HOH . F 4 HOH A 83 311 113 HOH HOH . F 4 HOH A 84 312 114 HOH HOH . F 4 HOH A 85 313 115 HOH HOH . F 4 HOH A 86 314 117 HOH HOH . F 4 HOH A 87 315 119 HOH HOH . F 4 HOH A 88 316 120 HOH HOH . F 4 HOH A 89 317 121 HOH HOH . F 4 HOH A 90 318 122 HOH HOH . F 4 HOH A 91 319 125 HOH HOH . F 4 HOH A 92 320 128 HOH HOH . F 4 HOH A 93 321 131 HOH HOH . F 4 HOH A 94 322 132 HOH HOH . F 4 HOH A 95 323 133 HOH HOH . F 4 HOH A 96 324 134 HOH HOH . F 4 HOH A 97 325 137 HOH HOH . F 4 HOH A 98 326 138 HOH HOH . F 4 HOH A 99 327 140 HOH HOH . F 4 HOH A 100 328 142 HOH HOH . F 4 HOH A 101 329 143 HOH HOH . F 4 HOH A 102 330 146 HOH HOH . F 4 HOH A 103 331 147 HOH HOH . F 4 HOH A 104 332 148 HOH HOH . F 4 HOH A 105 333 150 HOH HOH . F 4 HOH A 106 334 151 HOH HOH . F 4 HOH A 107 335 153 HOH HOH . F 4 HOH A 108 336 154 HOH HOH . F 4 HOH A 109 337 155 HOH HOH . F 4 HOH A 110 338 156 HOH HOH . F 4 HOH A 111 339 160 HOH HOH . F 4 HOH A 112 340 168 HOH HOH . F 4 HOH A 113 341 169 HOH HOH . F 4 HOH A 114 342 170 HOH HOH . F 4 HOH A 115 343 175 HOH HOH . F 4 HOH A 116 344 177 HOH HOH . F 4 HOH A 117 345 178 HOH HOH . F 4 HOH A 118 346 179 HOH HOH . F 4 HOH A 119 347 180 HOH HOH . F 4 HOH A 120 348 182 HOH HOH . F 4 HOH A 121 349 183 HOH HOH . F 4 HOH A 122 350 184 HOH HOH . F 4 HOH A 123 351 185 HOH HOH . F 4 HOH A 124 352 189 HOH HOH . F 4 HOH A 125 353 191 HOH HOH . F 4 HOH A 126 354 198 HOH HOH . F 4 HOH A 127 355 200 HOH HOH . F 4 HOH A 128 356 201 HOH HOH . F 4 HOH A 129 357 202 HOH HOH . F 4 HOH A 130 358 203 HOH HOH . F 4 HOH A 131 359 204 HOH HOH . F 4 HOH A 132 360 206 HOH HOH . F 4 HOH A 133 361 207 HOH HOH . F 4 HOH A 134 362 208 HOH HOH . F 4 HOH A 135 363 215 HOH HOH . F 4 HOH A 136 364 216 HOH HOH . F 4 HOH A 137 365 218 HOH HOH . F 4 HOH A 138 366 219 HOH HOH . F 4 HOH A 139 367 220 HOH HOH . F 4 HOH A 140 368 222 HOH HOH . F 4 HOH A 141 369 223 HOH HOH . F 4 HOH A 142 370 225 HOH HOH . F 4 HOH A 143 371 226 HOH HOH . F 4 HOH A 144 372 89 HOH HOH . G 4 HOH B 1 229 3 HOH HOH . G 4 HOH B 2 230 4 HOH HOH . G 4 HOH B 3 231 5 HOH HOH . G 4 HOH B 4 232 6 HOH HOH . G 4 HOH B 5 233 233 HOH HOH . G 4 HOH B 6 234 7 HOH HOH . G 4 HOH B 7 235 8 HOH HOH . G 4 HOH B 8 236 236 HOH HOH . G 4 HOH B 9 237 10 HOH HOH . G 4 HOH B 10 238 238 HOH HOH . G 4 HOH B 11 239 11 HOH HOH . G 4 HOH B 12 240 28 HOH HOH . G 4 HOH B 13 241 29 HOH HOH . G 4 HOH B 14 242 30 HOH HOH . G 4 HOH B 15 243 243 HOH HOH . G 4 HOH B 16 244 244 HOH HOH . G 4 HOH B 17 245 31 HOH HOH . G 4 HOH B 18 246 246 HOH HOH . G 4 HOH B 19 247 32 HOH HOH . G 4 HOH B 20 248 38 HOH HOH . G 4 HOH B 21 249 249 HOH HOH . G 4 HOH B 22 250 39 HOH HOH . G 4 HOH B 23 251 40 HOH HOH . G 4 HOH B 24 252 41 HOH HOH . G 4 HOH B 25 253 42 HOH HOH . G 4 HOH B 26 254 43 HOH HOH . G 4 HOH B 27 255 255 HOH HOH . G 4 HOH B 28 256 44 HOH HOH . G 4 HOH B 29 257 257 HOH HOH . G 4 HOH B 30 258 45 HOH HOH . G 4 HOH B 31 259 259 HOH HOH . G 4 HOH B 32 260 260 HOH HOH . G 4 HOH B 33 261 261 HOH HOH . G 4 HOH B 34 262 262 HOH HOH . G 4 HOH B 35 263 263 HOH HOH . G 4 HOH B 36 264 46 HOH HOH . G 4 HOH B 37 265 47 HOH HOH . G 4 HOH B 38 266 48 HOH HOH . G 4 HOH B 39 267 49 HOH HOH . G 4 HOH B 40 268 50 HOH HOH . G 4 HOH B 41 269 51 HOH HOH . G 4 HOH B 42 270 270 HOH HOH . G 4 HOH B 43 271 271 HOH HOH . G 4 HOH B 44 272 272 HOH HOH . G 4 HOH B 45 273 273 HOH HOH . G 4 HOH B 46 274 274 HOH HOH . G 4 HOH B 47 275 275 HOH HOH . G 4 HOH B 48 276 276 HOH HOH . G 4 HOH B 49 277 277 HOH HOH . G 4 HOH B 50 278 52 HOH HOH . G 4 HOH B 51 279 55 HOH HOH . G 4 HOH B 52 280 56 HOH HOH . G 4 HOH B 53 281 57 HOH HOH . G 4 HOH B 54 282 58 HOH HOH . G 4 HOH B 55 283 70 HOH HOH . G 4 HOH B 56 284 72 HOH HOH . G 4 HOH B 57 285 73 HOH HOH . G 4 HOH B 58 286 74 HOH HOH . G 4 HOH B 59 287 75 HOH HOH . G 4 HOH B 60 288 76 HOH HOH . G 4 HOH B 61 289 81 HOH HOH . G 4 HOH B 62 290 84 HOH HOH . G 4 HOH B 63 291 90 HOH HOH . G 4 HOH B 64 292 94 HOH HOH . G 4 HOH B 65 293 100 HOH HOH . G 4 HOH B 66 294 102 HOH HOH . G 4 HOH B 67 295 104 HOH HOH . G 4 HOH B 68 296 108 HOH HOH . G 4 HOH B 69 297 116 HOH HOH . G 4 HOH B 70 298 118 HOH HOH . G 4 HOH B 71 299 124 HOH HOH . G 4 HOH B 72 300 126 HOH HOH . G 4 HOH B 73 301 127 HOH HOH . G 4 HOH B 74 302 129 HOH HOH . G 4 HOH B 75 303 130 HOH HOH . G 4 HOH B 76 304 136 HOH HOH . G 4 HOH B 77 305 139 HOH HOH . G 4 HOH B 78 306 141 HOH HOH . G 4 HOH B 79 307 144 HOH HOH . G 4 HOH B 80 308 145 HOH HOH . G 4 HOH B 81 309 149 HOH HOH . G 4 HOH B 82 310 152 HOH HOH . G 4 HOH B 83 311 157 HOH HOH . G 4 HOH B 84 312 159 HOH HOH . G 4 HOH B 85 313 163 HOH HOH . G 4 HOH B 86 314 164 HOH HOH . G 4 HOH B 87 315 165 HOH HOH . G 4 HOH B 88 316 166 HOH HOH . G 4 HOH B 89 317 167 HOH HOH . G 4 HOH B 90 318 171 HOH HOH . G 4 HOH B 91 319 172 HOH HOH . G 4 HOH B 92 320 173 HOH HOH . G 4 HOH B 93 321 174 HOH HOH . G 4 HOH B 94 322 181 HOH HOH . G 4 HOH B 95 323 186 HOH HOH . G 4 HOH B 96 324 187 HOH HOH . G 4 HOH B 97 325 188 HOH HOH . G 4 HOH B 98 326 190 HOH HOH . G 4 HOH B 99 327 192 HOH HOH . G 4 HOH B 100 328 193 HOH HOH . G 4 HOH B 101 329 195 HOH HOH . G 4 HOH B 102 330 196 HOH HOH . G 4 HOH B 103 331 197 HOH HOH . G 4 HOH B 104 332 199 HOH HOH . G 4 HOH B 105 333 205 HOH HOH . G 4 HOH B 106 334 209 HOH HOH . G 4 HOH B 107 335 210 HOH HOH . G 4 HOH B 108 336 211 HOH HOH . G 4 HOH B 109 337 212 HOH HOH . G 4 HOH B 110 338 213 HOH HOH . G 4 HOH B 111 339 214 HOH HOH . G 4 HOH B 112 340 217 HOH HOH . G 4 HOH B 113 341 221 HOH HOH . G 4 HOH B 114 342 224 HOH HOH . G 4 HOH B 115 343 227 HOH HOH . G 4 HOH B 116 344 228 HOH HOH . H 4 HOH C 1 85 85 HOH HOH . H 4 HOH C 2 87 87 HOH HOH . H 4 HOH C 3 92 92 HOH HOH . H 4 HOH C 4 93 93 HOH HOH . H 4 HOH C 5 95 95 HOH HOH . H 4 HOH C 6 99 99 HOH HOH . H 4 HOH C 7 101 101 HOH HOH . H 4 HOH C 8 112 112 HOH HOH . H 4 HOH C 9 123 123 HOH HOH . H 4 HOH C 10 135 135 HOH HOH . H 4 HOH C 11 158 158 HOH HOH . H 4 HOH C 12 161 161 HOH HOH . H 4 HOH C 13 162 162 HOH HOH . H 4 HOH C 14 176 176 HOH HOH . H 4 HOH C 15 194 194 HOH HOH . H 4 HOH C 16 278 278 HOH HOH . H 4 HOH C 17 279 279 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 . . . E 3 -1.255 -1.533 7.424 1 25.57 ? C1 GOL 228 B 1 HETATM 2 O O1 GOL . . . E 3 0.042 -1.946 7.057 1 25.87 ? O1 GOL 228 B 1 HETATM 3 C C2 GOL . . . E 3 -1.493 -0.141 6.858 1 27.49 ? C2 GOL 228 B 1 HETATM 4 O O2 GOL . . . E 3 -2.243 0.636 7.773 1 37.72 ? O2 GOL 228 B 1 HETATM 5 C C3 GOL . . . E 3 -0.148 0.514 6.566 1 26.02 ? C3 GOL 228 B 1 HETATM 6 O O3 GOL . . . E 3 -0.204 1.899 6.843 1 29.76 ? O3 GOL 228 B 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #