data_5GVD # _model_server_result.job_id ckT9IRxIZoP0ZiddFG_2GQ _model_server_result.datetime_utc '2024-11-23 00:14:10' _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 5gvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":203}' # _entry.id 5GVD # _exptl.entry_id 5GVD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _entity.pdbx_number_of_molecules 3 _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 5GVD _cell.length_a 85.669 _cell.length_b 85.669 _cell.length_c 104.207 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GVD _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,I 1 1 B,D,E,F,G,H,J 2 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 E N N ? 3 F N N ? 3 G 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 D O4 PO4 . B PO4 201 1_555 H MG MG . B MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? metalc ? metalc2 H MG MG . B MG 205 1_555 J O HOH . B HOH 318 5_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc3 H MG MG . B MG 205 1_555 J O HOH . B HOH 365 5_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? # _chem_comp.formula 'C2 H6 O2' _chem_comp.formula_weight 62.068 _chem_comp.id EDO _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-ETHANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ETHYLENE GLYCOL' # 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 EDO sing 83 n n C1 C2 EDO sing 84 n n C1 H11 EDO sing 85 n n C1 H12 EDO sing 86 n n O1 HO1 EDO sing 87 n n C2 O2 EDO sing 88 n n C2 H21 EDO sing 89 n n C2 H22 EDO sing 90 n n O2 HO2 EDO sing 91 n n # _atom_sites.entry_id 5GVD _atom_sites.fract_transf_matrix[1][1] 0.011673 _atom_sites.fract_transf_matrix[1][2] 0.006739 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013479 _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] 0.009596 _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 PO4 A 1 201 1 PO4 PO4 . D 2 PO4 B 1 201 2 PO4 PO4 . E 3 EDO B 1 202 6 EDO EDO . F 3 EDO B 1 203 10 EDO EDO . G 3 EDO B 1 204 11 EDO EDO . H 4 MG B 1 205 12 MG MG . I 5 HOH A 1 301 191 HOH HOH . I 5 HOH A 2 302 181 HOH HOH . I 5 HOH A 3 303 94 HOH HOH . I 5 HOH A 4 304 206 HOH HOH . I 5 HOH A 5 305 215 HOH HOH . I 5 HOH A 6 306 167 HOH HOH . I 5 HOH A 7 307 103 HOH HOH . I 5 HOH A 8 308 55 HOH HOH . I 5 HOH A 9 309 43 HOH HOH . I 5 HOH A 10 310 171 HOH HOH . I 5 HOH A 11 311 235 HOH HOH . I 5 HOH A 12 312 76 HOH HOH . I 5 HOH A 13 313 110 HOH HOH . I 5 HOH A 14 314 135 HOH HOH . I 5 HOH A 15 315 160 HOH HOH . I 5 HOH A 16 316 212 HOH HOH . I 5 HOH A 17 317 12 HOH HOH . I 5 HOH A 18 318 2 HOH HOH . I 5 HOH A 19 319 118 HOH HOH . I 5 HOH A 20 320 52 HOH HOH . I 5 HOH A 21 321 192 HOH HOH . I 5 HOH A 22 322 223 HOH HOH . I 5 HOH A 23 323 132 HOH HOH . I 5 HOH A 24 324 60 HOH HOH . I 5 HOH A 25 325 117 HOH HOH . I 5 HOH A 26 326 44 HOH HOH . I 5 HOH A 27 327 34 HOH HOH . I 5 HOH A 28 328 114 HOH HOH . I 5 HOH A 29 329 151 HOH HOH . I 5 HOH A 30 330 95 HOH HOH . I 5 HOH A 31 331 14 HOH HOH . I 5 HOH A 32 332 180 HOH HOH . I 5 HOH A 33 333 75 HOH HOH . I 5 HOH A 34 334 45 HOH HOH . I 5 HOH A 35 335 21 HOH HOH . I 5 HOH A 36 336 231 HOH HOH . I 5 HOH A 37 337 138 HOH HOH . I 5 HOH A 38 338 144 HOH HOH . I 5 HOH A 39 339 99 HOH HOH . I 5 HOH A 40 340 102 HOH HOH . I 5 HOH A 41 341 146 HOH HOH . I 5 HOH A 42 342 80 HOH HOH . I 5 HOH A 43 343 33 HOH HOH . I 5 HOH A 44 344 1 HOH HOH . I 5 HOH A 45 345 195 HOH HOH . I 5 HOH A 46 346 32 HOH HOH . I 5 HOH A 47 347 68 HOH HOH . I 5 HOH A 48 348 100 HOH HOH . I 5 HOH A 49 349 211 HOH HOH . I 5 HOH A 50 350 10 HOH HOH . I 5 HOH A 51 351 35 HOH HOH . I 5 HOH A 52 352 113 HOH HOH . I 5 HOH A 53 353 65 HOH HOH . I 5 HOH A 54 354 13 HOH HOH . I 5 HOH A 55 355 62 HOH HOH . I 5 HOH A 56 356 49 HOH HOH . I 5 HOH A 57 357 6 HOH HOH . I 5 HOH A 58 358 173 HOH HOH . I 5 HOH A 59 359 230 HOH HOH . I 5 HOH A 60 360 112 HOH HOH . I 5 HOH A 61 361 239 HOH HOH . I 5 HOH A 62 362 30 HOH HOH . I 5 HOH A 63 363 214 HOH HOH . I 5 HOH A 64 364 210 HOH HOH . I 5 HOH A 65 365 177 HOH HOH . I 5 HOH A 66 366 154 HOH HOH . I 5 HOH A 67 367 11 HOH HOH . I 5 HOH A 68 368 219 HOH HOH . I 5 HOH A 69 369 39 HOH HOH . I 5 HOH A 70 370 41 HOH HOH . I 5 HOH A 71 371 72 HOH HOH . I 5 HOH A 72 372 190 HOH HOH . I 5 HOH A 73 373 42 HOH HOH . I 5 HOH A 74 374 57 HOH HOH . I 5 HOH A 75 375 196 HOH HOH . I 5 HOH A 76 376 162 HOH HOH . I 5 HOH A 77 377 8 HOH HOH . I 5 HOH A 78 378 115 HOH HOH . I 5 HOH A 79 379 143 HOH HOH . I 5 HOH A 80 380 142 HOH HOH . I 5 HOH A 81 381 104 HOH HOH . I 5 HOH A 82 382 77 HOH HOH . I 5 HOH A 83 383 108 HOH HOH . I 5 HOH A 84 384 130 HOH HOH . I 5 HOH A 85 385 197 HOH HOH . I 5 HOH A 86 386 84 HOH HOH . I 5 HOH A 87 387 101 HOH HOH . I 5 HOH A 88 388 236 HOH HOH . I 5 HOH A 89 389 200 HOH HOH . I 5 HOH A 90 390 111 HOH HOH . I 5 HOH A 91 391 136 HOH HOH . I 5 HOH A 92 392 131 HOH HOH . I 5 HOH A 93 393 133 HOH HOH . I 5 HOH A 94 394 126 HOH HOH . I 5 HOH A 95 395 92 HOH HOH . I 5 HOH A 96 396 204 HOH HOH . I 5 HOH A 97 397 166 HOH HOH . I 5 HOH A 98 398 238 HOH HOH . I 5 HOH A 99 399 127 HOH HOH . I 5 HOH A 100 400 123 HOH HOH . I 5 HOH A 101 401 54 HOH HOH . I 5 HOH A 102 402 189 HOH HOH . I 5 HOH A 103 403 158 HOH HOH . I 5 HOH A 104 404 164 HOH HOH . I 5 HOH A 105 405 205 HOH HOH . I 5 HOH A 106 406 207 HOH HOH . I 5 HOH A 107 407 124 HOH HOH . I 5 HOH A 108 408 217 HOH HOH . J 5 HOH B 1 301 93 HOH HOH . J 5 HOH B 2 302 163 HOH HOH . J 5 HOH B 3 303 221 HOH HOH . J 5 HOH B 4 304 179 HOH HOH . J 5 HOH B 5 305 156 HOH HOH . J 5 HOH B 6 306 69 HOH HOH . J 5 HOH B 7 307 165 HOH HOH . J 5 HOH B 8 308 193 HOH HOH . J 5 HOH B 9 309 46 HOH HOH . J 5 HOH B 10 310 81 HOH HOH . J 5 HOH B 11 311 176 HOH HOH . J 5 HOH B 12 312 26 HOH HOH . J 5 HOH B 13 313 194 HOH HOH . J 5 HOH B 14 314 218 HOH HOH . J 5 HOH B 15 315 152 HOH HOH . J 5 HOH B 16 316 237 HOH HOH . J 5 HOH B 17 317 227 HOH HOH . J 5 HOH B 18 318 48 HOH HOH . J 5 HOH B 19 319 228 HOH HOH . J 5 HOH B 20 320 22 HOH HOH . J 5 HOH B 21 321 23 HOH HOH . J 5 HOH B 22 322 40 HOH HOH . J 5 HOH B 23 323 139 HOH HOH . J 5 HOH B 24 324 147 HOH HOH . J 5 HOH B 25 325 88 HOH HOH . J 5 HOH B 26 326 232 HOH HOH . J 5 HOH B 27 327 61 HOH HOH . J 5 HOH B 28 328 224 HOH HOH . J 5 HOH B 29 329 229 HOH HOH . J 5 HOH B 30 330 175 HOH HOH . J 5 HOH B 31 331 25 HOH HOH . J 5 HOH B 32 332 16 HOH HOH . J 5 HOH B 33 333 37 HOH HOH . J 5 HOH B 34 334 150 HOH HOH . J 5 HOH B 35 335 90 HOH HOH . J 5 HOH B 36 336 208 HOH HOH . J 5 HOH B 37 337 15 HOH HOH . J 5 HOH B 38 338 188 HOH HOH . J 5 HOH B 39 339 203 HOH HOH . J 5 HOH B 40 340 24 HOH HOH . J 5 HOH B 41 341 134 HOH HOH . J 5 HOH B 42 342 174 HOH HOH . J 5 HOH B 43 343 9 HOH HOH . J 5 HOH B 44 344 67 HOH HOH . J 5 HOH B 45 345 159 HOH HOH . J 5 HOH B 46 346 56 HOH HOH . J 5 HOH B 47 347 109 HOH HOH . J 5 HOH B 48 348 51 HOH HOH . J 5 HOH B 49 349 19 HOH HOH . J 5 HOH B 50 350 182 HOH HOH . J 5 HOH B 51 351 220 HOH HOH . J 5 HOH B 52 352 184 HOH HOH . J 5 HOH B 53 353 20 HOH HOH . J 5 HOH B 54 354 89 HOH HOH . J 5 HOH B 55 355 29 HOH HOH . J 5 HOH B 56 356 129 HOH HOH . J 5 HOH B 57 357 226 HOH HOH . J 5 HOH B 58 358 4 HOH HOH . J 5 HOH B 59 359 141 HOH HOH . J 5 HOH B 60 360 120 HOH HOH . J 5 HOH B 61 361 47 HOH HOH . J 5 HOH B 62 362 50 HOH HOH . J 5 HOH B 63 363 17 HOH HOH . J 5 HOH B 64 364 18 HOH HOH . J 5 HOH B 65 365 172 HOH HOH . J 5 HOH B 66 366 140 HOH HOH . J 5 HOH B 67 367 119 HOH HOH . J 5 HOH B 68 368 216 HOH HOH . J 5 HOH B 69 369 3 HOH HOH . J 5 HOH B 70 370 234 HOH HOH . J 5 HOH B 71 371 83 HOH HOH . J 5 HOH B 72 372 125 HOH HOH . J 5 HOH B 73 373 128 HOH HOH . J 5 HOH B 74 374 157 HOH HOH . J 5 HOH B 75 375 145 HOH HOH . J 5 HOH B 76 376 28 HOH HOH . J 5 HOH B 77 377 27 HOH HOH . J 5 HOH B 78 378 79 HOH HOH . J 5 HOH B 79 379 38 HOH HOH . J 5 HOH B 80 380 122 HOH HOH . J 5 HOH B 81 381 5 HOH HOH . J 5 HOH B 82 382 97 HOH HOH . J 5 HOH B 83 383 66 HOH HOH . J 5 HOH B 84 384 116 HOH HOH . J 5 HOH B 85 385 31 HOH HOH . J 5 HOH B 86 386 7 HOH HOH . J 5 HOH B 87 387 36 HOH HOH . J 5 HOH B 88 388 106 HOH HOH . J 5 HOH B 89 389 137 HOH HOH . J 5 HOH B 90 390 170 HOH HOH . J 5 HOH B 91 391 70 HOH HOH . J 5 HOH B 92 392 155 HOH HOH . J 5 HOH B 93 393 201 HOH HOH . J 5 HOH B 94 394 199 HOH HOH . J 5 HOH B 95 395 202 HOH HOH . J 5 HOH B 96 396 71 HOH HOH . J 5 HOH B 97 397 59 HOH HOH . J 5 HOH B 98 398 153 HOH HOH . J 5 HOH B 99 399 87 HOH HOH . J 5 HOH B 100 400 105 HOH HOH . J 5 HOH B 101 401 233 HOH HOH . J 5 HOH B 102 402 149 HOH HOH . J 5 HOH B 103 403 225 HOH HOH . J 5 HOH B 104 404 98 HOH HOH . J 5 HOH B 105 405 121 HOH HOH . J 5 HOH B 106 406 222 HOH HOH . J 5 HOH B 107 407 213 HOH HOH . J 5 HOH B 108 408 183 HOH HOH . J 5 HOH B 109 409 85 HOH HOH . J 5 HOH B 110 410 169 HOH HOH . J 5 HOH B 111 411 241 HOH HOH . J 5 HOH B 112 412 96 HOH HOH . J 5 HOH B 113 413 185 HOH HOH . J 5 HOH B 114 414 240 HOH HOH . J 5 HOH B 115 415 187 HOH HOH . J 5 HOH B 116 416 178 HOH HOH . J 5 HOH B 117 417 82 HOH HOH . J 5 HOH B 118 418 209 HOH HOH . J 5 HOH B 119 419 91 HOH HOH . J 5 HOH B 120 420 78 HOH HOH . J 5 HOH B 121 421 53 HOH HOH . J 5 HOH B 122 422 198 HOH HOH . J 5 HOH B 123 423 64 HOH HOH . J 5 HOH B 124 424 63 HOH HOH . J 5 HOH B 125 425 58 HOH HOH . J 5 HOH B 126 426 73 HOH HOH . J 5 HOH B 127 427 168 HOH HOH . J 5 HOH B 128 428 86 HOH HOH . J 5 HOH B 129 429 107 HOH HOH . J 5 HOH B 130 430 186 HOH HOH . J 5 HOH B 131 431 148 HOH HOH . J 5 HOH B 132 432 161 HOH HOH . J 5 HOH B 133 433 74 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 EDO . . . F 3 20.515 67.692 37.414 1 25.59 ? C1 EDO 203 B 1 HETATM 2 O O1 EDO . . . F 3 21.219 67.553 38.629 1 20.93 ? O1 EDO 203 B 1 HETATM 3 C C2 EDO . . . F 3 19.681 68.963 37.403 1 27.51 ? C2 EDO 203 B 1 HETATM 4 O O2 EDO . . . F 3 19.203 68.98 36.058 1 45.44 ? O2 EDO 203 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 4 #