data_5MYI # _model_server_result.job_id wLWJ6tnkYLPuP9hDrmq9wQ _model_server_result.datetime_utc '2024-10-10 14:26:40' _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 5myi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":205}' # _entry.id 5MYI # _exptl.entry_id 5MYI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 106.12 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description DI(HYDROXYETHYL)ETHER _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 5MYI _cell.length_a 79.45 _cell.length_b 79.45 _cell.length_c 125.81 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MYI _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 10_664 -y+1,-x+1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 39.725 68.805718 -20.968333 # 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 ? 3 F 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 A OE1 GLU 73 D GLU 39 1_555 C CA CA . D CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc2 A OE1 GLU 76 D GLU 42 1_555 C CA CA . D CA 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc3 A OE1 GLU 76 D GLU 42 1_555 C CA CA . D CA 202 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc4 A O LYS 90 D LYS 56 1_555 H MG MG . D MG 207 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc5 A O GLY 92 D GLY 58 1_555 H MG MG . D MG 207 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc6 A OE1 GLU 101 D GLU 67 1_555 C CA CA . D CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc7 A OD2 ASP 104 D ASP 70 1_555 C CA CA . D CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc8 A O GLN 116 D GLN 82 1_555 B CA CA . D CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc9 A O GLY 117 D GLY 83 1_555 B CA CA . D CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc10 A OD2 ASP 131 D ASP 97 1_555 H MG MG . D MG 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc11 B CA CA . D CA 201 1_555 I O HOH . D HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc12 B CA CA . D CA 201 1_555 I O HOH . D HOH 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc13 B CA CA . D CA 201 1_555 I O HOH . D HOH 383 10_664 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc14 B CA CA . D CA 201 1_555 I O HOH . D HOH 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc15 B CA CA . D CA 201 1_555 I O HOH . D HOH 388 10_664 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc16 C CA CA . D CA 202 1_555 I O HOH . D HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc17 C CA CA . D CA 202 1_555 I O HOH . D HOH 375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc18 H MG MG . D MG 207 1_555 I O HOH . D HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc19 H MG MG . D MG 207 1_555 I O HOH . D HOH 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc20 H MG MG . D MG 207 1_555 I O HOH . D HOH 333 5_564 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc21 H MG MG . D MG 207 1_555 I O HOH . D HOH 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? # _chem_comp.formula 'C4 H10 O3' _chem_comp.formula_weight 106.12 _chem_comp.id PEG _chem_comp.mon_nstd_flag . _chem_comp.name DI(HYDROXYETHYL)ETHER _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 C1 O1 PEG sing 224 n n C1 C2 PEG sing 225 n n C1 H11 PEG sing 226 n n C1 H12 PEG sing 227 n n O1 HO1 PEG sing 228 n n C2 O2 PEG sing 229 n n C2 H21 PEG sing 230 n n C2 H22 PEG sing 231 n n O2 C3 PEG sing 232 n n C3 C4 PEG sing 233 n n C3 H31 PEG sing 234 n n C3 H32 PEG sing 235 n n C4 O4 PEG sing 236 n n C4 H41 PEG sing 237 n n C4 H42 PEG sing 238 n n O4 HO4 PEG sing 239 n n # _atom_sites.entry_id 5MYI _atom_sites.fract_transf_matrix[1][1] 0.012587 _atom_sites.fract_transf_matrix[1][2] 0.007267 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014534 _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] 0.007948 _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 CA D 1 201 1 CA CA . C 2 CA D 1 202 3 CA CA . D 3 PEG D 1 203 1 PEG PEG . E 3 PEG D 1 204 2 PEG PEG . F 3 PEG D 1 205 3 PEG PEG . G 4 CL D 1 206 1 CL CL . H 5 MG D 1 207 1 MG MG . I 6 HOH D 1 301 140 HOH HOH . I 6 HOH D 2 302 49 HOH HOH . I 6 HOH D 3 303 181 HOH HOH . I 6 HOH D 4 304 36 HOH HOH . I 6 HOH D 5 305 93 HOH HOH . I 6 HOH D 6 306 3 HOH HOH . I 6 HOH D 7 307 101 HOH HOH . I 6 HOH D 8 308 138 HOH HOH . I 6 HOH D 9 309 116 HOH HOH . I 6 HOH D 10 310 20 HOH HOH . I 6 HOH D 11 311 24 HOH HOH . I 6 HOH D 12 312 1 HOH HOH . I 6 HOH D 13 313 113 HOH HOH . I 6 HOH D 14 314 50 HOH HOH . I 6 HOH D 15 315 188 HOH HOH . I 6 HOH D 16 316 163 HOH HOH . I 6 HOH D 17 317 7 HOH HOH . I 6 HOH D 18 318 58 HOH HOH . I 6 HOH D 19 319 39 HOH HOH . I 6 HOH D 20 320 38 HOH HOH . I 6 HOH D 21 321 184 HOH HOH . I 6 HOH D 22 322 92 HOH HOH . I 6 HOH D 23 323 121 HOH HOH . I 6 HOH D 24 324 108 HOH HOH . I 6 HOH D 25 325 51 HOH HOH . I 6 HOH D 26 326 15 HOH HOH . I 6 HOH D 27 327 14 HOH HOH . I 6 HOH D 28 328 12 HOH HOH . I 6 HOH D 29 329 109 HOH HOH . I 6 HOH D 30 330 98 HOH HOH . I 6 HOH D 31 331 45 HOH HOH . I 6 HOH D 32 332 10 HOH HOH . I 6 HOH D 33 333 102 HOH HOH . I 6 HOH D 34 334 26 HOH HOH . I 6 HOH D 35 335 11 HOH HOH . I 6 HOH D 36 336 131 HOH HOH . I 6 HOH D 37 337 2 HOH HOH . I 6 HOH D 38 338 4 HOH HOH . I 6 HOH D 39 339 105 HOH HOH . I 6 HOH D 40 340 117 HOH HOH . I 6 HOH D 41 341 165 HOH HOH . I 6 HOH D 42 342 27 HOH HOH . I 6 HOH D 43 343 16 HOH HOH . I 6 HOH D 44 344 158 HOH HOH . I 6 HOH D 45 345 151 HOH HOH . I 6 HOH D 46 346 104 HOH HOH . I 6 HOH D 47 347 99 HOH HOH . I 6 HOH D 48 348 171 HOH HOH . I 6 HOH D 49 349 96 HOH HOH . I 6 HOH D 50 350 18 HOH HOH . I 6 HOH D 51 351 129 HOH HOH . I 6 HOH D 52 352 32 HOH HOH . I 6 HOH D 53 353 5 HOH HOH . I 6 HOH D 54 354 59 HOH HOH . I 6 HOH D 55 355 19 HOH HOH . I 6 HOH D 56 356 22 HOH HOH . I 6 HOH D 57 357 31 HOH HOH . I 6 HOH D 58 358 30 HOH HOH . I 6 HOH D 59 359 118 HOH HOH . I 6 HOH D 60 360 111 HOH HOH . I 6 HOH D 61 361 25 HOH HOH . I 6 HOH D 62 362 85 HOH HOH . I 6 HOH D 63 363 29 HOH HOH . I 6 HOH D 64 364 35 HOH HOH . I 6 HOH D 65 365 34 HOH HOH . I 6 HOH D 66 366 145 HOH HOH . I 6 HOH D 67 367 170 HOH HOH . I 6 HOH D 68 368 6 HOH HOH . I 6 HOH D 69 369 106 HOH HOH . I 6 HOH D 70 370 187 HOH HOH . I 6 HOH D 71 371 42 HOH HOH . I 6 HOH D 72 372 79 HOH HOH . I 6 HOH D 73 373 103 HOH HOH . I 6 HOH D 74 374 28 HOH HOH . I 6 HOH D 75 375 95 HOH HOH . I 6 HOH D 76 376 146 HOH HOH . I 6 HOH D 77 377 13 HOH HOH . I 6 HOH D 78 378 23 HOH HOH . I 6 HOH D 79 379 91 HOH HOH . I 6 HOH D 80 380 110 HOH HOH . I 6 HOH D 81 381 40 HOH HOH . I 6 HOH D 82 382 157 HOH HOH . I 6 HOH D 83 383 183 HOH HOH . I 6 HOH D 84 384 139 HOH HOH . I 6 HOH D 85 385 152 HOH HOH . I 6 HOH D 86 386 162 HOH HOH . I 6 HOH D 87 387 153 HOH HOH . I 6 HOH D 88 388 159 HOH HOH . I 6 HOH D 89 389 37 HOH HOH . I 6 HOH D 90 390 180 HOH HOH . I 6 HOH D 91 391 44 HOH HOH . I 6 HOH D 92 392 17 HOH HOH . I 6 HOH D 93 393 8 HOH HOH . I 6 HOH D 94 394 142 HOH HOH . I 6 HOH D 95 395 185 HOH HOH . I 6 HOH D 96 396 83 HOH HOH . I 6 HOH D 97 397 81 HOH HOH . I 6 HOH D 98 398 182 HOH HOH . I 6 HOH D 99 399 9 HOH HOH . I 6 HOH D 100 400 178 HOH HOH . I 6 HOH D 101 401 186 HOH HOH . I 6 HOH D 102 402 82 HOH HOH . I 6 HOH D 103 403 189 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 PEG . . . F 3 66.411 37.701 -12.351 1 78.72 ? C1 PEG 205 D 1 HETATM 2 O O1 PEG . . . F 3 67.814 37.506 -12.214 1 75.9 ? O1 PEG 205 D 1 HETATM 3 C C2 PEG . . . F 3 65.989 37.792 -13.841 1 69.63 ? C2 PEG 205 D 1 HETATM 4 O O2 PEG . . . F 3 65.89 39.166 -14.293 1 73.02 ? O2 PEG 205 D 1 HETATM 5 C C3 PEG . . . F 3 65.95 40.136 -13.253 1 72.08 ? C3 PEG 205 D 1 HETATM 6 C C4 PEG . . . F 3 66.022 41.542 -13.8 1 72.25 ? C4 PEG 205 D 1 HETATM 7 O O4 PEG . . . F 3 66.498 42.385 -12.774 1 75.42 ? O4 PEG 205 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 7 #