data_5YNX # _model_server_result.job_id S-MYLpzOguNlPa9UztfWXA _model_server_result.datetime_utc '2025-03-06 13:05:44' _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 5ynx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5YNX # _exptl.entry_id 5YNX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 78.133 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description BETA-MERCAPTOETHANOL _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 125.84 _cell.angle_gamma 90 _cell.entry_id 5YNX _cell.length_a 123.456 _cell.length_b 27.714 _cell.length_c 90.252 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YNX _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C2 H6 O S' _chem_comp.formula_weight 78.133 _chem_comp.id BME _chem_comp.mon_nstd_flag . _chem_comp.name BETA-MERCAPTOETHANOL _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 C2 BME sing 107 n n C1 O1 BME sing 108 n n C1 H11 BME sing 109 n n C1 H12 BME sing 110 n n C2 S2 BME sing 111 n n C2 H21 BME sing 112 n n C2 H22 BME sing 113 n n O1 HO1 BME sing 114 n n S2 HS2 BME sing 115 n n # _atom_sites.entry_id 5YNX _atom_sites.fract_transf_matrix[1][1] 0.0081 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00585 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.036083 _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] 0.013668 _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 1PE A 1 201 1 1PE 1PE . D 3 GOL A 1 202 1 GOL GOL . E 4 BME B 1 201 1 BME BME . F 3 GOL B 1 202 2 GOL GOL . G 5 HOH A 1 301 210 HOH HOH . G 5 HOH A 2 302 2 HOH HOH . G 5 HOH A 3 303 217 HOH HOH . G 5 HOH A 4 304 175 HOH HOH . G 5 HOH A 5 305 229 HOH HOH . G 5 HOH A 6 306 135 HOH HOH . G 5 HOH A 7 307 126 HOH HOH . G 5 HOH A 8 308 228 HOH HOH . G 5 HOH A 9 309 13 HOH HOH . G 5 HOH A 10 310 32 HOH HOH . G 5 HOH A 11 311 104 HOH HOH . G 5 HOH A 12 312 226 HOH HOH . G 5 HOH A 13 313 227 HOH HOH . G 5 HOH A 14 314 61 HOH HOH . G 5 HOH A 15 315 172 HOH HOH . G 5 HOH A 16 316 129 HOH HOH . G 5 HOH A 17 317 23 HOH HOH . G 5 HOH A 18 318 91 HOH HOH . G 5 HOH A 19 319 96 HOH HOH . G 5 HOH A 20 320 70 HOH HOH . G 5 HOH A 21 321 235 HOH HOH . G 5 HOH A 22 322 27 HOH HOH . G 5 HOH A 23 323 83 HOH HOH . G 5 HOH A 24 324 171 HOH HOH . G 5 HOH A 25 325 190 HOH HOH . G 5 HOH A 26 326 26 HOH HOH . G 5 HOH A 27 327 76 HOH HOH . G 5 HOH A 28 328 15 HOH HOH . G 5 HOH A 29 329 152 HOH HOH . G 5 HOH A 30 330 103 HOH HOH . G 5 HOH A 31 331 125 HOH HOH . G 5 HOH A 32 332 140 HOH HOH . G 5 HOH A 33 333 167 HOH HOH . G 5 HOH A 34 334 107 HOH HOH . G 5 HOH A 35 335 49 HOH HOH . G 5 HOH A 36 336 54 HOH HOH . G 5 HOH A 37 337 6 HOH HOH . G 5 HOH A 38 338 187 HOH HOH . G 5 HOH A 39 339 240 HOH HOH . G 5 HOH A 40 340 188 HOH HOH . G 5 HOH A 41 341 43 HOH HOH . G 5 HOH A 42 342 251 HOH HOH . G 5 HOH A 43 343 245 HOH HOH . G 5 HOH A 44 344 211 HOH HOH . G 5 HOH A 45 345 134 HOH HOH . G 5 HOH A 46 346 92 HOH HOH . G 5 HOH A 47 347 136 HOH HOH . G 5 HOH A 48 348 139 HOH HOH . G 5 HOH A 49 349 64 HOH HOH . G 5 HOH A 50 350 242 HOH HOH . G 5 HOH A 51 351 12 HOH HOH . G 5 HOH A 52 352 53 HOH HOH . G 5 HOH A 53 353 177 HOH HOH . G 5 HOH A 54 354 143 HOH HOH . G 5 HOH A 55 355 223 HOH HOH . G 5 HOH A 56 356 16 HOH HOH . G 5 HOH A 57 357 82 HOH HOH . G 5 HOH A 58 358 94 HOH HOH . G 5 HOH A 59 359 178 HOH HOH . G 5 HOH A 60 360 179 HOH HOH . G 5 HOH A 61 361 86 HOH HOH . G 5 HOH A 62 362 50 HOH HOH . G 5 HOH A 63 363 89 HOH HOH . G 5 HOH A 64 364 141 HOH HOH . G 5 HOH A 65 365 230 HOH HOH . G 5 HOH A 66 366 158 HOH HOH . G 5 HOH A 67 367 159 HOH HOH . G 5 HOH A 68 368 165 HOH HOH . G 5 HOH A 69 369 142 HOH HOH . G 5 HOH A 70 370 236 HOH HOH . G 5 HOH A 71 371 34 HOH HOH . G 5 HOH A 72 372 77 HOH HOH . G 5 HOH A 73 373 90 HOH HOH . G 5 HOH A 74 374 71 HOH HOH . G 5 HOH A 75 375 237 HOH HOH . G 5 HOH A 76 376 123 HOH HOH . G 5 HOH A 77 377 166 HOH HOH . G 5 HOH A 78 378 110 HOH HOH . G 5 HOH A 79 379 150 HOH HOH . G 5 HOH A 80 380 173 HOH HOH . G 5 HOH A 81 381 37 HOH HOH . G 5 HOH A 82 382 67 HOH HOH . G 5 HOH A 83 383 244 HOH HOH . G 5 HOH A 84 384 4 HOH HOH . G 5 HOH A 85 385 65 HOH HOH . G 5 HOH A 86 386 233 HOH HOH . G 5 HOH A 87 387 163 HOH HOH . G 5 HOH A 88 388 225 HOH HOH . G 5 HOH A 89 389 183 HOH HOH . G 5 HOH A 90 390 209 HOH HOH . G 5 HOH A 91 391 93 HOH HOH . G 5 HOH A 92 392 154 HOH HOH . G 5 HOH A 93 393 208 HOH HOH . G 5 HOH A 94 394 66 HOH HOH . G 5 HOH A 95 395 253 HOH HOH . G 5 HOH A 96 396 128 HOH HOH . G 5 HOH A 97 397 191 HOH HOH . G 5 HOH A 98 398 257 HOH HOH . G 5 HOH A 99 399 212 HOH HOH . G 5 HOH A 100 400 186 HOH HOH . G 5 HOH A 101 401 205 HOH HOH . G 5 HOH A 102 402 117 HOH HOH . G 5 HOH A 103 403 222 HOH HOH . G 5 HOH A 104 404 213 HOH HOH . G 5 HOH A 105 405 189 HOH HOH . G 5 HOH A 106 406 155 HOH HOH . G 5 HOH A 107 407 147 HOH HOH . G 5 HOH A 108 408 201 HOH HOH . G 5 HOH A 109 409 181 HOH HOH . G 5 HOH A 110 410 202 HOH HOH . G 5 HOH A 111 411 259 HOH HOH . G 5 HOH A 112 412 105 HOH HOH . G 5 HOH A 113 413 203 HOH HOH . G 5 HOH A 114 414 260 HOH HOH . G 5 HOH A 115 415 204 HOH HOH . H 5 HOH B 1 301 232 HOH HOH . H 5 HOH B 2 302 215 HOH HOH . H 5 HOH B 3 303 199 HOH HOH . H 5 HOH B 4 304 164 HOH HOH . H 5 HOH B 5 305 219 HOH HOH . H 5 HOH B 6 306 22 HOH HOH . H 5 HOH B 7 307 218 HOH HOH . H 5 HOH B 8 308 207 HOH HOH . H 5 HOH B 9 309 252 HOH HOH . H 5 HOH B 10 310 68 HOH HOH . H 5 HOH B 11 311 231 HOH HOH . H 5 HOH B 12 312 114 HOH HOH . H 5 HOH B 13 313 38 HOH HOH . H 5 HOH B 14 314 168 HOH HOH . H 5 HOH B 15 315 40 HOH HOH . H 5 HOH B 16 316 148 HOH HOH . H 5 HOH B 17 317 99 HOH HOH . H 5 HOH B 18 318 14 HOH HOH . H 5 HOH B 19 319 120 HOH HOH . H 5 HOH B 20 320 156 HOH HOH . H 5 HOH B 21 321 216 HOH HOH . H 5 HOH B 22 322 144 HOH HOH . H 5 HOH B 23 323 85 HOH HOH . H 5 HOH B 24 324 220 HOH HOH . H 5 HOH B 25 325 73 HOH HOH . H 5 HOH B 26 326 59 HOH HOH . H 5 HOH B 27 327 1 HOH HOH . H 5 HOH B 28 328 137 HOH HOH . H 5 HOH B 29 329 46 HOH HOH . H 5 HOH B 30 330 145 HOH HOH . H 5 HOH B 31 331 174 HOH HOH . H 5 HOH B 32 332 234 HOH HOH . H 5 HOH B 33 333 57 HOH HOH . H 5 HOH B 34 334 169 HOH HOH . H 5 HOH B 35 335 52 HOH HOH . H 5 HOH B 36 336 3 HOH HOH . H 5 HOH B 37 337 250 HOH HOH . H 5 HOH B 38 338 8 HOH HOH . H 5 HOH B 39 339 95 HOH HOH . H 5 HOH B 40 340 239 HOH HOH . H 5 HOH B 41 341 10 HOH HOH . H 5 HOH B 42 342 62 HOH HOH . H 5 HOH B 43 343 79 HOH HOH . H 5 HOH B 44 344 221 HOH HOH . H 5 HOH B 45 345 78 HOH HOH . H 5 HOH B 46 346 9 HOH HOH . H 5 HOH B 47 347 115 HOH HOH . H 5 HOH B 48 348 247 HOH HOH . H 5 HOH B 49 349 88 HOH HOH . H 5 HOH B 50 350 18 HOH HOH . H 5 HOH B 51 351 111 HOH HOH . H 5 HOH B 52 352 31 HOH HOH . H 5 HOH B 53 353 30 HOH HOH . H 5 HOH B 54 354 17 HOH HOH . H 5 HOH B 55 355 84 HOH HOH . H 5 HOH B 56 356 47 HOH HOH . H 5 HOH B 57 357 7 HOH HOH . H 5 HOH B 58 358 112 HOH HOH . H 5 HOH B 59 359 102 HOH HOH . H 5 HOH B 60 360 5 HOH HOH . H 5 HOH B 61 361 98 HOH HOH . H 5 HOH B 62 362 41 HOH HOH . H 5 HOH B 63 363 121 HOH HOH . H 5 HOH B 64 364 29 HOH HOH . H 5 HOH B 65 365 243 HOH HOH . H 5 HOH B 66 366 238 HOH HOH . H 5 HOH B 67 367 35 HOH HOH . H 5 HOH B 68 368 20 HOH HOH . H 5 HOH B 69 369 138 HOH HOH . H 5 HOH B 70 370 51 HOH HOH . H 5 HOH B 71 371 58 HOH HOH . H 5 HOH B 72 372 25 HOH HOH . H 5 HOH B 73 373 24 HOH HOH . H 5 HOH B 74 374 108 HOH HOH . H 5 HOH B 75 375 100 HOH HOH . H 5 HOH B 76 376 127 HOH HOH . H 5 HOH B 77 377 44 HOH HOH . H 5 HOH B 78 378 170 HOH HOH . H 5 HOH B 79 379 60 HOH HOH . H 5 HOH B 80 380 48 HOH HOH . H 5 HOH B 81 381 11 HOH HOH . H 5 HOH B 82 382 132 HOH HOH . H 5 HOH B 83 383 241 HOH HOH . H 5 HOH B 84 384 39 HOH HOH . H 5 HOH B 85 385 55 HOH HOH . H 5 HOH B 86 386 246 HOH HOH . H 5 HOH B 87 387 119 HOH HOH . H 5 HOH B 88 388 33 HOH HOH . H 5 HOH B 89 389 160 HOH HOH . H 5 HOH B 90 390 124 HOH HOH . H 5 HOH B 91 391 131 HOH HOH . H 5 HOH B 92 392 80 HOH HOH . H 5 HOH B 93 393 248 HOH HOH . H 5 HOH B 94 394 81 HOH HOH . H 5 HOH B 95 395 122 HOH HOH . H 5 HOH B 96 396 161 HOH HOH . H 5 HOH B 97 397 180 HOH HOH . H 5 HOH B 98 398 87 HOH HOH . H 5 HOH B 99 399 56 HOH HOH . H 5 HOH B 100 400 19 HOH HOH . H 5 HOH B 101 401 36 HOH HOH . H 5 HOH B 102 402 133 HOH HOH . H 5 HOH B 103 403 72 HOH HOH . H 5 HOH B 104 404 69 HOH HOH . H 5 HOH B 105 405 21 HOH HOH . H 5 HOH B 106 406 198 HOH HOH . H 5 HOH B 107 407 146 HOH HOH . H 5 HOH B 108 408 192 HOH HOH . H 5 HOH B 109 409 28 HOH HOH . H 5 HOH B 110 410 101 HOH HOH . H 5 HOH B 111 411 194 HOH HOH . H 5 HOH B 112 412 224 HOH HOH . H 5 HOH B 113 413 182 HOH HOH . H 5 HOH B 114 414 74 HOH HOH . H 5 HOH B 115 415 214 HOH HOH . H 5 HOH B 116 416 200 HOH HOH . H 5 HOH B 117 417 196 HOH HOH . H 5 HOH B 118 418 258 HOH HOH . H 5 HOH B 119 419 109 HOH HOH . H 5 HOH B 120 420 193 HOH HOH . H 5 HOH B 121 421 116 HOH HOH . H 5 HOH B 122 422 185 HOH HOH . H 5 HOH B 123 423 157 HOH HOH . H 5 HOH B 124 424 153 HOH HOH . H 5 HOH B 125 425 149 HOH HOH . H 5 HOH B 126 426 184 HOH HOH . H 5 HOH B 127 427 256 HOH HOH . H 5 HOH B 128 428 261 HOH HOH . H 5 HOH B 129 429 176 HOH HOH . H 5 HOH B 130 430 162 HOH HOH . H 5 HOH B 131 431 113 HOH HOH . H 5 HOH B 132 432 97 HOH HOH . H 5 HOH B 133 433 63 HOH HOH . H 5 HOH B 134 434 195 HOH HOH . H 5 HOH B 135 435 45 HOH HOH . H 5 HOH B 136 436 249 HOH HOH . H 5 HOH B 137 437 197 HOH HOH . H 5 HOH B 138 438 106 HOH HOH . H 5 HOH B 139 439 130 HOH HOH . H 5 HOH B 140 440 206 HOH HOH . H 5 HOH B 141 441 255 HOH HOH . H 5 HOH B 142 442 118 HOH HOH . H 5 HOH B 143 443 42 HOH HOH . H 5 HOH B 144 444 254 HOH HOH . H 5 HOH B 145 445 151 HOH HOH . H 5 HOH B 146 446 75 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 BME . . . E 4 -19.672 -3.072 16.881 1 39.27 ? C1 BME 201 B 1 HETATM 2 C C2 BME . . . E 4 -20.722 -3.55 15.937 1 43.73 ? C2 BME 201 B 1 HETATM 3 O O1 BME . . . E 4 -18.57 -2.449 16.205 1 63.35 ? O1 BME 201 B 1 HETATM 4 S S2 BME . . . E 4 -21.419 -5.126 16.457 1 80.69 ? S2 BME 201 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 4 #