data_8VJF # _model_server_result.job_id MbzATVEBxUasjY6fDaeh6A _model_server_result.datetime_utc '2024-11-15 04:38:59' _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 8vjf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 8VJF # _exptl.entry_id 8VJF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 154.251 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,3-DIHYDROXY-1,4-DITHIOBUTANE _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 90 _cell.angle_gamma 120 _cell.entry_id 8VJF _cell.length_a 68.867 _cell.length_b 68.867 _cell.length_c 78.738 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VJF _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 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,I _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 D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 A SG CYS 116 A CYS 113 1_555 B CH3 ACE 1 B ACE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.739 ? covale ? covale2 B C ACE 1 B ACE 1 1_555 B N MTY 2 B MTY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale3 B C MTY 2 B MTY 2 1_555 B N YCP 3 B YCP 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale4 B C YCP 3 B YCP 3 1_555 B N TRP 4 B TRP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale5 B C TRP 4 B TRP 4 1_555 B N NH2 5 B NH2 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? # _chem_comp.formula 'C4 H10 O2 S2' _chem_comp.formula_weight 154.251 _chem_comp.id DTT _chem_comp.mon_nstd_flag . _chem_comp.name 2,3-DIHYDROXY-1,4-DITHIOBUTANE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1,4-DITHIOTHREITOL # 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 S1 C1 DTT sing 89 n n S1 HS1 DTT sing 90 n n C1 C2 DTT sing 91 n n C1 H11 DTT sing 92 n n C1 H12 DTT sing 93 n n C2 O2 DTT sing 94 n n C2 C3 DTT sing 95 n n C2 H2 DTT sing 96 n n O2 HO2 DTT sing 97 n n C3 O3 DTT sing 98 n n C3 C4 DTT sing 99 n n C3 H3 DTT sing 100 n n O3 HO3 DTT sing 101 n n C4 S4 DTT sing 102 n n C4 H41 DTT sing 103 n n C4 H42 DTT sing 104 n n S4 HS2 DTT sing 105 n n # _atom_sites.entry_id 8VJF _atom_sites.fract_transf_matrix[1][1] 0.014521 _atom_sites.fract_transf_matrix[1][2] 0.008384 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016767 _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] 0.0127 _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 3 P33 A 1 201 206 P33 PEG . D 4 DTT A 1 202 207 DTT DTT . E 5 SO4 A 1 203 2 SO4 SO4 . F 5 SO4 A 1 204 4 SO4 SO4 . G 5 SO4 A 1 205 5 SO4 SO4 . H 6 HOH A 1 301 197 HOH HOH . H 6 HOH A 2 302 62 HOH HOH . H 6 HOH A 3 303 115 HOH HOH . H 6 HOH A 4 304 5 HOH HOH . H 6 HOH A 5 305 85 HOH HOH . H 6 HOH A 6 306 18 HOH HOH . H 6 HOH A 7 307 121 HOH HOH . H 6 HOH A 8 308 212 HOH HOH . H 6 HOH A 9 309 205 HOH HOH . H 6 HOH A 10 310 55 HOH HOH . H 6 HOH A 11 311 37 HOH HOH . H 6 HOH A 12 312 91 HOH HOH . H 6 HOH A 13 313 2 HOH HOH . H 6 HOH A 14 314 177 HOH HOH . H 6 HOH A 15 315 89 HOH HOH . H 6 HOH A 16 316 203 HOH HOH . H 6 HOH A 17 317 46 HOH HOH . H 6 HOH A 18 318 214 HOH HOH . H 6 HOH A 19 319 103 HOH HOH . H 6 HOH A 20 320 77 HOH HOH . H 6 HOH A 21 321 21 HOH HOH . H 6 HOH A 22 322 68 HOH HOH . H 6 HOH A 23 323 99 HOH HOH . H 6 HOH A 24 324 172 HOH HOH . H 6 HOH A 25 325 23 HOH HOH . H 6 HOH A 26 326 195 HOH HOH . H 6 HOH A 27 327 17 HOH HOH . H 6 HOH A 28 328 66 HOH HOH . H 6 HOH A 29 329 111 HOH HOH . H 6 HOH A 30 330 33 HOH HOH . H 6 HOH A 31 331 86 HOH HOH . H 6 HOH A 32 332 56 HOH HOH . H 6 HOH A 33 333 114 HOH HOH . H 6 HOH A 34 334 79 HOH HOH . H 6 HOH A 35 335 28 HOH HOH . H 6 HOH A 36 336 47 HOH HOH . H 6 HOH A 37 337 109 HOH HOH . H 6 HOH A 38 338 180 HOH HOH . H 6 HOH A 39 339 13 HOH HOH . H 6 HOH A 40 340 57 HOH HOH . H 6 HOH A 41 341 151 HOH HOH . H 6 HOH A 42 342 139 HOH HOH . H 6 HOH A 43 343 204 HOH HOH . H 6 HOH A 44 344 58 HOH HOH . H 6 HOH A 45 345 36 HOH HOH . H 6 HOH A 46 346 96 HOH HOH . H 6 HOH A 47 347 74 HOH HOH . H 6 HOH A 48 348 171 HOH HOH . H 6 HOH A 49 349 61 HOH HOH . H 6 HOH A 50 350 10 HOH HOH . H 6 HOH A 51 351 88 HOH HOH . H 6 HOH A 52 352 11 HOH HOH . H 6 HOH A 53 353 202 HOH HOH . H 6 HOH A 54 354 71 HOH HOH . H 6 HOH A 55 355 32 HOH HOH . H 6 HOH A 56 356 25 HOH HOH . H 6 HOH A 57 357 14 HOH HOH . H 6 HOH A 58 358 175 HOH HOH . H 6 HOH A 59 359 60 HOH HOH . H 6 HOH A 60 360 34 HOH HOH . H 6 HOH A 61 361 170 HOH HOH . H 6 HOH A 62 362 207 HOH HOH . H 6 HOH A 63 363 188 HOH HOH . H 6 HOH A 64 364 4 HOH HOH . H 6 HOH A 65 365 94 HOH HOH . H 6 HOH A 66 366 53 HOH HOH . H 6 HOH A 67 367 15 HOH HOH . H 6 HOH A 68 368 6 HOH HOH . H 6 HOH A 69 369 176 HOH HOH . H 6 HOH A 70 370 98 HOH HOH . H 6 HOH A 71 371 160 HOH HOH . H 6 HOH A 72 372 107 HOH HOH . H 6 HOH A 73 373 174 HOH HOH . H 6 HOH A 74 374 51 HOH HOH . H 6 HOH A 75 375 141 HOH HOH . H 6 HOH A 76 376 102 HOH HOH . H 6 HOH A 77 377 100 HOH HOH . H 6 HOH A 78 378 154 HOH HOH . H 6 HOH A 79 379 194 HOH HOH . H 6 HOH A 80 380 134 HOH HOH . H 6 HOH A 81 381 16 HOH HOH . H 6 HOH A 82 382 20 HOH HOH . H 6 HOH A 83 383 196 HOH HOH . H 6 HOH A 84 384 152 HOH HOH . H 6 HOH A 85 385 110 HOH HOH . H 6 HOH A 86 386 125 HOH HOH . H 6 HOH A 87 387 104 HOH HOH . H 6 HOH A 88 388 213 HOH HOH . H 6 HOH A 89 389 12 HOH HOH . H 6 HOH A 90 390 65 HOH HOH . H 6 HOH A 91 391 73 HOH HOH . H 6 HOH A 92 392 209 HOH HOH . H 6 HOH A 93 393 35 HOH HOH . H 6 HOH A 94 394 191 HOH HOH . H 6 HOH A 95 395 155 HOH HOH . H 6 HOH A 96 396 161 HOH HOH . H 6 HOH A 97 397 206 HOH HOH . H 6 HOH A 98 398 101 HOH HOH . H 6 HOH A 99 399 116 HOH HOH . H 6 HOH A 100 400 95 HOH HOH . H 6 HOH A 101 401 165 HOH HOH . H 6 HOH A 102 402 148 HOH HOH . H 6 HOH A 103 403 105 HOH HOH . H 6 HOH A 104 404 190 HOH HOH . H 6 HOH A 105 405 90 HOH HOH . H 6 HOH A 106 406 9 HOH HOH . H 6 HOH A 107 407 182 HOH HOH . H 6 HOH A 108 408 198 HOH HOH . H 6 HOH A 109 409 156 HOH HOH . H 6 HOH A 110 410 124 HOH HOH . H 6 HOH A 111 411 76 HOH HOH . H 6 HOH A 112 412 106 HOH HOH . H 6 HOH A 113 413 164 HOH HOH . H 6 HOH A 114 414 138 HOH HOH . H 6 HOH A 115 415 169 HOH HOH . H 6 HOH A 116 416 29 HOH HOH . H 6 HOH A 117 417 52 HOH HOH . H 6 HOH A 118 418 211 HOH HOH . H 6 HOH A 119 419 49 HOH HOH . H 6 HOH A 120 420 183 HOH HOH . H 6 HOH A 121 421 22 HOH HOH . H 6 HOH A 122 422 97 HOH HOH . H 6 HOH A 123 423 130 HOH HOH . H 6 HOH A 124 424 44 HOH HOH . H 6 HOH A 125 425 8 HOH HOH . H 6 HOH A 126 426 78 HOH HOH . H 6 HOH A 127 427 162 HOH HOH . H 6 HOH A 128 428 123 HOH HOH . H 6 HOH A 129 429 137 HOH HOH . H 6 HOH A 130 430 108 HOH HOH . H 6 HOH A 131 431 45 HOH HOH . H 6 HOH A 132 432 146 HOH HOH . H 6 HOH A 133 433 153 HOH HOH . H 6 HOH A 134 434 179 HOH HOH . H 6 HOH A 135 435 75 HOH HOH . H 6 HOH A 136 436 64 HOH HOH . H 6 HOH A 137 437 59 HOH HOH . H 6 HOH A 138 438 112 HOH HOH . H 6 HOH A 139 439 122 HOH HOH . H 6 HOH A 140 440 185 HOH HOH . H 6 HOH A 141 441 199 HOH HOH . H 6 HOH A 142 442 144 HOH HOH . H 6 HOH A 143 443 136 HOH HOH . H 6 HOH A 144 444 143 HOH HOH . H 6 HOH A 145 445 178 HOH HOH . H 6 HOH A 146 446 184 HOH HOH . H 6 HOH A 147 447 210 HOH HOH . I 6 HOH B 1 101 70 HOH HOH . I 6 HOH B 2 102 67 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 S S1 DTT . . . D 4 38.918 -34.753 13.619 1 54.67 ? S1 DTT 202 A 1 HETATM 2 C C1 DTT . . . D 4 39.164 -35.461 11.957 1 54.28 ? C1 DTT 202 A 1 HETATM 3 C C2 DTT . . . D 4 40.56 -35.309 11.348 1 51.54 ? C2 DTT 202 A 1 HETATM 4 O O2 DTT . . . D 4 40.478 -34.97 9.981 1 43.14 ? O2 DTT 202 A 1 HETATM 5 C C3 DTT . . . D 4 41.332 -36.613 11.445 1 61.57 ? C3 DTT 202 A 1 HETATM 6 O O3 DTT . . . D 4 40.402 -37.673 11.422 1 69.39 ? O3 DTT 202 A 1 HETATM 7 C C4 DTT . . . D 4 42.3 -36.776 10.275 1 65.41 ? C4 DTT 202 A 1 HETATM 8 S S4 DTT . . . D 4 43.73 -35.661 10.29 1 71.67 ? S4 DTT 202 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 8 #