data_5E89 # _model_server_result.job_id fLwGlR3GslTaV-PPklBvRg _model_server_result.datetime_utc '2025-01-10 15:35:56' _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 5e89 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 5E89 # _exptl.entry_id 5E89 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 648.635 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-1-thio-beta-D-galactopyranoside' _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 90 _cell.entry_id 5E89 _cell.length_a 37.045 _cell.length_b 58.298 _cell.length_c 63.728 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5E89 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C28 H30 F2 N6 O8 S' _chem_comp.formula_weight 648.635 _chem_comp.id TD2 _chem_comp.mon_nstd_flag . _chem_comp.name '3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-1-thio-beta-D-galactopyranoside' _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 O61 C61 TD2 sing 290 n n C61 C51 TD2 sing 291 n n C51 O51 TD2 sing 292 n n C51 C41 TD2 sing 293 n n O51 C11 TD2 sing 294 n n O6 C6 TD2 sing 295 n n C5 C6 TD2 sing 296 n n C5 O5 TD2 sing 297 n n C5 C4 TD2 sing 298 n n C41 O41 TD2 sing 299 n n C41 C31 TD2 sing 300 n n O5 C1 TD2 sing 301 n n C4 C3 TD2 sing 302 n n C4 O4 TD2 sing 303 n n C1 C2 TD2 sing 304 n n C1 S1 TD2 sing 305 n n C3 C2 TD2 sing 306 n n C3 N71 TD2 sing 307 n n N8 N71 TD2 sing 308 n y N8 N9 TD2 doub 309 n y C11 S1 TD2 sing 310 n n C11 C21 TD2 sing 311 n n O21 C2 TD2 sing 312 n n C31 C21 TD2 sing 313 n n C31 N7 TD2 sing 314 n n N71 C71 TD2 sing 315 n y N9 C10 TD2 sing 316 n y C21 O2 TD2 sing 317 n n N11 N7 TD2 sing 318 n y N11 N10 TD2 doub 319 n y N7 C8 TD2 sing 320 n y C71 C10 TD2 doub 321 n y N10 C9 TD2 sing 322 n y C10 C22 TD2 sing 323 n n C8 C9 TD2 doub 324 n y C9 C12 TD2 sing 325 n n C23 C22 TD2 doub 326 n y C23 C24 TD2 sing 327 n y C22 C27 TD2 sing 328 n y C24 C25 TD2 doub 329 n y C12 C13 TD2 doub 330 n y C12 C17 TD2 sing 331 n y C27 C26 TD2 doub 332 n y C13 C14 TD2 sing 333 n y C17 C16 TD2 doub 334 n y C25 C26 TD2 sing 335 n y C26 F28 TD2 sing 336 n n C14 F18 TD2 sing 337 n n C14 C15 TD2 doub 338 n y C16 C15 TD2 sing 339 n y C1 H1 TD2 sing 340 n n C2 H2 TD2 sing 341 n n C3 H3 TD2 sing 342 n n C4 H4 TD2 sing 343 n n C5 H5 TD2 sing 344 n n C6 H6 TD2 sing 345 n n C6 H7 TD2 sing 346 n n C13 H8 TD2 sing 347 n n C11 H9 TD2 sing 348 n n C51 H10 TD2 sing 349 n n C61 H11 TD2 sing 350 n n C61 H12 TD2 sing 351 n n O6 H13 TD2 sing 352 n n O61 H14 TD2 sing 353 n n C41 H15 TD2 sing 354 n n O4 H16 TD2 sing 355 n n O41 H17 TD2 sing 356 n n C31 H18 TD2 sing 357 n n C21 H19 TD2 sing 358 n n O2 H20 TD2 sing 359 n n O21 H21 TD2 sing 360 n n C8 H22 TD2 sing 361 n n C71 H23 TD2 sing 362 n n C15 H24 TD2 sing 363 n n C16 H25 TD2 sing 364 n n C17 H26 TD2 sing 365 n n C23 H27 TD2 sing 366 n n C24 H28 TD2 sing 367 n n C25 H29 TD2 sing 368 n n C27 H30 TD2 sing 369 n n # _atom_sites.entry_id 5E89 _atom_sites.fract_transf_matrix[1][1] 0.026994 _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] 0.017153 _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] 0.015692 _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 CL A 1 301 1 CL CL . C 3 TD2 A 1 302 1 TD2 TDM . D 4 HOH A 1 401 178 HOH HOH . D 4 HOH A 2 402 175 HOH HOH . D 4 HOH A 3 403 173 HOH HOH . D 4 HOH A 4 404 73 HOH HOH . D 4 HOH A 5 405 68 HOH HOH . D 4 HOH A 6 406 84 HOH HOH . D 4 HOH A 7 407 33 HOH HOH . D 4 HOH A 8 408 14 HOH HOH . D 4 HOH A 9 409 108 HOH HOH . D 4 HOH A 10 410 101 HOH HOH . D 4 HOH A 11 411 26 HOH HOH . D 4 HOH A 12 412 170 HOH HOH . D 4 HOH A 13 413 45 HOH HOH . D 4 HOH A 14 414 38 HOH HOH . D 4 HOH A 15 415 17 HOH HOH . D 4 HOH A 16 416 29 HOH HOH . D 4 HOH A 17 417 116 HOH HOH . D 4 HOH A 18 418 113 HOH HOH . D 4 HOH A 19 419 94 HOH HOH . D 4 HOH A 20 420 83 HOH HOH . D 4 HOH A 21 421 2 HOH HOH . D 4 HOH A 22 422 90 HOH HOH . D 4 HOH A 23 423 59 HOH HOH . D 4 HOH A 24 424 54 HOH HOH . D 4 HOH A 25 425 124 HOH HOH . D 4 HOH A 26 426 182 HOH HOH . D 4 HOH A 27 427 87 HOH HOH . D 4 HOH A 28 428 118 HOH HOH . D 4 HOH A 29 429 24 HOH HOH . D 4 HOH A 30 430 103 HOH HOH . D 4 HOH A 31 431 76 HOH HOH . D 4 HOH A 32 432 92 HOH HOH . D 4 HOH A 33 433 7 HOH HOH . D 4 HOH A 34 434 141 HOH HOH . D 4 HOH A 35 435 85 HOH HOH . D 4 HOH A 36 436 143 HOH HOH . D 4 HOH A 37 437 61 HOH HOH . D 4 HOH A 38 438 22 HOH HOH . D 4 HOH A 39 439 50 HOH HOH . D 4 HOH A 40 440 154 HOH HOH . D 4 HOH A 41 441 123 HOH HOH . D 4 HOH A 42 442 156 HOH HOH . D 4 HOH A 43 443 181 HOH HOH . D 4 HOH A 44 444 176 HOH HOH . D 4 HOH A 45 445 5 HOH HOH . D 4 HOH A 46 446 48 HOH HOH . D 4 HOH A 47 447 58 HOH HOH . D 4 HOH A 48 448 46 HOH HOH . D 4 HOH A 49 449 4 HOH HOH . D 4 HOH A 50 450 140 HOH HOH . D 4 HOH A 51 451 163 HOH HOH . D 4 HOH A 52 452 3 HOH HOH . D 4 HOH A 53 453 12 HOH HOH . D 4 HOH A 54 454 136 HOH HOH . D 4 HOH A 55 455 91 HOH HOH . D 4 HOH A 56 456 196 HOH HOH . D 4 HOH A 57 457 52 HOH HOH . D 4 HOH A 58 458 65 HOH HOH . D 4 HOH A 59 459 10 HOH HOH . D 4 HOH A 60 460 15 HOH HOH . D 4 HOH A 61 461 67 HOH HOH . D 4 HOH A 62 462 37 HOH HOH . D 4 HOH A 63 463 18 HOH HOH . D 4 HOH A 64 464 11 HOH HOH . D 4 HOH A 65 465 93 HOH HOH . D 4 HOH A 66 466 8 HOH HOH . D 4 HOH A 67 467 74 HOH HOH . D 4 HOH A 68 468 80 HOH HOH . D 4 HOH A 69 469 71 HOH HOH . D 4 HOH A 70 470 1 HOH HOH . D 4 HOH A 71 471 100 HOH HOH . D 4 HOH A 72 472 149 HOH HOH . D 4 HOH A 73 473 20 HOH HOH . D 4 HOH A 74 474 40 HOH HOH . D 4 HOH A 75 475 174 HOH HOH . D 4 HOH A 76 476 36 HOH HOH . D 4 HOH A 77 477 60 HOH HOH . D 4 HOH A 78 478 57 HOH HOH . D 4 HOH A 79 479 105 HOH HOH . D 4 HOH A 80 480 6 HOH HOH . D 4 HOH A 81 481 192 HOH HOH . D 4 HOH A 82 482 107 HOH HOH . D 4 HOH A 83 483 69 HOH HOH . D 4 HOH A 84 484 39 HOH HOH . D 4 HOH A 85 485 66 HOH HOH . D 4 HOH A 86 486 28 HOH HOH . D 4 HOH A 87 487 35 HOH HOH . D 4 HOH A 88 488 128 HOH HOH . D 4 HOH A 89 489 104 HOH HOH . D 4 HOH A 90 490 183 HOH HOH . D 4 HOH A 91 491 49 HOH HOH . D 4 HOH A 92 492 75 HOH HOH . D 4 HOH A 93 493 34 HOH HOH . D 4 HOH A 94 494 19 HOH HOH . D 4 HOH A 95 495 53 HOH HOH . D 4 HOH A 96 496 171 HOH HOH . D 4 HOH A 97 497 16 HOH HOH . D 4 HOH A 98 498 23 HOH HOH . D 4 HOH A 99 499 114 HOH HOH . D 4 HOH A 100 500 115 HOH HOH . D 4 HOH A 101 501 77 HOH HOH . D 4 HOH A 102 502 42 HOH HOH . D 4 HOH A 103 503 97 HOH HOH . D 4 HOH A 104 504 62 HOH HOH . D 4 HOH A 105 505 13 HOH HOH . D 4 HOH A 106 506 194 HOH HOH . D 4 HOH A 107 507 79 HOH HOH . D 4 HOH A 108 508 160 HOH HOH . D 4 HOH A 109 509 21 HOH HOH . D 4 HOH A 110 510 117 HOH HOH . D 4 HOH A 111 511 47 HOH HOH . D 4 HOH A 112 512 64 HOH HOH . D 4 HOH A 113 513 44 HOH HOH . D 4 HOH A 114 514 99 HOH HOH . D 4 HOH A 115 515 144 HOH HOH . D 4 HOH A 116 516 27 HOH HOH . D 4 HOH A 117 517 195 HOH HOH . D 4 HOH A 118 518 88 HOH HOH . D 4 HOH A 119 519 41 HOH HOH . D 4 HOH A 120 520 9 HOH HOH . D 4 HOH A 121 521 56 HOH HOH . D 4 HOH A 122 522 161 HOH HOH . D 4 HOH A 123 523 32 HOH HOH . D 4 HOH A 124 524 98 HOH HOH . D 4 HOH A 125 525 95 HOH HOH . D 4 HOH A 126 526 119 HOH HOH . D 4 HOH A 127 527 96 HOH HOH . D 4 HOH A 128 528 184 HOH HOH . D 4 HOH A 129 529 137 HOH HOH . D 4 HOH A 130 530 129 HOH HOH . D 4 HOH A 131 531 31 HOH HOH . D 4 HOH A 132 532 142 HOH HOH . D 4 HOH A 133 533 81 HOH HOH . D 4 HOH A 134 534 86 HOH HOH . D 4 HOH A 135 535 30 HOH HOH . D 4 HOH A 136 536 43 HOH HOH . D 4 HOH A 137 537 169 HOH HOH . D 4 HOH A 138 538 109 HOH HOH . D 4 HOH A 139 539 51 HOH HOH . D 4 HOH A 140 540 187 HOH HOH . D 4 HOH A 141 541 139 HOH HOH . D 4 HOH A 142 542 133 HOH HOH . D 4 HOH A 143 543 188 HOH HOH . D 4 HOH A 144 544 55 HOH HOH . D 4 HOH A 145 545 72 HOH HOH . D 4 HOH A 146 546 106 HOH HOH . D 4 HOH A 147 547 25 HOH HOH . D 4 HOH A 148 548 70 HOH HOH . D 4 HOH A 149 549 185 HOH HOH . D 4 HOH A 150 550 78 HOH HOH . D 4 HOH A 151 551 193 HOH HOH . D 4 HOH A 152 552 110 HOH HOH . D 4 HOH A 153 553 191 HOH HOH . D 4 HOH A 154 554 186 HOH HOH . D 4 HOH A 155 555 89 HOH HOH . D 4 HOH A 156 556 189 HOH HOH . D 4 HOH A 157 557 121 HOH HOH . D 4 HOH A 158 558 63 HOH HOH . D 4 HOH A 159 559 155 HOH HOH . D 4 HOH A 160 560 112 HOH HOH . D 4 HOH A 161 561 126 HOH HOH . D 4 HOH A 162 562 190 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 TD2 . . . C 3 20.135 -8.964 -1.133 0.7 12.63 ? C1 TD2 302 A 1 HETATM 2 C C2 TD2 . . . C 3 18.66 -9.24 -1.018 0.7 12.78 ? C2 TD2 302 A 1 HETATM 3 C C3 TD2 . . . C 3 17.9 -7.998 -1.393 0.7 12.73 ? C3 TD2 302 A 1 HETATM 4 C C4 TD2 . . . C 3 18.42 -6.832 -0.563 0.7 9.66 ? C4 TD2 302 A 1 HETATM 5 C C5 TD2 . . . C 3 19.915 -6.68 -0.75 0.7 9.91 ? C5 TD2 302 A 1 HETATM 6 C C6 TD2 . . . C 3 20.457 -5.525 0.069 0.7 10.07 ? C6 TD2 302 A 1 HETATM 7 N N9 TD2 . . . C 3 14.316 -8.125 -1.862 0.7 20.67 ? N9 TD2 302 A 1 HETATM 8 C C12 TD2 . . . C 3 27.446 -11.14 4.117 0.7 35.7 ? C12 TD2 302 A 1 HETATM 9 C C13 TD2 . . . C 3 26.775 -12.252 4.575 0.7 36.9 ? C13 TD2 302 A 1 HETATM 10 C C14 TD2 . . . C 3 27.081 -12.811 5.799 0.7 42.63 ? C14 TD2 302 A 1 HETATM 11 C C11 TD2 . . . C 3 22.587 -9.957 -0.907 0.7 18.03 ? C11 TD2 302 A 1 HETATM 12 S S1 TD2 . . . C 3 20.937 -10.391 -0.552 0.7 18.53 ? S1 TD2 302 A 1 HETATM 13 O O5 TD2 . . . C 3 20.529 -7.883 -0.332 0.7 9.34 ? O5 TD2 302 A 1 HETATM 14 O O51 TD2 . . . C 3 23.04 -10.794 -1.973 0.7 23.61 ? O51 TD2 302 A 1 HETATM 15 C C51 TD2 . . . C 3 24.367 -10.521 -2.345 0.7 26.31 ? C51 TD2 302 A 1 HETATM 16 C C61 TD2 . . . C 3 24.772 -11.404 -3.526 0.7 32.94 ? C61 TD2 302 A 1 HETATM 17 O O6 TD2 . . . C 3 21.837 -5.419 -0.2 0.7 13.03 ? O6 TD2 302 A 1 HETATM 18 O O61 TD2 . . . C 3 24.155 -10.845 -4.676 0.7 36.66 ? O61 TD2 302 A 1 HETATM 19 C C41 TD2 . . . C 3 25.334 -10.741 -1.205 0.7 25.6 ? C41 TD2 302 A 1 HETATM 20 O O4 TD2 . . . C 3 18.113 -7.037 0.813 0.7 6.11 ? O4 TD2 302 A 1 HETATM 21 O O41 TD2 . . . C 3 25.488 -12.123 -0.872 0.7 28.27 ? O41 TD2 302 A 1 HETATM 22 C C31 TD2 . . . C 3 24.851 -9.95 -0.018 0.7 21.52 ? C31 TD2 302 A 1 HETATM 23 C C21 TD2 . . . C 3 23.409 -10.258 0.323 0.7 18.19 ? C21 TD2 302 A 1 HETATM 24 O O2 TD2 . . . C 3 23.001 -9.456 1.431 0.7 13.33 ? O2 TD2 302 A 1 HETATM 25 O O21 TD2 . . . C 3 18.302 -10.279 -1.925 0.7 17.34 ? O21 TD2 302 A 1 HETATM 26 N N7 TD2 . . . C 3 25.748 -10.166 1.111 0.7 25.47 ? N7 TD2 302 A 1 HETATM 27 C C8 TD2 . . . C 3 25.828 -10.95 2.156 0.7 28.05 ? C8 TD2 302 A 1 HETATM 28 C C9 TD2 . . . C 3 26.987 -10.581 2.824 0.7 31.07 ? C9 TD2 302 A 1 HETATM 29 N N10 TD2 . . . C 3 27.563 -9.555 2.191 0.7 31.02 ? N10 TD2 302 A 1 HETATM 30 N N11 TD2 . . . C 3 26.798 -9.278 1.082 0.7 28.75 ? N11 TD2 302 A 1 HETATM 31 N N71 TD2 . . . C 3 16.454 -8.15 -1.188 0.7 14.56 ? N71 TD2 302 A 1 HETATM 32 N N8 TD2 . . . C 3 15.633 -7.954 -2.3 0.7 20.35 ? N8 TD2 302 A 1 HETATM 33 C C10 TD2 . . . C 3 14.418 -8.406 -0.55 0.7 17.35 ? C10 TD2 302 A 1 HETATM 34 C C71 TD2 . . . C 3 15.732 -8.428 -0.138 0.7 15.07 ? C71 TD2 302 A 1 HETATM 35 C C15 TD2 . . . C 3 28.052 -12.223 6.589 0.7 44.7 ? C15 TD2 302 A 1 HETATM 36 C C16 TD2 . . . C 3 28.697 -11.067 6.157 0.7 43.32 ? C16 TD2 302 A 1 HETATM 37 C C17 TD2 . . . C 3 28.383 -10.503 4.924 0.7 38.67 ? C17 TD2 302 A 1 HETATM 38 C C22 TD2 . . . C 3 13.149 -8.648 0.202 0.7 19.17 ? C22 TD2 302 A 1 HETATM 39 C C23 TD2 . . . C 3 11.983 -9.01 -0.464 0.7 23.22 ? C23 TD2 302 A 1 HETATM 40 C C24 TD2 . . . C 3 10.815 -9.233 0.252 0.7 25.6 ? C24 TD2 302 A 1 HETATM 41 C C25 TD2 . . . C 3 10.814 -9.105 1.637 0.7 24.27 ? C25 TD2 302 A 1 HETATM 42 C C26 TD2 . . . C 3 11.968 -8.766 2.288 0.7 20.81 ? C26 TD2 302 A 1 HETATM 43 C C27 TD2 . . . C 3 13.134 -8.507 1.589 0.7 17.54 ? C27 TD2 302 A 1 HETATM 44 F F18 TD2 . . . C 3 26.379 -13.944 6.071 0.7 48.17 ? F18 TD2 302 A 1 HETATM 45 F F28 TD2 . . . C 3 11.908 -8.646 3.626 0.7 24.14 ? F28 TD2 302 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 45 #