data_5E88 # _model_server_result.job_id VQtjjM_L9C64QPHfs1n4ng _model_server_result.datetime_utc '2025-01-26 18:29:14' _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 5e88 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 5E88 # _exptl.entry_id 5E88 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 624.71 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '3-deoxy-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-1-thio-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-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 5E88 _cell.length_a 36.464 _cell.length_b 58.034 _cell.length_c 63.122 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5E88 _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 'C24 H28 N6 O8 S3' _chem_comp.formula_weight 624.71 _chem_comp.id 5KT _chem_comp.mon_nstd_flag . _chem_comp.name '3-deoxy-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-1-thio-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranoside' _chem_comp.type d-saccharide _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 O6' C6' 5KT sing 1 n n C6' C5' 5KT sing 2 n n C5' O5' 5KT sing 3 n n C5' C4' 5KT sing 4 n n N2 N3 5KT doub 5 n y N2 N1 5KT sing 6 n y O5' C1' 5KT sing 7 n n O2 C2 5KT sing 8 n n N3 CB 5KT sing 9 n y C3 N1 5KT sing 10 n n C3 C2 5KT sing 11 n n C3 C4 5KT sing 12 n n C4' O4' 5KT sing 13 n n C4' C3' 5KT sing 14 n n C1 C2 5KT sing 15 n n C1 S1 5KT sing 16 n n C1 O5 5KT sing 17 n n N1 CA 5KT sing 18 n y C1' S1 5KT sing 19 n n C1' C2' 5KT sing 20 n n C5 C4 5KT sing 21 n n C5 O5 5KT sing 22 n n C5 C6 5KT sing 23 n n C4 O4 5KT sing 24 n n CB CA 5KT doub 25 n y CB CD 5KT sing 26 n n O6 C6 5KT sing 27 n n CF CD 5KT sing 28 n y CF CG 5KT doub 29 n y C3' C2' 5KT sing 30 n n C3' N1' 5KT sing 31 n n CD CE 5KT doub 32 n y C2' O2' 5KT sing 33 n n CG S2 5KT sing 34 n y N1' CA' 5KT sing 35 n y N1' N2' 5KT sing 36 n y CE S2 5KT sing 37 n y CA' CB' 5KT doub 38 n y N2' N3' 5KT doub 39 n y CB' N3' 5KT sing 40 n y CB' CD' 5KT sing 41 n n CD' CF' 5KT sing 42 n y CD' CE' 5KT doub 43 n y CF' CG' 5KT doub 44 n y CE' S2' 5KT sing 45 n y CG' S2' 5KT sing 46 n y C6 H1 5KT sing 47 n n C6 H2 5KT sing 48 n n C5 H3 5KT sing 49 n n C2 H4 5KT sing 50 n n C4 H5 5KT sing 51 n n C5' H6 5KT sing 52 n n C4' H7 5KT sing 53 n n C2' H8 5KT sing 54 n n C6' H9 5KT sing 55 n n C6' H10 5KT sing 56 n n O6 H11 5KT sing 57 n n O4 H12 5KT sing 58 n n C3 H13 5KT sing 59 n n CF H14 5KT sing 60 n n CE H15 5KT sing 61 n n CG H16 5KT sing 62 n n CA H17 5KT sing 63 n n O2 H18 5KT sing 64 n n C1 H19 5KT sing 65 n n C1' H20 5KT sing 66 n n O6' H21 5KT sing 67 n n O2' H22 5KT sing 68 n n C3' H23 5KT sing 69 n n O4' H24 5KT sing 70 n n CA' H25 5KT sing 71 n n CF' H26 5KT sing 72 n n CE' H27 5KT sing 73 n n CG' H28 5KT sing 74 n n # _atom_sites.entry_id 5E88 _atom_sites.fract_transf_matrix[1][1] 0.027424 _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] 0.017231 _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] 0.015842 _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 5KT A 1 302 1 5KT TDM . D 4 HOH A 1 401 155 HOH HOH . D 4 HOH A 2 402 127 HOH HOH . D 4 HOH A 3 403 70 HOH HOH . D 4 HOH A 4 404 123 HOH HOH . D 4 HOH A 5 405 14 HOH HOH . D 4 HOH A 6 406 77 HOH HOH . D 4 HOH A 7 407 32 HOH HOH . D 4 HOH A 8 408 9 HOH HOH . D 4 HOH A 9 409 169 HOH HOH . D 4 HOH A 10 410 48 HOH HOH . D 4 HOH A 11 411 8 HOH HOH . D 4 HOH A 12 412 33 HOH HOH . D 4 HOH A 13 413 153 HOH HOH . D 4 HOH A 14 414 64 HOH HOH . D 4 HOH A 15 415 25 HOH HOH . D 4 HOH A 16 416 57 HOH HOH . D 4 HOH A 17 417 37 HOH HOH . D 4 HOH A 18 418 113 HOH HOH . D 4 HOH A 19 419 29 HOH HOH . D 4 HOH A 20 420 2 HOH HOH . D 4 HOH A 21 421 165 HOH HOH . D 4 HOH A 22 422 95 HOH HOH . D 4 HOH A 23 423 6 HOH HOH . D 4 HOH A 24 424 160 HOH HOH . D 4 HOH A 25 425 124 HOH HOH . D 4 HOH A 26 426 4 HOH HOH . D 4 HOH A 27 427 50 HOH HOH . D 4 HOH A 28 428 11 HOH HOH . D 4 HOH A 29 429 71 HOH HOH . D 4 HOH A 30 430 17 HOH HOH . D 4 HOH A 31 431 5 HOH HOH . D 4 HOH A 32 432 116 HOH HOH . D 4 HOH A 33 433 3 HOH HOH . D 4 HOH A 34 434 12 HOH HOH . D 4 HOH A 35 435 140 HOH HOH . D 4 HOH A 36 436 58 HOH HOH . D 4 HOH A 37 437 126 HOH HOH . D 4 HOH A 38 438 68 HOH HOH . D 4 HOH A 39 439 152 HOH HOH . D 4 HOH A 40 440 117 HOH HOH . D 4 HOH A 41 441 65 HOH HOH . D 4 HOH A 42 442 55 HOH HOH . D 4 HOH A 43 443 41 HOH HOH . D 4 HOH A 44 444 103 HOH HOH . D 4 HOH A 45 445 19 HOH HOH . D 4 HOH A 46 446 170 HOH HOH . D 4 HOH A 47 447 20 HOH HOH . D 4 HOH A 48 448 31 HOH HOH . D 4 HOH A 49 449 42 HOH HOH . D 4 HOH A 50 450 73 HOH HOH . D 4 HOH A 51 451 1 HOH HOH . D 4 HOH A 52 452 10 HOH HOH . D 4 HOH A 53 453 74 HOH HOH . D 4 HOH A 54 454 76 HOH HOH . D 4 HOH A 55 455 44 HOH HOH . D 4 HOH A 56 456 159 HOH HOH . D 4 HOH A 57 457 98 HOH HOH . D 4 HOH A 58 458 141 HOH HOH . D 4 HOH A 59 459 23 HOH HOH . D 4 HOH A 60 460 61 HOH HOH . D 4 HOH A 61 461 16 HOH HOH . D 4 HOH A 62 462 53 HOH HOH . D 4 HOH A 63 463 62 HOH HOH . D 4 HOH A 64 464 56 HOH HOH . D 4 HOH A 65 465 52 HOH HOH . D 4 HOH A 66 466 80 HOH HOH . D 4 HOH A 67 467 100 HOH HOH . D 4 HOH A 68 468 150 HOH HOH . D 4 HOH A 69 469 78 HOH HOH . D 4 HOH A 70 470 83 HOH HOH . D 4 HOH A 71 471 75 HOH HOH . D 4 HOH A 72 472 36 HOH HOH . D 4 HOH A 73 473 40 HOH HOH . D 4 HOH A 74 474 104 HOH HOH . D 4 HOH A 75 475 101 HOH HOH . D 4 HOH A 76 476 87 HOH HOH . D 4 HOH A 77 477 67 HOH HOH . D 4 HOH A 78 478 145 HOH HOH . D 4 HOH A 79 479 176 HOH HOH . D 4 HOH A 80 480 88 HOH HOH . D 4 HOH A 81 481 85 HOH HOH . D 4 HOH A 82 482 24 HOH HOH . D 4 HOH A 83 483 178 HOH HOH . D 4 HOH A 84 484 135 HOH HOH . D 4 HOH A 85 485 39 HOH HOH . D 4 HOH A 86 486 63 HOH HOH . D 4 HOH A 87 487 130 HOH HOH . D 4 HOH A 88 488 60 HOH HOH . D 4 HOH A 89 489 27 HOH HOH . D 4 HOH A 90 490 7 HOH HOH . D 4 HOH A 91 491 72 HOH HOH . D 4 HOH A 92 492 172 HOH HOH . D 4 HOH A 93 493 136 HOH HOH . D 4 HOH A 94 494 166 HOH HOH . D 4 HOH A 95 495 28 HOH HOH . D 4 HOH A 96 496 177 HOH HOH . D 4 HOH A 97 497 15 HOH HOH . D 4 HOH A 98 498 163 HOH HOH . D 4 HOH A 99 499 43 HOH HOH . D 4 HOH A 100 500 91 HOH HOH . D 4 HOH A 101 501 115 HOH HOH . D 4 HOH A 102 502 38 HOH HOH . D 4 HOH A 103 503 22 HOH HOH . D 4 HOH A 104 504 26 HOH HOH . D 4 HOH A 105 505 118 HOH HOH . D 4 HOH A 106 506 49 HOH HOH . D 4 HOH A 107 507 111 HOH HOH . D 4 HOH A 108 508 34 HOH HOH . D 4 HOH A 109 509 82 HOH HOH . D 4 HOH A 110 510 30 HOH HOH . D 4 HOH A 111 511 137 HOH HOH . D 4 HOH A 112 512 13 HOH HOH . D 4 HOH A 113 513 18 HOH HOH . D 4 HOH A 114 514 167 HOH HOH . D 4 HOH A 115 515 47 HOH HOH . D 4 HOH A 116 516 107 HOH HOH . D 4 HOH A 117 517 66 HOH HOH . D 4 HOH A 118 518 46 HOH HOH . D 4 HOH A 119 519 146 HOH HOH . D 4 HOH A 120 520 175 HOH HOH . D 4 HOH A 121 521 110 HOH HOH . D 4 HOH A 122 522 51 HOH HOH . D 4 HOH A 123 523 151 HOH HOH . D 4 HOH A 124 524 154 HOH HOH . D 4 HOH A 125 525 164 HOH HOH . D 4 HOH A 126 526 54 HOH HOH . D 4 HOH A 127 527 173 HOH HOH . D 4 HOH A 128 528 171 HOH HOH . D 4 HOH A 129 529 158 HOH HOH . D 4 HOH A 130 530 35 HOH HOH . D 4 HOH A 131 531 161 HOH HOH . D 4 HOH A 132 532 132 HOH HOH . D 4 HOH A 133 533 81 HOH HOH . D 4 HOH A 134 534 105 HOH HOH . D 4 HOH A 135 535 156 HOH HOH . D 4 HOH A 136 536 92 HOH HOH . D 4 HOH A 137 537 21 HOH HOH . D 4 HOH A 138 538 149 HOH HOH . D 4 HOH A 139 539 134 HOH HOH . D 4 HOH A 140 540 122 HOH HOH . D 4 HOH A 141 541 84 HOH HOH . D 4 HOH A 142 542 97 HOH HOH . D 4 HOH A 143 543 174 HOH HOH . D 4 HOH A 144 544 86 HOH HOH . D 4 HOH A 145 545 162 HOH HOH . D 4 HOH A 146 546 179 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 C6 5KT . . . C 3 20.532 -5.614 -0.151 1 15 ? C6 5KT 302 A 1 HETATM 2 C C5 5KT . . . C 3 19.956 -6.775 -0.956 1 14.02 ? C5 5KT 302 A 1 HETATM 3 S S1 5KT . . . C 3 21.089 -10.503 -0.702 1 20.7 ? S1 5KT 302 A 1 HETATM 4 C C2 5KT . . . C 3 18.681 -9.373 -1.174 1 19.7 ? C2 5KT 302 A 1 HETATM 5 N N3 5KT . . . C 3 14.329 -8.071 -1.961 1 28.69 ? N3 5KT 302 A 1 HETATM 6 C C4 5KT . . . C 3 18.46 -6.931 -0.742 1 14.89 ? C4 5KT 302 A 1 HETATM 7 C C5' 5KT . . . C 3 24.583 -10.52 -2.494 1 27.21 ? C5' 5KT 302 A 1 HETATM 8 C C4' 5KT . . . C 3 25.536 -10.735 -1.319 1 28.4 ? C4' 5KT 302 A 1 HETATM 9 N N3' 5KT . . . C 3 26.853 -11.013 2.822 1 35.15 ? N3' 5KT 302 A 1 HETATM 10 C C2' 5KT . . . C 3 23.629 -10.254 0.211 1 21.3 ? C2' 5KT 302 A 1 HETATM 11 N N1' 5KT . . . C 3 25.96 -9.959 1.044 1 28.42 ? N1' 5KT 302 A 1 HETATM 12 C C6' 5KT . . . C 3 24.997 -11.347 -3.709 1 34 ? C6' 5KT 302 A 1 HETATM 13 O O6 5KT . . . C 3 21.919 -5.476 -0.474 1 15.65 ? O6 5KT 302 A 1 HETATM 14 O O5 5KT . . . C 3 20.609 -7.984 -0.563 1 14.99 ? O5 5KT 302 A 1 HETATM 15 O O4 5KT . . . C 3 18.188 -7.118 0.65 1 13.97 ? O4 5KT 302 A 1 HETATM 16 C C3 5KT . . . C 3 17.913 -8.112 -1.537 1 16.58 ? C3 5KT 302 A 1 HETATM 17 N N1 5KT . . . C 3 16.46 -8.231 -1.269 1 19.9 ? N1 5KT 302 A 1 HETATM 18 N N2 5KT . . . C 3 15.66 -7.936 -2.385 1 24.68 ? N2 5KT 302 A 1 HETATM 19 C CB 5KT . . . C 3 14.423 -8.416 -0.662 1 22.52 ? CB 5KT 302 A 1 HETATM 20 C CD 5KT . . . C 3 13.205 -8.653 0.168 1 25.54 ? CD 5KT 302 A 1 HETATM 21 C CF 5KT . . . C 3 11.951 -8.712 -0.418 1 32.59 ? CF 5KT 302 A 1 HETATM 22 C CE 5KT . . . C 3 13.259 -8.806 1.536 1 21.52 ? CE 5KT 302 A 1 HETATM 23 S S2 5KT . . . C 3 11.667 -9.065 2.197 1 32.36 ? S2 5KT 302 A 1 HETATM 24 C CG 5KT . . . C 3 11.02 -8.934 0.581 1 28.77 ? CG 5KT 302 A 1 HETATM 25 C CA 5KT . . . C 3 15.719 -8.522 -0.189 1 21.29 ? CA 5KT 302 A 1 HETATM 26 O O2 5KT . . . C 3 18.264 -10.434 -2.04 1 23.23 ? O2 5KT 302 A 1 HETATM 27 C C1 5KT . . . C 3 20.181 -9.122 -1.317 1 16.62 ? C1 5KT 302 A 1 HETATM 28 C C1' 5KT . . . C 3 22.758 -10.054 -1.03 1 21.32 ? C1' 5KT 302 A 1 HETATM 29 O O5' 5KT . . . C 3 23.245 -10.861 -2.113 1 23.44 ? O5' 5KT 302 A 1 HETATM 30 O O6' 5KT . . . C 3 24.196 -10.972 -4.834 1 47.7 ? O6' 5KT 302 A 1 HETATM 31 O O2' 5KT . . . C 3 23.15 -9.468 1.314 1 17.02 ? O2' 5KT 302 A 1 HETATM 32 C C3' 5KT . . . C 3 25.065 -9.874 -0.145 1 24.71 ? C3' 5KT 302 A 1 HETATM 33 O O4' 5KT . . . C 3 25.576 -12.123 -0.962 1 30.92 ? O4' 5KT 302 A 1 HETATM 34 N N2' 5KT . . . C 3 25.959 -11.174 1.746 1 30.19 ? N2' 5KT 302 A 1 HETATM 35 C CB' 5KT . . . C 3 27.309 -9.753 2.684 1 39.57 ? CB' 5KT 302 A 1 HETATM 36 C CA' 5KT . . . C 3 26.778 -9.068 1.617 1 31.41 ? CA' 5KT 302 A 1 HETATM 37 C CD' 5KT . . . C 3 28.272 -9.147 3.654 1 50.17 ? CD' 5KT 302 A 1 HETATM 38 C CF' 5KT . . . C 3 28.447 -7.774 3.708 1 53.49 ? CF' 5KT 302 A 1 HETATM 39 C CE' 5KT . . . C 3 28.963 -9.937 4.554 1 55.99 ? CE' 5KT 302 A 1 HETATM 40 S S2' 5KT . . . C 3 29.951 -8.884 5.536 1 67.54 ? S2' 5KT 302 A 1 HETATM 41 C CG' 5KT . . . C 3 29.363 -7.464 4.698 1 63.25 ? CG' 5KT 302 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 41 #