data_5XSJ # _model_server_result.job_id qt5ImprYbXxvCXWupFhreQ _model_server_result.datetime_utc '2024-11-22 16:31:34' _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 5xsj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 5XSJ # _exptl.entry_id 5XSJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description beta-D-xylopyranose _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 5XSJ _cell.length_a 105.681 _cell.length_b 143.688 _cell.length_c 87.133 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XSJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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' 3_454 -x-1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 -105.681 0 -43.5665 # _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 'C5 H10 O5' _chem_comp.formula_weight 150.13 _chem_comp.id XYP _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-xylopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-D-xylose;D-xylose;xylose # 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 O1 C1 XYP sing 376 n n O1 HO1 XYP sing 377 n n C1 C2 XYP sing 378 n n C1 O5 XYP sing 379 n n C1 H1 XYP sing 380 n n C2 C3 XYP sing 381 n n C2 O2 XYP sing 382 n n C2 H2 XYP sing 383 n n C3 C4 XYP sing 384 n n C3 O3 XYP sing 385 n n C3 H3 XYP sing 386 n n C4 C5 XYP sing 387 n n C4 O4 XYP sing 388 n n C4 H4 XYP sing 389 n n C5 O5 XYP sing 390 n n C5 H51 XYP sing 391 n n C5 H52 XYP sing 392 n n O2 HO2 XYP sing 393 n n O3 HO3 XYP sing 394 n n O4 HO4 XYP sing 395 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version XYP DXylpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 XYP b-D-xylopyranose 'COMMON NAME' GMML 1 XYP b-D-Xylp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 XYP Xyl 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5XSJ _atom_sites.fract_transf_matrix[1][1] 0.009462 _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] 0.00696 _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] 0.011477 _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 XYP X 1 500 500 XYP XYP . D 4 HOH X 1 601 177 HOH HOH . D 4 HOH X 2 602 226 HOH HOH . D 4 HOH X 3 603 252 HOH HOH . D 4 HOH X 4 604 39 HOH HOH . D 4 HOH X 5 605 214 HOH HOH . D 4 HOH X 6 606 261 HOH HOH . D 4 HOH X 7 607 139 HOH HOH . D 4 HOH X 8 608 236 HOH HOH . D 4 HOH X 9 609 83 HOH HOH . D 4 HOH X 10 610 239 HOH HOH . D 4 HOH X 11 611 192 HOH HOH . D 4 HOH X 12 612 159 HOH HOH . D 4 HOH X 13 613 50 HOH HOH . D 4 HOH X 14 614 72 HOH HOH . D 4 HOH X 15 615 75 HOH HOH . D 4 HOH X 16 616 170 HOH HOH . D 4 HOH X 17 617 117 HOH HOH . D 4 HOH X 18 618 88 HOH HOH . D 4 HOH X 19 619 167 HOH HOH . D 4 HOH X 20 620 89 HOH HOH . D 4 HOH X 21 621 151 HOH HOH . D 4 HOH X 22 622 99 HOH HOH . D 4 HOH X 23 623 153 HOH HOH . D 4 HOH X 24 624 66 HOH HOH . D 4 HOH X 25 625 18 HOH HOH . D 4 HOH X 26 626 114 HOH HOH . D 4 HOH X 27 627 13 HOH HOH . D 4 HOH X 28 628 85 HOH HOH . D 4 HOH X 29 629 143 HOH HOH . D 4 HOH X 30 630 32 HOH HOH . D 4 HOH X 31 631 35 HOH HOH . D 4 HOH X 32 632 224 HOH HOH . D 4 HOH X 33 633 65 HOH HOH . D 4 HOH X 34 634 216 HOH HOH . D 4 HOH X 35 635 26 HOH HOH . D 4 HOH X 36 636 46 HOH HOH . D 4 HOH X 37 637 229 HOH HOH . D 4 HOH X 38 638 260 HOH HOH . D 4 HOH X 39 639 23 HOH HOH . D 4 HOH X 40 640 19 HOH HOH . D 4 HOH X 41 641 91 HOH HOH . D 4 HOH X 42 642 10 HOH HOH . D 4 HOH X 43 643 86 HOH HOH . D 4 HOH X 44 644 110 HOH HOH . D 4 HOH X 45 645 40 HOH HOH . D 4 HOH X 46 646 36 HOH HOH . D 4 HOH X 47 647 56 HOH HOH . D 4 HOH X 48 648 21 HOH HOH . D 4 HOH X 49 649 5 HOH HOH . D 4 HOH X 50 650 73 HOH HOH . D 4 HOH X 51 651 16 HOH HOH . D 4 HOH X 52 652 53 HOH HOH . D 4 HOH X 53 653 263 HOH HOH . D 4 HOH X 54 654 28 HOH HOH . D 4 HOH X 55 655 3 HOH HOH . D 4 HOH X 56 656 255 HOH HOH . D 4 HOH X 57 657 22 HOH HOH . D 4 HOH X 58 658 178 HOH HOH . D 4 HOH X 59 659 12 HOH HOH . D 4 HOH X 60 660 34 HOH HOH . D 4 HOH X 61 661 112 HOH HOH . D 4 HOH X 62 662 262 HOH HOH . D 4 HOH X 63 663 124 HOH HOH . D 4 HOH X 64 664 60 HOH HOH . D 4 HOH X 65 665 107 HOH HOH . D 4 HOH X 66 666 24 HOH HOH . D 4 HOH X 67 667 7 HOH HOH . D 4 HOH X 68 668 74 HOH HOH . D 4 HOH X 69 669 15 HOH HOH . D 4 HOH X 70 670 163 HOH HOH . D 4 HOH X 71 671 106 HOH HOH . D 4 HOH X 72 672 33 HOH HOH . D 4 HOH X 73 673 158 HOH HOH . D 4 HOH X 74 674 195 HOH HOH . D 4 HOH X 75 675 49 HOH HOH . D 4 HOH X 76 676 166 HOH HOH . D 4 HOH X 77 677 59 HOH HOH . D 4 HOH X 78 678 184 HOH HOH . D 4 HOH X 79 679 98 HOH HOH . D 4 HOH X 80 680 179 HOH HOH . D 4 HOH X 81 681 233 HOH HOH . D 4 HOH X 82 682 138 HOH HOH . D 4 HOH X 83 683 164 HOH HOH . D 4 HOH X 84 684 148 HOH HOH . D 4 HOH X 85 685 38 HOH HOH . D 4 HOH X 86 686 235 HOH HOH . D 4 HOH X 87 687 63 HOH HOH . D 4 HOH X 88 688 123 HOH HOH . D 4 HOH X 89 689 2 HOH HOH . D 4 HOH X 90 690 29 HOH HOH . D 4 HOH X 91 691 211 HOH HOH . D 4 HOH X 92 692 25 HOH HOH . D 4 HOH X 93 693 84 HOH HOH . D 4 HOH X 94 694 108 HOH HOH . D 4 HOH X 95 695 94 HOH HOH . D 4 HOH X 96 696 82 HOH HOH . D 4 HOH X 97 697 254 HOH HOH . D 4 HOH X 98 698 249 HOH HOH . D 4 HOH X 99 699 45 HOH HOH . D 4 HOH X 100 700 31 HOH HOH . D 4 HOH X 101 701 6 HOH HOH . D 4 HOH X 102 702 100 HOH HOH . D 4 HOH X 103 703 109 HOH HOH . D 4 HOH X 104 704 62 HOH HOH . D 4 HOH X 105 705 69 HOH HOH . D 4 HOH X 106 706 215 HOH HOH . D 4 HOH X 107 707 137 HOH HOH . D 4 HOH X 108 708 78 HOH HOH . D 4 HOH X 109 709 245 HOH HOH . D 4 HOH X 110 710 103 HOH HOH . D 4 HOH X 111 711 80 HOH HOH . D 4 HOH X 112 712 48 HOH HOH . D 4 HOH X 113 713 207 HOH HOH . D 4 HOH X 114 714 188 HOH HOH . D 4 HOH X 115 715 128 HOH HOH . D 4 HOH X 116 716 52 HOH HOH . D 4 HOH X 117 717 30 HOH HOH . D 4 HOH X 118 718 122 HOH HOH . D 4 HOH X 119 719 230 HOH HOH . D 4 HOH X 120 720 79 HOH HOH . D 4 HOH X 121 721 172 HOH HOH . D 4 HOH X 122 722 126 HOH HOH . D 4 HOH X 123 723 57 HOH HOH . D 4 HOH X 124 724 152 HOH HOH . D 4 HOH X 125 725 203 HOH HOH . D 4 HOH X 126 726 119 HOH HOH . D 4 HOH X 127 727 71 HOH HOH . D 4 HOH X 128 728 251 HOH HOH . D 4 HOH X 129 729 218 HOH HOH . D 4 HOH X 130 730 134 HOH HOH . D 4 HOH X 131 731 201 HOH HOH . D 4 HOH X 132 732 42 HOH HOH . D 4 HOH X 133 733 43 HOH HOH . D 4 HOH X 134 734 257 HOH HOH . D 4 HOH X 135 735 157 HOH HOH . D 4 HOH X 136 736 87 HOH HOH . D 4 HOH X 137 737 101 HOH HOH . D 4 HOH X 138 738 104 HOH HOH . D 4 HOH X 139 739 125 HOH HOH . D 4 HOH X 140 740 186 HOH HOH . D 4 HOH X 141 741 248 HOH HOH . D 4 HOH X 142 742 41 HOH HOH . D 4 HOH X 143 743 92 HOH HOH . D 4 HOH X 144 744 102 HOH HOH . D 4 HOH X 145 745 243 HOH HOH . D 4 HOH X 146 746 213 HOH HOH . D 4 HOH X 147 747 90 HOH HOH . D 4 HOH X 148 748 202 HOH HOH . D 4 HOH X 149 749 144 HOH HOH . D 4 HOH X 150 750 160 HOH HOH . D 4 HOH X 151 751 231 HOH HOH . D 4 HOH X 152 752 194 HOH HOH . D 4 HOH X 153 753 70 HOH HOH . D 4 HOH X 154 754 131 HOH HOH . D 4 HOH X 155 755 240 HOH HOH . D 4 HOH X 156 756 37 HOH HOH . D 4 HOH X 157 757 113 HOH HOH . D 4 HOH X 158 758 95 HOH HOH . D 4 HOH X 159 759 238 HOH HOH . D 4 HOH X 160 760 58 HOH HOH . D 4 HOH X 161 761 241 HOH HOH . D 4 HOH X 162 762 181 HOH HOH . D 4 HOH X 163 763 1 HOH HOH . D 4 HOH X 164 764 180 HOH HOH . D 4 HOH X 165 765 142 HOH HOH . D 4 HOH X 166 766 173 HOH HOH . D 4 HOH X 167 767 220 HOH HOH . D 4 HOH X 168 768 196 HOH HOH . D 4 HOH X 169 769 206 HOH HOH . D 4 HOH X 170 770 190 HOH HOH . D 4 HOH X 171 771 197 HOH HOH . D 4 HOH X 172 772 221 HOH HOH . D 4 HOH X 173 773 156 HOH HOH . D 4 HOH X 174 774 205 HOH HOH . D 4 HOH X 175 775 130 HOH HOH . D 4 HOH X 176 776 182 HOH HOH . D 4 HOH X 177 777 155 HOH HOH . D 4 HOH X 178 778 129 HOH HOH . D 4 HOH X 179 779 121 HOH HOH . D 4 HOH X 180 780 149 HOH HOH . D 4 HOH X 181 781 174 HOH HOH . D 4 HOH X 182 782 232 HOH HOH . D 4 HOH X 183 783 242 HOH HOH . D 4 HOH X 184 784 191 HOH HOH . D 4 HOH X 185 785 247 HOH HOH . D 4 HOH X 186 786 234 HOH HOH . D 4 HOH X 187 787 223 HOH HOH . D 4 HOH X 188 788 136 HOH HOH . D 4 HOH X 189 789 183 HOH HOH . D 4 HOH X 190 790 217 HOH HOH . D 4 HOH X 191 791 169 HOH HOH . E 4 HOH L 1 301 204 HOH HOH . E 4 HOH L 2 302 171 HOH HOH . E 4 HOH L 3 303 228 HOH HOH . E 4 HOH L 4 304 127 HOH HOH . E 4 HOH L 5 305 135 HOH HOH . E 4 HOH L 6 306 64 HOH HOH . E 4 HOH L 7 307 17 HOH HOH . E 4 HOH L 8 308 185 HOH HOH . E 4 HOH L 9 309 4 HOH HOH . E 4 HOH L 10 310 27 HOH HOH . E 4 HOH L 11 311 162 HOH HOH . E 4 HOH L 12 312 161 HOH HOH . E 4 HOH L 13 313 253 HOH HOH . E 4 HOH L 14 314 96 HOH HOH . E 4 HOH L 15 315 68 HOH HOH . E 4 HOH L 16 316 145 HOH HOH . E 4 HOH L 17 317 47 HOH HOH . E 4 HOH L 18 318 61 HOH HOH . E 4 HOH L 19 319 9 HOH HOH . E 4 HOH L 20 320 44 HOH HOH . E 4 HOH L 21 321 225 HOH HOH . E 4 HOH L 22 322 105 HOH HOH . E 4 HOH L 23 323 8 HOH HOH . E 4 HOH L 24 324 76 HOH HOH . E 4 HOH L 25 325 14 HOH HOH . E 4 HOH L 26 326 133 HOH HOH . E 4 HOH L 27 327 210 HOH HOH . E 4 HOH L 28 328 67 HOH HOH . E 4 HOH L 29 329 250 HOH HOH . E 4 HOH L 30 330 168 HOH HOH . E 4 HOH L 31 331 97 HOH HOH . E 4 HOH L 32 332 141 HOH HOH . E 4 HOH L 33 333 55 HOH HOH . E 4 HOH L 34 334 11 HOH HOH . E 4 HOH L 35 335 209 HOH HOH . E 4 HOH L 36 336 120 HOH HOH . E 4 HOH L 37 337 77 HOH HOH . E 4 HOH L 38 338 175 HOH HOH . E 4 HOH L 39 339 20 HOH HOH . E 4 HOH L 40 340 116 HOH HOH . E 4 HOH L 41 341 111 HOH HOH . E 4 HOH L 42 342 212 HOH HOH . E 4 HOH L 43 343 54 HOH HOH . E 4 HOH L 44 344 258 HOH HOH . E 4 HOH L 45 345 81 HOH HOH . E 4 HOH L 46 346 93 HOH HOH . E 4 HOH L 47 347 140 HOH HOH . E 4 HOH L 48 348 150 HOH HOH . E 4 HOH L 49 349 256 HOH HOH . E 4 HOH L 50 350 154 HOH HOH . E 4 HOH L 51 351 237 HOH HOH . E 4 HOH L 52 352 115 HOH HOH . E 4 HOH L 53 353 146 HOH HOH . E 4 HOH L 54 354 259 HOH HOH . E 4 HOH L 55 355 132 HOH HOH . E 4 HOH L 56 356 208 HOH HOH . E 4 HOH L 57 357 189 HOH HOH . E 4 HOH L 58 358 199 HOH HOH . E 4 HOH L 59 359 246 HOH HOH . E 4 HOH L 60 360 200 HOH HOH . E 4 HOH L 61 361 51 HOH HOH . E 4 HOH L 62 362 193 HOH HOH . E 4 HOH L 63 363 187 HOH HOH . E 4 HOH L 64 364 244 HOH HOH . E 4 HOH L 65 365 198 HOH HOH . E 4 HOH L 66 366 176 HOH HOH . E 4 HOH L 67 367 227 HOH HOH . E 4 HOH L 68 368 147 HOH HOH . E 4 HOH L 69 369 222 HOH HOH . E 4 HOH L 70 370 118 HOH HOH . E 4 HOH L 71 371 219 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 O O1 XYP . . . C 3 -32.962 -29.464 -4.309 1 53.11 ? O1 XYP 500 X 1 HETATM 2 C C1 XYP . . . C 3 -33.432 -28.379 -5.035 1 50.51 ? C1 XYP 500 X 1 HETATM 3 C C2 XYP . . . C 3 -33.555 -28.764 -6.487 1 45.45 ? C2 XYP 500 X 1 HETATM 4 C C3 XYP . . . C 3 -34.393 -27.74 -7.23 1 50.15 ? C3 XYP 500 X 1 HETATM 5 C C4 XYP . . . C 3 -35.686 -27.431 -6.502 1 42.27 ? C4 XYP 500 X 1 HETATM 6 C C5 XYP . . . C 3 -35.381 -27.098 -5.068 1 46.2 ? C5 XYP 500 X 1 HETATM 7 O O2 XYP . . . C 3 -32.252 -28.811 -7.009 1 62.35 ? O2 XYP 500 X 1 HETATM 8 O O3 XYP . . . C 3 -34.732 -28.19 -8.51 1 84.63 ? O3 XYP 500 X 1 HETATM 9 O O4 XYP . . . C 3 -36.297 -26.314 -7.091 1 52.49 ? O4 XYP 500 X 1 HETATM 10 O O5 XYP . . . C 3 -34.698 -28.179 -4.509 1 63.89 ? O5 XYP 500 X 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 10 #