data_5QB5 # _model_server_result.job_id IQTTXMQA6IpxnQ7hDRmcEQ _model_server_result.datetime_utc '2024-10-20 20:39:21' _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 5qb5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 5QB5 # _exptl.entry_id 5QB5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 253.317 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1S,2S,3S,4R,5R)-2-amino-4-(phenylsulfanyl)-6,8-dioxabicyclo[3.2.1]octan-3-ol _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 109.53 _cell.angle_gamma 90 _cell.entry_id 5QB5 _cell.length_a 45.241 _cell.length_b 73.115 _cell.length_c 52.91 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5QB5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 255 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 255 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 290 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 290 _struct_conn.ptnr2_symmetry 1_555 _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 2.039 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C12 H15 N O3 S' _chem_comp.formula_weight 253.317 _chem_comp.id D5V _chem_comp.mon_nstd_flag . _chem_comp.name (1S,2S,3S,4R,5R)-2-amino-4-(phenylsulfanyl)-6,8-dioxabicyclo[3.2.1]octan-3-ol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5QB5 _atom_sites.fract_transf_matrix[1][1] 0.022104 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00784 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013677 _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] 0.020054 _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 GOL A 1 401 1 GOL GOL . C 2 GOL A 1 402 3 GOL GOL . D 2 GOL A 1 403 4 GOL GOL . E 3 ACT A 1 404 1 ACT ACT . F 4 D5V A 1 405 1 D5V XXX . G 5 HOH A 1 501 897 HOH HOH . G 5 HOH A 2 502 830 HOH HOH . G 5 HOH A 3 503 1540 HOH HOH . G 5 HOH A 4 504 867 HOH HOH . G 5 HOH A 5 505 1894 HOH HOH . G 5 HOH A 6 506 1633 HOH HOH . G 5 HOH A 7 507 1026 HOH HOH . G 5 HOH A 8 508 1459 HOH HOH . G 5 HOH A 9 509 569 HOH HOH . G 5 HOH A 10 510 995 HOH HOH . G 5 HOH A 11 511 2679 HOH HOH . G 5 HOH A 12 512 2669 HOH HOH . G 5 HOH A 13 513 1388 HOH HOH . G 5 HOH A 14 514 2283 HOH HOH . G 5 HOH A 15 515 2151 HOH HOH . G 5 HOH A 16 516 508 HOH HOH . G 5 HOH A 17 517 1005 HOH HOH . G 5 HOH A 18 518 1369 HOH HOH . G 5 HOH A 19 519 1308 HOH HOH . G 5 HOH A 20 520 1410 HOH HOH . G 5 HOH A 21 521 747 HOH HOH . G 5 HOH A 22 522 786 HOH HOH . G 5 HOH A 23 523 955 HOH HOH . G 5 HOH A 24 524 1070 HOH HOH . G 5 HOH A 25 525 1997 HOH HOH . G 5 HOH A 26 526 1800 HOH HOH . G 5 HOH A 27 527 2183 HOH HOH . G 5 HOH A 28 528 835 HOH HOH . G 5 HOH A 29 529 1936 HOH HOH . G 5 HOH A 30 530 1269 HOH HOH . G 5 HOH A 31 531 1019 HOH HOH . G 5 HOH A 32 532 1627 HOH HOH . G 5 HOH A 33 533 1401 HOH HOH . G 5 HOH A 34 534 905 HOH HOH . G 5 HOH A 35 535 2095 HOH HOH . G 5 HOH A 36 536 1958 HOH HOH . G 5 HOH A 37 537 2093 HOH HOH . G 5 HOH A 38 538 1610 HOH HOH . G 5 HOH A 39 539 1448 HOH HOH . G 5 HOH A 40 540 1282 HOH HOH . G 5 HOH A 41 541 1407 HOH HOH . G 5 HOH A 42 542 2533 HOH HOH . G 5 HOH A 43 543 804 HOH HOH . G 5 HOH A 44 544 501 HOH HOH . G 5 HOH A 45 545 2660 HOH HOH . G 5 HOH A 46 546 957 HOH HOH . G 5 HOH A 47 547 2354 HOH HOH . G 5 HOH A 48 548 638 HOH HOH . G 5 HOH A 49 549 1125 HOH HOH . G 5 HOH A 50 550 1246 HOH HOH . G 5 HOH A 51 551 1631 HOH HOH . G 5 HOH A 52 552 858 HOH HOH . G 5 HOH A 53 553 2216 HOH HOH . G 5 HOH A 54 554 589 HOH HOH . G 5 HOH A 55 555 2698 HOH HOH . G 5 HOH A 56 556 2657 HOH HOH . G 5 HOH A 57 557 1523 HOH HOH . G 5 HOH A 58 558 775 HOH HOH . G 5 HOH A 59 559 2102 HOH HOH . G 5 HOH A 60 560 1210 HOH HOH . G 5 HOH A 61 561 2057 HOH HOH . G 5 HOH A 62 562 877 HOH HOH . G 5 HOH A 63 563 925 HOH HOH . G 5 HOH A 64 564 1236 HOH HOH . G 5 HOH A 65 565 1394 HOH HOH . G 5 HOH A 66 566 959 HOH HOH . G 5 HOH A 67 567 744 HOH HOH . G 5 HOH A 68 568 988 HOH HOH . G 5 HOH A 69 569 1594 HOH HOH . G 5 HOH A 70 570 2357 HOH HOH . G 5 HOH A 71 571 896 HOH HOH . G 5 HOH A 72 572 2163 HOH HOH . G 5 HOH A 73 573 2085 HOH HOH . G 5 HOH A 74 574 2307 HOH HOH . G 5 HOH A 75 575 2308 HOH HOH . G 5 HOH A 76 576 1503 HOH HOH . G 5 HOH A 77 577 1593 HOH HOH . G 5 HOH A 78 578 1304 HOH HOH . G 5 HOH A 79 579 2459 HOH HOH . G 5 HOH A 80 580 1651 HOH HOH . G 5 HOH A 81 581 1820 HOH HOH . G 5 HOH A 82 582 2167 HOH HOH . G 5 HOH A 83 583 1111 HOH HOH . G 5 HOH A 84 584 2644 HOH HOH . G 5 HOH A 85 585 1999 HOH HOH . G 5 HOH A 86 586 1853 HOH HOH . G 5 HOH A 87 587 992 HOH HOH . G 5 HOH A 88 588 1115 HOH HOH . G 5 HOH A 89 589 1463 HOH HOH . G 5 HOH A 90 590 1883 HOH HOH . G 5 HOH A 91 591 1658 HOH HOH . G 5 HOH A 92 592 1856 HOH HOH . G 5 HOH A 93 593 1081 HOH HOH . G 5 HOH A 94 594 582 HOH HOH . G 5 HOH A 95 595 1329 HOH HOH . G 5 HOH A 96 596 1010 HOH HOH . G 5 HOH A 97 597 807 HOH HOH . G 5 HOH A 98 598 971 HOH HOH . G 5 HOH A 99 599 2166 HOH HOH . G 5 HOH A 100 600 1124 HOH HOH . G 5 HOH A 101 601 2110 HOH HOH . G 5 HOH A 102 602 1538 HOH HOH . G 5 HOH A 103 603 1180 HOH HOH . G 5 HOH A 104 604 932 HOH HOH . G 5 HOH A 105 605 621 HOH HOH . G 5 HOH A 106 606 733 HOH HOH . G 5 HOH A 107 607 819 HOH HOH . G 5 HOH A 108 608 978 HOH HOH . G 5 HOH A 109 609 1286 HOH HOH . G 5 HOH A 110 610 1223 HOH HOH . G 5 HOH A 111 611 1461 HOH HOH . G 5 HOH A 112 612 588 HOH HOH . G 5 HOH A 113 613 1107 HOH HOH . G 5 HOH A 114 614 1340 HOH HOH . G 5 HOH A 115 615 1167 HOH HOH . G 5 HOH A 116 616 1851 HOH HOH . G 5 HOH A 117 617 690 HOH HOH . G 5 HOH A 118 618 1745 HOH HOH . G 5 HOH A 119 619 1832 HOH HOH . G 5 HOH A 120 620 1244 HOH HOH . G 5 HOH A 121 621 1290 HOH HOH . G 5 HOH A 122 622 2535 HOH HOH . G 5 HOH A 123 623 826 HOH HOH . G 5 HOH A 124 624 1417 HOH HOH . G 5 HOH A 125 625 1716 HOH HOH . G 5 HOH A 126 626 612 HOH HOH . G 5 HOH A 127 627 1782 HOH HOH . G 5 HOH A 128 628 1384 HOH HOH . G 5 HOH A 129 629 1572 HOH HOH . G 5 HOH A 130 630 798 HOH HOH . G 5 HOH A 131 631 1391 HOH HOH . G 5 HOH A 132 632 1638 HOH HOH . G 5 HOH A 133 633 731 HOH HOH . G 5 HOH A 134 634 1149 HOH HOH . G 5 HOH A 135 635 1475 HOH HOH . G 5 HOH A 136 636 1316 HOH HOH . G 5 HOH A 137 637 1700 HOH HOH . G 5 HOH A 138 638 760 HOH HOH . G 5 HOH A 139 639 1014 HOH HOH . G 5 HOH A 140 640 1237 HOH HOH . G 5 HOH A 141 641 686 HOH HOH . G 5 HOH A 142 642 1531 HOH HOH . G 5 HOH A 143 643 1731 HOH HOH . G 5 HOH A 144 644 881 HOH HOH . G 5 HOH A 145 645 813 HOH HOH . G 5 HOH A 146 646 738 HOH HOH . G 5 HOH A 147 647 2210 HOH HOH . G 5 HOH A 148 648 1092 HOH HOH . G 5 HOH A 149 649 1226 HOH HOH . G 5 HOH A 150 650 2290 HOH HOH . G 5 HOH A 151 651 1359 HOH HOH . G 5 HOH A 152 652 938 HOH HOH . G 5 HOH A 153 653 1515 HOH HOH . G 5 HOH A 154 654 2159 HOH HOH . G 5 HOH A 155 655 1770 HOH HOH . G 5 HOH A 156 656 1784 HOH HOH . G 5 HOH A 157 657 1365 HOH HOH . G 5 HOH A 158 658 1718 HOH HOH . G 5 HOH A 159 659 2611 HOH HOH . G 5 HOH A 160 660 2344 HOH HOH . G 5 HOH A 161 661 1095 HOH HOH . G 5 HOH A 162 662 677 HOH HOH . G 5 HOH A 163 663 1709 HOH HOH . G 5 HOH A 164 664 629 HOH HOH . G 5 HOH A 165 665 2162 HOH HOH . G 5 HOH A 166 666 1689 HOH HOH . G 5 HOH A 167 667 748 HOH HOH . G 5 HOH A 168 668 2055 HOH HOH . G 5 HOH A 169 669 1140 HOH HOH . G 5 HOH A 170 670 1173 HOH HOH . G 5 HOH A 171 671 1038 HOH HOH . G 5 HOH A 172 672 1221 HOH HOH . G 5 HOH A 173 673 1207 HOH HOH . G 5 HOH A 174 674 1346 HOH HOH . G 5 HOH A 175 675 2688 HOH HOH . G 5 HOH A 176 676 2364 HOH HOH . G 5 HOH A 177 677 970 HOH HOH . G 5 HOH A 178 678 1906 HOH HOH . G 5 HOH A 179 679 1547 HOH HOH . G 5 HOH A 180 680 1776 HOH HOH . G 5 HOH A 181 681 1292 HOH HOH . G 5 HOH A 182 682 2125 HOH HOH . G 5 HOH A 183 683 1980 HOH HOH . G 5 HOH A 184 684 1792 HOH HOH . G 5 HOH A 185 685 1089 HOH HOH . G 5 HOH A 186 686 996 HOH HOH . G 5 HOH A 187 687 2505 HOH HOH . G 5 HOH A 188 688 948 HOH HOH . G 5 HOH A 189 689 1739 HOH HOH . G 5 HOH A 190 690 2451 HOH HOH . G 5 HOH A 191 691 1612 HOH HOH . G 5 HOH A 192 692 1699 HOH HOH . G 5 HOH A 193 693 1805 HOH HOH . G 5 HOH A 194 694 1637 HOH HOH . G 5 HOH A 195 695 1110 HOH HOH . G 5 HOH A 196 696 2330 HOH HOH . G 5 HOH A 197 697 1677 HOH HOH . G 5 HOH A 198 698 852 HOH HOH . G 5 HOH A 199 699 1640 HOH HOH . G 5 HOH A 200 700 1932 HOH HOH . G 5 HOH A 201 701 2618 HOH HOH . G 5 HOH A 202 702 2198 HOH HOH . G 5 HOH A 203 703 2060 HOH HOH . G 5 HOH A 204 704 2483 HOH HOH . G 5 HOH A 205 705 1791 HOH HOH . G 5 HOH A 206 706 580 HOH HOH . G 5 HOH A 207 707 1565 HOH HOH . G 5 HOH A 208 708 2137 HOH HOH . G 5 HOH A 209 709 1757 HOH HOH . G 5 HOH A 210 710 1562 HOH HOH . G 5 HOH A 211 711 1118 HOH HOH . G 5 HOH A 212 712 1566 HOH HOH . G 5 HOH A 213 713 2107 HOH HOH . G 5 HOH A 214 714 1977 HOH HOH . G 5 HOH A 215 715 2070 HOH HOH . G 5 HOH A 216 716 678 HOH HOH . G 5 HOH A 217 717 1535 HOH HOH . G 5 HOH A 218 718 770 HOH HOH . G 5 HOH A 219 719 2274 HOH HOH . G 5 HOH A 220 720 1419 HOH HOH . G 5 HOH A 221 721 843 HOH HOH . G 5 HOH A 222 722 1769 HOH HOH . G 5 HOH A 223 723 1928 HOH HOH . G 5 HOH A 224 724 1116 HOH HOH . G 5 HOH A 225 725 1477 HOH HOH . G 5 HOH A 226 726 1508 HOH HOH . G 5 HOH A 227 727 1172 HOH HOH . G 5 HOH A 228 728 864 HOH HOH . G 5 HOH A 229 729 1309 HOH HOH . G 5 HOH A 230 730 1225 HOH HOH . G 5 HOH A 231 731 1987 HOH HOH . G 5 HOH A 232 732 1345 HOH HOH . G 5 HOH A 233 733 2180 HOH HOH . G 5 HOH A 234 734 2677 HOH HOH . G 5 HOH A 235 735 2114 HOH HOH . G 5 HOH A 236 736 1451 HOH HOH . G 5 HOH A 237 737 1839 HOH HOH . G 5 HOH A 238 738 967 HOH HOH . G 5 HOH A 239 739 1672 HOH HOH . G 5 HOH A 240 740 1079 HOH HOH . G 5 HOH A 241 741 1772 HOH HOH . G 5 HOH A 242 742 950 HOH HOH . G 5 HOH A 243 743 2694 HOH HOH . G 5 HOH A 244 744 1073 HOH HOH . G 5 HOH A 245 745 1190 HOH HOH . G 5 HOH A 246 746 1682 HOH HOH . G 5 HOH A 247 747 1694 HOH HOH . G 5 HOH A 248 748 1421 HOH HOH . G 5 HOH A 249 749 895 HOH HOH . G 5 HOH A 250 750 1260 HOH HOH . G 5 HOH A 251 751 2189 HOH HOH . G 5 HOH A 252 752 1534 HOH HOH . G 5 HOH A 253 753 2539 HOH HOH . G 5 HOH A 254 754 2387 HOH HOH . G 5 HOH A 255 755 1706 HOH HOH . G 5 HOH A 256 756 1361 HOH HOH . G 5 HOH A 257 757 1306 HOH HOH . G 5 HOH A 258 758 1738 HOH HOH . G 5 HOH A 259 759 1733 HOH HOH . G 5 HOH A 260 760 1690 HOH HOH . G 5 HOH A 261 761 1991 HOH HOH . G 5 HOH A 262 762 2735 HOH HOH . G 5 HOH A 263 763 2404 HOH HOH . G 5 HOH A 264 764 2168 HOH HOH . G 5 HOH A 265 765 2140 HOH HOH . G 5 HOH A 266 766 2756 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 C4 D5V . A . F 4 -4.718 1.116 11.171 0.65 18.31 ? C4 D5V 405 A 1 HETATM 2 C C5 D5V . A . F 4 -5.55 0.138 10.655 0.65 19.25 ? C5 D5V 405 A 1 HETATM 3 C C6 D5V . A . F 4 -1.586 3.013 10.219 0.65 15.88 ? C6 D5V 405 A 1 HETATM 4 C C7 D5V . A . F 4 -0.054 2.997 10.258 0.65 15.92 ? C7 D5V 405 A 1 HETATM 5 C C8 D5V . A . F 4 0.525 3.854 9.132 0.65 15.91 ? C8 D5V 405 A 1 HETATM 6 C C9 D5V . A . F 4 -0.318 5.117 8.965 0.65 16.58 ? C9 D5V 405 A 1 HETATM 7 C C10 D5V . A . F 4 -1.47 4.95 7.979 0.65 16.56 ? C10 D5V 405 A 1 HETATM 8 C C11 D5V . A . F 4 -2.118 4.472 10.095 0.65 16.28 ? C11 D5V 405 A 1 HETATM 9 O O2 D5V . A . F 4 0.428 1.662 10.14 0.65 15.46 ? O2 D5V 405 A 1 HETATM 10 N N D5V . A . F 4 1.939 4.226 9.454 0.65 16.35 1 N D5V 405 A 1 HETATM 11 O O1 D5V . A . F 4 -1.023 5.356 10.204 0.65 17.07 ? O1 D5V 405 A 1 HETATM 12 O O D5V . A . F 4 -2.61 4.641 8.79 0.65 15.88 ? O D5V 405 A 1 HETATM 13 S S D5V . A . F 4 -2.251 2.218 11.715 0.65 16.44 ? S D5V 405 A 1 HETATM 14 C C3 D5V . A . F 4 -3.342 0.99 11.044 0.65 17.21 ? C3 D5V 405 A 1 HETATM 15 C C2 D5V . A . F 4 -2.811 -0.113 10.392 0.65 17.57 ? C2 D5V 405 A 1 HETATM 16 C C1 D5V . A . F 4 -3.654 -1.084 9.88 0.65 18.89 ? C1 D5V 405 A 1 HETATM 17 C C D5V . A . F 4 -5.02 -0.961 10.013 0.65 19.25 ? C D5V 405 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 17 #