data_1J01 # _model_server_result.job_id tF4QvEpqQ5I9gAa2A3mBYw _model_server_result.datetime_utc '2024-10-18 17:28:57' _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 1j01 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 1J01 # _exptl.entry_id 1J01 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 263.244 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(3S,4R)-3-hydroxy-2-oxopiperidin-4-yl beta-D-xylopyranoside' _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 1J01 _cell.length_a 86.996 _cell.length_b 86.996 _cell.length_c 80.364 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1J01 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _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 2 _struct_asym.id B _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 disulf ? disulf1 A SG CYS 167 A CYS 167 1_555 A SG CYS 199 A CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 261 A CYS 261 1_555 A SG CYS 267 A CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? # _chem_comp.formula 'C10 H17 N O7' _chem_comp.formula_weight 263.244 _chem_comp.id XIL _chem_comp.mon_nstd_flag n _chem_comp.name '(3S,4R)-3-hydroxy-2-oxopiperidin-4-yl beta-D-xylopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms '3-HYDROXY-4-(3,4,5-TRIHYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-PIPERIDIN-2-ONE;(3S,4R)-3-hydroxy-2-oxopiperidin-4-yl beta-D-xyloside;(3S,4R)-3-hydroxy-2-oxopiperidin-4-yl D-xyloside;(3S,4R)-3-hydroxy-2-oxopiperidin-4-yl xyloside' # 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 C1 C2 XIL sing 376 n n C1 O5 XIL sing 377 n n C1 O1 XIL sing 378 n n C1 H1 XIL sing 379 n n C2 O2 XIL sing 380 n n C2 C3 XIL sing 381 n n C2 H2 XIL sing 382 n n O2 HO2 XIL sing 383 n n C3 O3 XIL sing 384 n n C3 C4 XIL sing 385 n n C3 H3 XIL sing 386 n n O3 HO3 XIL sing 387 n n C4 O4 XIL sing 388 n n C4 C5 XIL sing 389 n n C4 H4 XIL sing 390 n n O4 HO4 XIL sing 391 n n C5 O5 XIL sing 392 n n C5 H51 XIL sing 393 n n C5 H52 XIL sing 394 n n N1' C2' XIL sing 395 n n N1' C6' XIL sing 396 n n N1' HN' XIL sing 397 n n C2' C3' XIL sing 398 n n C2' O2' XIL doub 399 n n C3' O3' XIL sing 400 n n C3' C4' XIL sing 401 n n C3' H3' XIL sing 402 n n O3' HO' XIL sing 403 n n C4' O1 XIL sing 404 n n C4' C5' XIL sing 405 n n C4' H4' XIL sing 406 n n C5' C6' XIL sing 407 n n C5' "H5'1" XIL sing 408 n n C5' "H5'2" XIL sing 409 n n C6' "H6'1" XIL sing 410 n n C6' "H6'2" XIL sing 411 n n # _atom_sites.entry_id 1J01 _atom_sites.fract_transf_matrix[1][1] 0.011495 _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] 0.011495 _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] 0.012443 _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 XIL A 1 601 601 XIL XYL . C 3 HOH A 1 602 1 HOH TIP . C 3 HOH A 2 603 2 HOH TIP . C 3 HOH A 3 604 3 HOH TIP . C 3 HOH A 4 605 4 HOH TIP . C 3 HOH A 5 606 5 HOH TIP . C 3 HOH A 6 607 6 HOH TIP . C 3 HOH A 7 608 7 HOH TIP . C 3 HOH A 8 609 8 HOH TIP . C 3 HOH A 9 610 9 HOH TIP . C 3 HOH A 10 611 10 HOH TIP . C 3 HOH A 11 612 11 HOH TIP . C 3 HOH A 12 613 12 HOH TIP . C 3 HOH A 13 614 13 HOH TIP . C 3 HOH A 14 615 14 HOH TIP . C 3 HOH A 15 616 15 HOH TIP . C 3 HOH A 16 617 16 HOH TIP . C 3 HOH A 17 618 17 HOH TIP . C 3 HOH A 18 619 18 HOH TIP . C 3 HOH A 19 620 19 HOH TIP . C 3 HOH A 20 621 20 HOH TIP . C 3 HOH A 21 622 21 HOH TIP . C 3 HOH A 22 623 22 HOH TIP . C 3 HOH A 23 624 23 HOH TIP . C 3 HOH A 24 625 24 HOH TIP . C 3 HOH A 25 626 25 HOH TIP . C 3 HOH A 26 627 26 HOH TIP . C 3 HOH A 27 628 27 HOH TIP . C 3 HOH A 28 629 28 HOH TIP . C 3 HOH A 29 630 29 HOH TIP . C 3 HOH A 30 631 30 HOH TIP . C 3 HOH A 31 632 31 HOH TIP . C 3 HOH A 32 633 32 HOH TIP . C 3 HOH A 33 634 33 HOH TIP . C 3 HOH A 34 635 34 HOH TIP . C 3 HOH A 35 636 35 HOH TIP . C 3 HOH A 36 637 36 HOH TIP . C 3 HOH A 37 638 37 HOH TIP . C 3 HOH A 38 639 38 HOH TIP . C 3 HOH A 39 640 39 HOH TIP . C 3 HOH A 40 641 40 HOH TIP . C 3 HOH A 41 642 41 HOH TIP . C 3 HOH A 42 643 42 HOH TIP . C 3 HOH A 43 644 43 HOH TIP . C 3 HOH A 44 645 44 HOH TIP . C 3 HOH A 45 646 45 HOH TIP . C 3 HOH A 46 647 46 HOH TIP . C 3 HOH A 47 648 47 HOH TIP . C 3 HOH A 48 649 48 HOH TIP . C 3 HOH A 49 650 49 HOH TIP . C 3 HOH A 50 651 50 HOH TIP . C 3 HOH A 51 652 51 HOH TIP . C 3 HOH A 52 653 52 HOH TIP . C 3 HOH A 53 654 53 HOH TIP . C 3 HOH A 54 655 54 HOH TIP . C 3 HOH A 55 656 55 HOH TIP . C 3 HOH A 56 657 56 HOH TIP . C 3 HOH A 57 658 57 HOH TIP . C 3 HOH A 58 659 58 HOH TIP . C 3 HOH A 59 660 59 HOH TIP . C 3 HOH A 60 661 60 HOH TIP . C 3 HOH A 61 662 61 HOH TIP . C 3 HOH A 62 663 62 HOH TIP . C 3 HOH A 63 664 63 HOH TIP . C 3 HOH A 64 665 64 HOH TIP . C 3 HOH A 65 666 65 HOH TIP . C 3 HOH A 66 667 66 HOH TIP . C 3 HOH A 67 668 67 HOH TIP . C 3 HOH A 68 669 68 HOH TIP . C 3 HOH A 69 670 69 HOH TIP . C 3 HOH A 70 671 70 HOH TIP . C 3 HOH A 71 672 71 HOH TIP . C 3 HOH A 72 673 72 HOH TIP . C 3 HOH A 73 674 73 HOH TIP . C 3 HOH A 74 675 74 HOH TIP . C 3 HOH A 75 676 75 HOH TIP . C 3 HOH A 76 677 76 HOH TIP . C 3 HOH A 77 678 77 HOH TIP . C 3 HOH A 78 679 78 HOH TIP . C 3 HOH A 79 680 79 HOH TIP . C 3 HOH A 80 681 80 HOH TIP . C 3 HOH A 81 682 81 HOH TIP . C 3 HOH A 82 683 82 HOH TIP . C 3 HOH A 83 684 83 HOH TIP . C 3 HOH A 84 685 84 HOH TIP . C 3 HOH A 85 686 85 HOH TIP . C 3 HOH A 86 687 86 HOH TIP . C 3 HOH A 87 688 87 HOH TIP . C 3 HOH A 88 689 88 HOH TIP . C 3 HOH A 89 690 89 HOH TIP . C 3 HOH A 90 691 90 HOH TIP . C 3 HOH A 91 692 91 HOH TIP . C 3 HOH A 92 693 92 HOH TIP . C 3 HOH A 93 694 93 HOH TIP . C 3 HOH A 94 695 94 HOH TIP . C 3 HOH A 95 696 95 HOH TIP . C 3 HOH A 96 697 96 HOH TIP . C 3 HOH A 97 698 97 HOH TIP . C 3 HOH A 98 699 98 HOH TIP . C 3 HOH A 99 700 99 HOH TIP . C 3 HOH A 100 701 100 HOH TIP . C 3 HOH A 101 702 101 HOH TIP . C 3 HOH A 102 703 102 HOH TIP . C 3 HOH A 103 704 103 HOH TIP . C 3 HOH A 104 705 104 HOH TIP . C 3 HOH A 105 706 105 HOH TIP . C 3 HOH A 106 707 106 HOH TIP . C 3 HOH A 107 708 107 HOH TIP . C 3 HOH A 108 709 108 HOH TIP . C 3 HOH A 109 710 109 HOH TIP . C 3 HOH A 110 711 110 HOH TIP . C 3 HOH A 111 712 111 HOH TIP . C 3 HOH A 112 713 112 HOH TIP . C 3 HOH A 113 714 113 HOH TIP . C 3 HOH A 114 715 114 HOH TIP . C 3 HOH A 115 716 115 HOH TIP . C 3 HOH A 116 717 116 HOH TIP . C 3 HOH A 117 718 117 HOH TIP . C 3 HOH A 118 719 118 HOH TIP . C 3 HOH A 119 720 119 HOH TIP . C 3 HOH A 120 721 120 HOH TIP . C 3 HOH A 121 722 121 HOH TIP . C 3 HOH A 122 723 122 HOH TIP . C 3 HOH A 123 724 123 HOH TIP . C 3 HOH A 124 725 124 HOH TIP . C 3 HOH A 125 726 125 HOH TIP . C 3 HOH A 126 727 126 HOH TIP . C 3 HOH A 127 728 127 HOH TIP . C 3 HOH A 128 729 128 HOH TIP . C 3 HOH A 129 730 129 HOH TIP . C 3 HOH A 130 731 130 HOH TIP . C 3 HOH A 131 732 131 HOH TIP . C 3 HOH A 132 733 132 HOH TIP . C 3 HOH A 133 734 133 HOH TIP . C 3 HOH A 134 735 134 HOH TIP . C 3 HOH A 135 736 135 HOH TIP . C 3 HOH A 136 737 136 HOH TIP . C 3 HOH A 137 738 137 HOH TIP . C 3 HOH A 138 739 138 HOH TIP . C 3 HOH A 139 740 139 HOH TIP . C 3 HOH A 140 741 140 HOH TIP . C 3 HOH A 141 742 141 HOH TIP . C 3 HOH A 142 743 142 HOH TIP . C 3 HOH A 143 744 143 HOH TIP . C 3 HOH A 144 745 144 HOH TIP . C 3 HOH A 145 746 145 HOH TIP . C 3 HOH A 146 747 146 HOH TIP . C 3 HOH A 147 748 147 HOH TIP . C 3 HOH A 148 749 148 HOH TIP . C 3 HOH A 149 750 149 HOH TIP . C 3 HOH A 150 751 150 HOH TIP . C 3 HOH A 151 752 151 HOH TIP . C 3 HOH A 152 753 152 HOH TIP . C 3 HOH A 153 754 153 HOH TIP . C 3 HOH A 154 755 154 HOH TIP . C 3 HOH A 155 756 155 HOH TIP . C 3 HOH A 156 757 156 HOH TIP . C 3 HOH A 157 758 157 HOH TIP . C 3 HOH A 158 759 158 HOH TIP . C 3 HOH A 159 760 159 HOH TIP . C 3 HOH A 160 761 160 HOH TIP . # 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 XIL . . . B 2 16.939 65.278 38.689 1 20.46 ? C1 XIL 601 A 1 HETATM 2 C C2 XIL . . . B 2 16.736 64.264 39.823 1 20.2 ? C2 XIL 601 A 1 HETATM 3 O O2 XIL . . . B 2 17.611 63.163 39.627 1 19.94 ? O2 XIL 601 A 1 HETATM 4 C C3 XIL . . . B 2 15.286 63.764 39.853 1 20.41 ? C3 XIL 601 A 1 HETATM 5 O O3 XIL . . . B 2 15.075 62.968 41.013 1 20.86 ? O3 XIL 601 A 1 HETATM 6 C C4 XIL . . . B 2 14.307 64.934 39.857 1 20.24 ? C4 XIL 601 A 1 HETATM 7 O O4 XIL . . . B 2 12.986 64.439 39.71 1 19.59 ? O4 XIL 601 A 1 HETATM 8 C C5 XIL . . . B 2 14.626 65.9 38.709 1 20.95 ? C5 XIL 601 A 1 HETATM 9 O O5 XIL . . . B 2 15.995 66.354 38.807 1 20.18 ? O5 XIL 601 A 1 HETATM 10 N N1' XIL . . . B 2 20.301 67.776 35.697 1 19.77 ? N1' XIL 601 A 1 HETATM 11 C C2' XIL . . . B 2 20.34 68.338 37 1 20.11 ? C2' XIL 601 A 1 HETATM 12 C C3' XIL . . . B 2 19.648 67.693 38.053 1 19.56 ? C3' XIL 601 A 1 HETATM 13 O O2' XIL . . . B 2 21.192 69.177 37.263 1 19.88 ? O2' XIL 601 A 1 HETATM 14 O O3' XIL . . . B 2 19.226 68.461 39.162 1 19.48 ? O3' XIL 601 A 1 HETATM 15 C C4' XIL . . . B 2 18.55 66.655 37.644 1 19.98 ? C4' XIL 601 A 1 HETATM 16 O O1 XIL . . . B 2 18.277 65.824 38.768 1 19.47 ? O1 XIL 601 A 1 HETATM 17 C C5' XIL . . . B 2 19.028 65.85 36.431 1 20.37 ? C5' XIL 601 A 1 HETATM 18 C C6' XIL . . . B 2 19.271 66.834 35.322 1 19.22 ? C6' XIL 601 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 18 #