data_3RX7 # _model_server_result.job_id 9BwalQuXcfkCz3Bjicw05A _model_server_result.datetime_utc '2024-11-26 15:24:02' _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 3rx7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":605}' # _entry.id 3RX7 # _exptl.entry_id 3RX7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.313 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside' _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 3RX7 _cell.length_a 85.22 _cell.length_b 129.09 _cell.length_c 49.19 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RX7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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,E,F _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 5 _struct_asym.id E _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 metalc ? metalc1 A SG CYS 104 A CYS 104 1_555 C ZN ZN . A ZN 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc2 A SG CYS 121 A CYS 121 1_555 C ZN ZN . A ZN 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc3 A ND1 HIS 122 A HIS 122 1_555 C ZN ZN . A ZN 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc4 A NE2 HIS 142 A HIS 142 1_555 C ZN ZN . A ZN 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc5 A OD2 ASP 302 A ASP 302 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc6 A O GLU 304 A GLU 304 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc7 A OD2 ASP 307 A ASP 307 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc8 A OD1 ASP 307 A ASP 307 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc9 A OE2 GLU 308 A GLU 308 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc10 A OE1 GLU 308 A GLU 308 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc11 A O ALA 344 A ALA 344 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc12 B CA CA . A CA 538 1_555 F O HOH . A HOH 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? # _chem_comp.formula 'C12 H23 N O8' _chem_comp.formula_weight 309.313 _chem_comp.id 9MR _chem_comp.mon_nstd_flag n _chem_comp.name '(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'CELLOBIOSE-LIKE ISOFAGOMINE;(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucoside;(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl D-glucoside;(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl glucoside' # 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 O2 C2 9MR sing 1 n n O2 HO2 9MR sing 2 n n C2 C1 9MR sing 3 n n C2 C3 9MR sing 4 n n C2 H2 9MR sing 5 n n C3 C4 9MR sing 6 n n C3 O3 9MR sing 7 n n C3 H3 9MR sing 8 n n O3 HO3 9MR sing 9 n n C4 C5 9MR sing 10 n n C4 O4 9MR sing 11 n n C4 H4 9MR sing 12 n n O4 HO4 9MR sing 13 n n C5 C6 9MR sing 14 n n C5 O5 9MR sing 15 n n C5 H5 9MR sing 16 n n C6 O6 9MR sing 17 n n C6 H61 9MR sing 18 n n C6 H62 9MR sing 19 n n O6 HO6 9MR sing 20 n n O5 C1 9MR sing 21 n n C1 O1 9MR sing 22 n n C1 H1 9MR sing 23 n n O1 C3A 9MR sing 24 n n C3A C2A 9MR sing 25 n n C3A C4A 9MR sing 26 n n C3A H3A 9MR sing 27 n n C4A C5M 9MR sing 28 n n C4A O4A 9MR sing 29 n n C4A H4A 9MR sing 30 n n O4A HO4A 9MR sing 31 n n C5M N5A 9MR sing 32 n n C5M H5M1 9MR sing 33 n n C5M H5M2 9MR sing 34 n n N5A C1A 9MR sing 35 n n N5A HN5A 9MR sing 36 n n C1A C2A 9MR sing 37 n n C1A H1A1 9MR sing 38 n n C1A H1A2 9MR sing 39 n n C2A C6A 9MR sing 40 n n C2A H2A 9MR sing 41 n n C6A O6A 9MR sing 42 n n C6A H6A1 9MR sing 43 n n C6A H6A2 9MR sing 44 n n O6A HO6A 9MR sing 45 n n # _atom_sites.entry_id 3RX7 _atom_sites.fract_transf_matrix[1][1] 0.011734 _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] 0.007747 _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] 0.020329 _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 CA A 1 538 1 CA CA . C 3 ZN A 1 539 2 ZN ZN . D 4 G3I A 1 604 604 G3I G3I . E 5 9MR A 1 605 605 9MR 9MR . F 6 HOH A 1 540 1 HOH HOH . F 6 HOH A 2 541 2 HOH HOH . F 6 HOH A 3 542 3 HOH HOH . F 6 HOH A 4 543 4 HOH HOH . F 6 HOH A 5 544 5 HOH HOH . F 6 HOH A 6 545 6 HOH HOH . F 6 HOH A 7 546 7 HOH HOH . F 6 HOH A 8 547 8 HOH HOH . F 6 HOH A 9 548 9 HOH HOH . F 6 HOH A 10 549 10 HOH HOH . F 6 HOH A 11 550 11 HOH HOH . F 6 HOH A 12 551 12 HOH HOH . F 6 HOH A 13 552 13 HOH HOH . F 6 HOH A 14 553 14 HOH HOH . F 6 HOH A 15 554 15 HOH HOH . F 6 HOH A 16 555 16 HOH HOH . F 6 HOH A 17 556 17 HOH HOH . F 6 HOH A 18 557 18 HOH HOH . F 6 HOH A 19 558 19 HOH HOH . F 6 HOH A 20 559 20 HOH HOH . F 6 HOH A 21 560 21 HOH HOH . F 6 HOH A 22 561 22 HOH HOH . F 6 HOH A 23 562 23 HOH HOH . F 6 HOH A 24 563 24 HOH HOH . F 6 HOH A 25 564 25 HOH HOH . F 6 HOH A 26 565 26 HOH HOH . F 6 HOH A 27 566 27 HOH HOH . F 6 HOH A 28 567 28 HOH HOH . F 6 HOH A 29 568 29 HOH HOH . F 6 HOH A 30 569 30 HOH HOH . F 6 HOH A 31 570 31 HOH HOH . F 6 HOH A 32 571 32 HOH HOH . F 6 HOH A 33 572 33 HOH HOH . F 6 HOH A 34 573 34 HOH HOH . F 6 HOH A 35 574 35 HOH HOH . F 6 HOH A 36 575 36 HOH HOH . F 6 HOH A 37 576 37 HOH HOH . F 6 HOH A 38 577 38 HOH HOH . F 6 HOH A 39 578 39 HOH HOH . F 6 HOH A 40 579 40 HOH HOH . F 6 HOH A 41 580 41 HOH HOH . F 6 HOH A 42 581 42 HOH HOH . F 6 HOH A 43 582 43 HOH HOH . F 6 HOH A 44 583 44 HOH HOH . F 6 HOH A 45 584 45 HOH HOH . F 6 HOH A 46 585 46 HOH HOH . F 6 HOH A 47 586 47 HOH HOH . F 6 HOH A 48 587 48 HOH HOH . F 6 HOH A 49 588 49 HOH HOH . F 6 HOH A 50 589 50 HOH HOH . F 6 HOH A 51 590 51 HOH HOH . F 6 HOH A 52 591 52 HOH HOH . F 6 HOH A 53 592 53 HOH HOH . F 6 HOH A 54 593 54 HOH HOH . F 6 HOH A 55 594 55 HOH HOH . F 6 HOH A 56 595 56 HOH HOH . F 6 HOH A 57 596 57 HOH HOH . F 6 HOH A 58 597 58 HOH HOH . F 6 HOH A 59 598 59 HOH HOH . F 6 HOH A 60 599 60 HOH HOH . F 6 HOH A 61 600 61 HOH HOH . F 6 HOH A 62 601 62 HOH HOH . F 6 HOH A 63 602 63 HOH HOH . F 6 HOH A 64 603 64 HOH HOH . F 6 HOH A 65 606 65 HOH HOH . F 6 HOH A 66 607 66 HOH HOH . F 6 HOH A 67 608 67 HOH HOH . F 6 HOH A 68 609 68 HOH HOH . F 6 HOH A 69 610 69 HOH HOH . F 6 HOH A 70 611 70 HOH HOH . F 6 HOH A 71 612 71 HOH HOH . F 6 HOH A 72 613 72 HOH HOH . F 6 HOH A 73 614 73 HOH HOH . F 6 HOH A 74 615 74 HOH HOH . F 6 HOH A 75 616 75 HOH HOH . F 6 HOH A 76 617 76 HOH HOH . F 6 HOH A 77 618 77 HOH HOH . F 6 HOH A 78 619 78 HOH HOH . F 6 HOH A 79 620 79 HOH HOH . F 6 HOH A 80 621 80 HOH HOH . F 6 HOH A 81 622 81 HOH HOH . F 6 HOH A 82 623 82 HOH HOH . F 6 HOH A 83 624 83 HOH HOH . F 6 HOH A 84 625 84 HOH HOH . F 6 HOH A 85 626 85 HOH HOH . F 6 HOH A 86 627 86 HOH HOH . F 6 HOH A 87 628 87 HOH HOH . F 6 HOH A 88 629 88 HOH HOH . F 6 HOH A 89 630 89 HOH HOH . F 6 HOH A 90 631 90 HOH HOH . F 6 HOH A 91 632 91 HOH HOH . F 6 HOH A 92 633 92 HOH HOH . F 6 HOH A 93 634 93 HOH HOH . F 6 HOH A 94 635 94 HOH HOH . F 6 HOH A 95 636 95 HOH HOH . F 6 HOH A 96 637 96 HOH HOH . F 6 HOH A 97 638 97 HOH HOH . F 6 HOH A 98 639 98 HOH HOH . F 6 HOH A 99 640 99 HOH HOH . F 6 HOH A 100 641 100 HOH HOH . F 6 HOH A 101 642 101 HOH HOH . F 6 HOH A 102 643 102 HOH HOH . F 6 HOH A 103 644 103 HOH HOH . F 6 HOH A 104 645 104 HOH HOH . F 6 HOH A 105 646 105 HOH HOH . F 6 HOH A 106 647 106 HOH HOH . F 6 HOH A 107 648 107 HOH HOH . F 6 HOH A 108 649 108 HOH HOH . F 6 HOH A 109 650 109 HOH HOH . F 6 HOH A 110 651 110 HOH HOH . F 6 HOH A 111 652 111 HOH HOH . F 6 HOH A 112 653 112 HOH HOH . F 6 HOH A 113 654 113 HOH HOH . F 6 HOH A 114 655 114 HOH HOH . F 6 HOH A 115 656 115 HOH HOH . F 6 HOH A 116 657 116 HOH HOH . F 6 HOH A 117 658 117 HOH HOH . F 6 HOH A 118 659 118 HOH HOH . F 6 HOH A 119 660 119 HOH HOH . F 6 HOH A 120 661 120 HOH HOH . F 6 HOH A 121 662 121 HOH HOH . F 6 HOH A 122 663 122 HOH HOH . F 6 HOH A 123 664 123 HOH HOH . F 6 HOH A 124 665 124 HOH HOH . F 6 HOH A 125 666 125 HOH HOH . F 6 HOH A 126 667 126 HOH HOH . F 6 HOH A 127 668 127 HOH HOH . F 6 HOH A 128 669 128 HOH HOH . F 6 HOH A 129 670 129 HOH HOH . F 6 HOH A 130 671 130 HOH HOH . F 6 HOH A 131 672 131 HOH HOH . F 6 HOH A 132 673 132 HOH HOH . F 6 HOH A 133 674 133 HOH HOH . F 6 HOH A 134 675 134 HOH HOH . F 6 HOH A 135 676 135 HOH HOH . F 6 HOH A 136 677 136 HOH HOH . F 6 HOH A 137 678 137 HOH HOH . F 6 HOH A 138 679 138 HOH HOH . F 6 HOH A 139 680 139 HOH HOH . F 6 HOH A 140 681 140 HOH HOH . F 6 HOH A 141 682 141 HOH HOH . F 6 HOH A 142 683 142 HOH HOH . F 6 HOH A 143 684 143 HOH HOH . F 6 HOH A 144 685 144 HOH HOH . F 6 HOH A 145 686 145 HOH HOH . F 6 HOH A 146 687 146 HOH HOH . F 6 HOH A 147 688 147 HOH HOH . F 6 HOH A 148 689 148 HOH HOH . F 6 HOH A 149 690 149 HOH HOH . F 6 HOH A 150 691 150 HOH HOH . F 6 HOH A 151 692 151 HOH HOH . F 6 HOH A 152 693 152 HOH HOH . F 6 HOH A 153 694 153 HOH HOH . F 6 HOH A 154 695 154 HOH HOH . F 6 HOH A 155 696 155 HOH HOH . F 6 HOH A 156 697 156 HOH HOH . F 6 HOH A 157 698 157 HOH HOH . F 6 HOH A 158 699 158 HOH HOH . F 6 HOH A 159 700 159 HOH HOH . F 6 HOH A 160 701 160 HOH HOH . F 6 HOH A 161 702 161 HOH HOH . F 6 HOH A 162 703 162 HOH HOH . F 6 HOH A 163 704 163 HOH HOH . F 6 HOH A 164 705 164 HOH HOH . F 6 HOH A 165 706 165 HOH HOH . F 6 HOH A 166 707 166 HOH HOH . F 6 HOH A 167 708 167 HOH HOH . F 6 HOH A 168 709 168 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 O2 9MR . . . E 5 -17.027 35.914 -29.911 1 30.21 ? O2 9MR 605 A 1 HETATM 2 C C2 9MR . . . E 5 -15.724 35.423 -29.79 1 31.87 ? C2 9MR 605 A 1 HETATM 3 C C3 9MR . . . E 5 -15.165 35.36 -28.294 1 30.88 ? C3 9MR 605 A 1 HETATM 4 O O3 9MR . . . E 5 -15.951 34.41 -27.637 1 28.64 ? O3 9MR 605 A 1 HETATM 5 C C4 9MR . . . E 5 -13.748 34.885 -28.227 1 31 ? C4 9MR 605 A 1 HETATM 6 O O4 9MR . . . E 5 -13.032 34.935 -26.99 1 32.36 ? O4 9MR 605 A 1 HETATM 7 C C5 9MR . . . E 5 -12.754 35.501 -29.235 1 33.01 ? C5 9MR 605 A 1 HETATM 8 C C6 9MR . . . E 5 -11.957 34.144 -29.51 1 37.21 ? C6 9MR 605 A 1 HETATM 9 O O6 9MR . . . E 5 -10.757 34.687 -29.687 1 40.52 ? O6 9MR 605 A 1 HETATM 10 O O5 9MR . . . E 5 -13.338 35.662 -30.469 1 31.69 ? O5 9MR 605 A 1 HETATM 11 C C1 9MR . . . E 5 -14.71 36.264 -30.637 1 33.22 ? C1 9MR 605 A 1 HETATM 12 O O1 9MR . . . E 5 -15.21 36.219 -31.994 1 35.48 ? O1 9MR 605 A 1 HETATM 13 C C3A 9MR . . . E 5 -14.438 37.063 -32.828 1 40.32 ? C3A 9MR 605 A 1 HETATM 14 C C4A 9MR . . . E 5 -13.324 36.257 -33.691 1 42.28 ? C4A 9MR 605 A 1 HETATM 15 O O4A 9MR . . . E 5 -12.147 35.708 -32.968 1 42.66 ? O4A 9MR 605 A 1 HETATM 16 C C5M 9MR . . . E 5 -12.899 36.98 -35.09 1 43.42 ? C5M 9MR 605 A 1 HETATM 17 N N5A 9MR . . . E 5 -13.461 38.442 -35.268 1 44.78 ? N5A 9MR 605 A 1 HETATM 18 C C1A 9MR . . . E 5 -14.646 38.797 -34.475 1 42.77 ? C1A 9MR 605 A 1 HETATM 19 C C2A 9MR . . . E 5 -15.434 37.753 -33.774 1 42.99 ? C2A 9MR 605 A 1 HETATM 20 C C6A 9MR . . . E 5 -16.769 38.362 -33.17 1 46.75 ? C6A 9MR 605 A 1 HETATM 21 O O6A 9MR . . . E 5 -16.506 39.522 -32.365 1 47.8 ? O6A 9MR 605 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #