data_5U1E # _model_server_result.job_id CyItjFbkYTcwdJblyWn3YQ _model_server_result.datetime_utc '2025-02-18 00:37:57' _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 5u1e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5U1E # _exptl.entry_id 5U1E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.514 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-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 5U1E _cell.length_a 66.718 _cell.length_b 68.168 _cell.length_c 69.799 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5U1E _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C18 H37 N5 O10' _chem_comp.formula_weight 483.514 _chem_comp.id 9CS _chem_comp.mon_nstd_flag . _chem_comp.name '(1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Kanamycin B;Bekanamycin' # 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 O5 9CS sing 1 n n C1 O9 9CS sing 2 n n C1 C2 9CS sing 3 n n C1 H1 9CS sing 4 n n C2 C3 9CS sing 5 n n C2 N6 9CS sing 6 n n C2 H2 9CS sing 7 n n C3 C4 9CS sing 8 n n C3 O7 9CS sing 9 n n C3 H3 9CS sing 10 n n C4 C5 9CS sing 11 n n C4 O8 9CS sing 12 n n C4 H4 9CS sing 13 n n C5 C6 9CS sing 14 n n C5 O5 9CS sing 15 n n C5 H5 9CS sing 16 n n C6 N1 9CS sing 17 n n C6 H61 9CS sing 18 n n C6 H62 9CS sing 19 n n C7 C12 9CS sing 20 n n C7 N3 9CS sing 21 n n C7 C8 9CS sing 22 n n C7 H7 9CS sing 23 n n C8 C9 9CS sing 24 n n C8 O11 9CS sing 25 n n C8 H8 9CS sing 26 n n C9 C10 9CS sing 27 n n C9 O10 9CS sing 28 n n C9 H9 9CS sing 29 n n C10 C11 9CS sing 30 n n C10 O9 9CS sing 31 n n C10 H10 9CS sing 32 n n C11 N2 9CS sing 33 n n C11 C12 9CS sing 34 n n C11 H11 9CS sing 35 n n C12 H121 9CS sing 36 n n C12 H122 9CS sing 37 n n C13 O11 9CS sing 38 n n C13 C14 9CS sing 39 n n C13 O12 9CS sing 40 n n C13 H13 9CS sing 41 n n C14 O13 9CS sing 42 n n C14 C15 9CS sing 43 n n C14 H14 9CS sing 44 n n C15 N4 9CS sing 45 n n C15 C16 9CS sing 46 n n C15 H15 9CS sing 47 n n C16 C17 9CS sing 48 n n C16 O14 9CS sing 49 n n C16 H16 9CS sing 50 n n C17 O12 9CS sing 51 n n C17 C18 9CS sing 52 n n C17 H17 9CS sing 53 n n C18 O15 9CS sing 54 n n C18 H181 9CS sing 55 n n C18 H182 9CS sing 56 n n N1 HN11 9CS sing 57 n n N1 HN12 9CS sing 58 n n N2 HN21 9CS sing 59 n n N2 HN22 9CS sing 60 n n N3 HN31 9CS sing 61 n n N3 HN32 9CS sing 62 n n N4 HN41 9CS sing 63 n n N4 HN42 9CS sing 64 n n O7 HO7 9CS sing 65 n n O8 HO8 9CS sing 66 n n O10 HO10 9CS sing 67 n n O13 HO13 9CS sing 68 n n O14 HO14 9CS sing 69 n n O15 HO15 9CS sing 70 n n N6 HN61 9CS sing 71 n n N6 HN62 9CS sing 72 n n # _atom_sites.entry_id 5U1E _atom_sites.fract_transf_matrix[1][1] 0.014988 _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] 0.01467 _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] 0.014327 _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 9CS A 1 401 1 9CS LIG . C 3 SAH A 1 402 1 SAH SAM . D 4 HOH A 1 501 54 HOH HOH . D 4 HOH A 2 502 42 HOH HOH . D 4 HOH A 3 503 97 HOH HOH . D 4 HOH A 4 504 108 HOH HOH . D 4 HOH A 5 505 114 HOH HOH . D 4 HOH A 6 506 72 HOH HOH . D 4 HOH A 7 507 22 HOH HOH . D 4 HOH A 8 508 104 HOH HOH . D 4 HOH A 9 509 17 HOH HOH . D 4 HOH A 10 510 52 HOH HOH . D 4 HOH A 11 511 24 HOH HOH . D 4 HOH A 12 512 60 HOH HOH . D 4 HOH A 13 513 25 HOH HOH . D 4 HOH A 14 514 78 HOH HOH . D 4 HOH A 15 515 71 HOH HOH . D 4 HOH A 16 516 38 HOH HOH . D 4 HOH A 17 517 8 HOH HOH . D 4 HOH A 18 518 2 HOH HOH . D 4 HOH A 19 519 70 HOH HOH . D 4 HOH A 20 520 112 HOH HOH . D 4 HOH A 21 521 12 HOH HOH . D 4 HOH A 22 522 27 HOH HOH . D 4 HOH A 23 523 18 HOH HOH . D 4 HOH A 24 524 120 HOH HOH . D 4 HOH A 25 525 21 HOH HOH . D 4 HOH A 26 526 73 HOH HOH . D 4 HOH A 27 527 102 HOH HOH . D 4 HOH A 28 528 32 HOH HOH . D 4 HOH A 29 529 14 HOH HOH . D 4 HOH A 30 530 11 HOH HOH . D 4 HOH A 31 531 75 HOH HOH . D 4 HOH A 32 532 20 HOH HOH . D 4 HOH A 33 533 41 HOH HOH . D 4 HOH A 34 534 56 HOH HOH . D 4 HOH A 35 535 9 HOH HOH . D 4 HOH A 36 536 103 HOH HOH . D 4 HOH A 37 537 6 HOH HOH . D 4 HOH A 38 538 4 HOH HOH . D 4 HOH A 39 539 39 HOH HOH . D 4 HOH A 40 540 37 HOH HOH . D 4 HOH A 41 541 81 HOH HOH . D 4 HOH A 42 542 15 HOH HOH . D 4 HOH A 43 543 122 HOH HOH . D 4 HOH A 44 544 92 HOH HOH . D 4 HOH A 45 545 13 HOH HOH . D 4 HOH A 46 546 1 HOH HOH . D 4 HOH A 47 547 19 HOH HOH . D 4 HOH A 48 548 5 HOH HOH . D 4 HOH A 49 549 80 HOH HOH . D 4 HOH A 50 550 85 HOH HOH . D 4 HOH A 51 551 26 HOH HOH . D 4 HOH A 52 552 49 HOH HOH . D 4 HOH A 53 553 77 HOH HOH . D 4 HOH A 54 554 55 HOH HOH . D 4 HOH A 55 555 62 HOH HOH . D 4 HOH A 56 556 16 HOH HOH . D 4 HOH A 57 557 50 HOH HOH . D 4 HOH A 58 558 3 HOH HOH . D 4 HOH A 59 559 36 HOH HOH . D 4 HOH A 60 560 40 HOH HOH . D 4 HOH A 61 561 87 HOH HOH . D 4 HOH A 62 562 43 HOH HOH . D 4 HOH A 63 563 123 HOH HOH . D 4 HOH A 64 564 53 HOH HOH . D 4 HOH A 65 565 79 HOH HOH . D 4 HOH A 66 566 126 HOH HOH . D 4 HOH A 67 567 10 HOH HOH . D 4 HOH A 68 568 83 HOH HOH . D 4 HOH A 69 569 35 HOH HOH . D 4 HOH A 70 570 90 HOH HOH . D 4 HOH A 71 571 30 HOH HOH . D 4 HOH A 72 572 23 HOH HOH . D 4 HOH A 73 573 51 HOH HOH . D 4 HOH A 74 574 58 HOH HOH . D 4 HOH A 75 575 57 HOH HOH . D 4 HOH A 76 576 117 HOH HOH . D 4 HOH A 77 577 101 HOH HOH . D 4 HOH A 78 578 124 HOH HOH . D 4 HOH A 79 579 44 HOH HOH . D 4 HOH A 80 580 48 HOH HOH . D 4 HOH A 81 581 93 HOH HOH . D 4 HOH A 82 582 69 HOH HOH . D 4 HOH A 83 583 68 HOH HOH . D 4 HOH A 84 584 116 HOH HOH . D 4 HOH A 85 585 84 HOH HOH . D 4 HOH A 86 586 61 HOH HOH . D 4 HOH A 87 587 74 HOH HOH . D 4 HOH A 88 588 95 HOH HOH . D 4 HOH A 89 589 28 HOH HOH . D 4 HOH A 90 590 111 HOH HOH . D 4 HOH A 91 591 33 HOH HOH . D 4 HOH A 92 592 45 HOH HOH . D 4 HOH A 93 593 29 HOH HOH . D 4 HOH A 94 594 110 HOH HOH . D 4 HOH A 95 595 118 HOH HOH . D 4 HOH A 96 596 105 HOH HOH . D 4 HOH A 97 597 59 HOH HOH . D 4 HOH A 98 598 67 HOH HOH . D 4 HOH A 99 599 7 HOH HOH . D 4 HOH A 100 600 96 HOH HOH . D 4 HOH A 101 601 46 HOH HOH . D 4 HOH A 102 602 47 HOH HOH . D 4 HOH A 103 603 100 HOH HOH . D 4 HOH A 104 604 125 HOH HOH . D 4 HOH A 105 605 63 HOH HOH . D 4 HOH A 106 606 82 HOH HOH . D 4 HOH A 107 607 91 HOH HOH . D 4 HOH A 108 608 113 HOH HOH . D 4 HOH A 109 609 121 HOH HOH . D 4 HOH A 110 610 109 HOH HOH . D 4 HOH A 111 611 64 HOH HOH . D 4 HOH A 112 612 106 HOH HOH . D 4 HOH A 113 613 86 HOH HOH . D 4 HOH A 114 614 94 HOH HOH . D 4 HOH A 115 615 98 HOH HOH . D 4 HOH A 116 616 115 HOH HOH . D 4 HOH A 117 617 99 HOH HOH . D 4 HOH A 118 618 88 HOH HOH . D 4 HOH A 119 619 66 HOH HOH . D 4 HOH A 120 620 119 HOH HOH . D 4 HOH A 121 621 89 HOH HOH . D 4 HOH A 122 622 107 HOH HOH . D 4 HOH A 123 623 34 HOH HOH . D 4 HOH A 124 624 76 HOH HOH . D 4 HOH A 125 625 65 HOH HOH . D 4 HOH A 126 626 31 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 C1 9CS . . . B 2 -4.817 -18.073 17.728 1 35.21 ? C1 9CS 401 A 1 HETATM 2 C C2 9CS . . . B 2 -4.426 -17.568 19.125 1 37.58 ? C2 9CS 401 A 1 HETATM 3 C C3 9CS . . . B 2 -2.95 -17.418 19.222 1 35.1 ? C3 9CS 401 A 1 HETATM 4 C C4 9CS . . . B 2 -2.279 -18.708 18.954 1 33.21 ? C4 9CS 401 A 1 HETATM 5 C C5 9CS . . . B 2 -2.664 -19.248 17.569 1 27.76 ? C5 9CS 401 A 1 HETATM 6 C C6 9CS . . . B 2 -2.088 -20.603 17.371 1 36.18 ? C6 9CS 401 A 1 HETATM 7 C C7 9CS . . . B 2 -5.983 -15.567 13.177 1 30.17 ? C7 9CS 401 A 1 HETATM 8 C C8 9CS . . . B 2 -6.328 -14.876 14.474 1 27.43 ? C8 9CS 401 A 1 HETATM 9 C C9 9CS . . . B 2 -5.433 -15.369 15.611 1 26.93 ? C9 9CS 401 A 1 HETATM 10 C C10 9CS . . . B 2 -5.416 -16.884 15.799 1 30.38 ? C10 9CS 401 A 1 HETATM 11 C C11 9CS . . . B 2 -5.138 -17.63 14.504 1 36.98 ? C11 9CS 401 A 1 HETATM 12 C C12 9CS . . . B 2 -5.933 -17.101 13.313 1 23.54 ? C12 9CS 401 A 1 HETATM 13 C C13 9CS . . . B 2 -7.398 -12.783 14.238 1 26.03 ? C13 9CS 401 A 1 HETATM 14 C C14 9CS . . . B 2 -7.304 -11.334 13.749 1 23.72 ? C14 9CS 401 A 1 HETATM 15 C C15 9CS . . . B 2 -6.725 -10.368 14.752 1 23.73 ? C15 9CS 401 A 1 HETATM 16 C C16 9CS . . . B 2 -7.377 -10.517 16.055 1 26.31 ? C16 9CS 401 A 1 HETATM 17 C C17 9CS . . . B 2 -7.262 -11.955 16.531 1 28.01 ? C17 9CS 401 A 1 HETATM 18 C C18 9CS . . . B 2 -7.925 -12.122 17.828 1 26.39 ? C18 9CS 401 A 1 HETATM 19 N N1 9CS . . . B 2 -2.25 -21.044 16.004 1 38.89 ? N1 9CS 401 A 1 HETATM 20 N N2 9CS . . . B 2 -5.431 -19.042 14.704 1 28.53 ? N2 9CS 401 A 1 HETATM 21 N N3 9CS . . . B 2 -6.933 -15.179 12.181 1 24.05 ? N3 9CS 401 A 1 HETATM 22 N N4 9CS . . . B 2 -6.849 -8.987 14.242 1 29.9 ? N4 9CS 401 A 1 HETATM 23 O O5 9CS . . . B 2 -4.142 -19.347 17.46 1 30.43 ? O5 9CS 401 A 1 HETATM 24 O O7 9CS . . . B 2 -2.579 -16.96 20.557 1 30.77 ? O7 9CS 401 A 1 HETATM 25 O O8 9CS . . . B 2 -0.854 -18.574 19.086 1 30.48 ? O8 9CS 401 A 1 HETATM 26 O O9 9CS . . . B 2 -4.395 -17.179 16.761 1 29.07 ? O9 9CS 401 A 1 HETATM 27 O O10 9CS . . . B 2 -5.844 -14.846 16.865 1 30.64 ? O10 9CS 401 A 1 HETATM 28 O O11 9CS . . . B 2 -6.153 -13.445 14.273 1 27.33 ? O11 9CS 401 A 1 HETATM 29 O O12 9CS . . . B 2 -7.937 -12.903 15.579 1 23.96 ? O12 9CS 401 A 1 HETATM 30 O O13 9CS . . . B 2 -6.512 -11.262 12.55 1 24.94 ? O13 9CS 401 A 1 HETATM 31 O O14 9CS . . . B 2 -6.819 -9.585 17.028 1 23.6 ? O14 9CS 401 A 1 HETATM 32 O O15 9CS . . . B 2 -7.856 -13.493 18.166 1 30.3 ? O15 9CS 401 A 1 HETATM 33 N N6 9CS . . . B 2 -5.098 -16.328 19.417 1 36.28 ? N6 9CS 401 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 33 #