data_5YSW # _model_server_result.job_id nqlZTZGCCw2xrDRdvcxKXQ _model_server_result.datetime_utc '2024-11-05 01:16:31' _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 5ysw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 5YSW # _exptl.entry_id 5YSW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 755.805 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S,12E,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-21-(acetyloxy)-5,6,17,19-tetrahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-9-yl hydroxyacetate' _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 94 _cell.angle_gamma 90 _cell.entry_id 5YSW _cell.length_a 35.082 _cell.length_b 70.709 _cell.length_c 80.975 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YSW _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 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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _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 387 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 366 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 501 _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 2.435 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C39 H49 N O14' _chem_comp.formula_weight 755.805 _chem_comp.id 9LF _chem_comp.mon_nstd_flag . _chem_comp.name '(2S,12E,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-21-(acetyloxy)-5,6,17,19-tetrahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-9-yl hydroxyacetate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Rifamycin L' # 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 O25 C24 9LF sing 1 n n C24 C22 9LF sing 2 n n O32 C31 9LF doub 3 n n C22 O23 9LF doub 4 n n C22 O21 9LF sing 5 n n N30 C31 9LF sing 6 n n N30 C18 9LF sing 7 n n C31 C33 9LF sing 8 n n C19 C18 9LF doub 9 n y C19 C20 9LF sing 10 n y C18 C16 9LF sing 11 n y O21 C20 9LF sing 12 n n C20 C26 9LF doub 13 n y C34 C33 9LF sing 14 n n C33 C35 9LF doub 15 e n C16 O17 9LF sing 16 n n C16 C15 9LF doub 17 n y C26 C15 9LF sing 18 n y C26 C27 9LF sing 19 n y O29 C28 9LF doub 20 n n C35 C36 9LF sing 21 n n C15 C13 9LF sing 22 n y C27 C28 9LF sing 23 n n C27 C10 9LF doub 24 n y C01 O02 9LF sing 25 n n C28 C07 9LF sing 26 n n C36 C37 9LF doub 27 e n C13 O14 9LF sing 28 n n C13 C11 9LF doub 29 n y C37 C38 9LF sing 30 n n C10 C11 9LF sing 31 n y C10 O09 9LF sing 32 n n C39 C38 9LF sing 33 n n C08 C07 9LF sing 34 n n C11 C12 9LF sing 35 n n C07 O09 9LF sing 36 n n C07 O06 9LF sing 37 n n O02 C03 9LF sing 38 n n C38 C40 9LF sing 39 n n C04 C03 9LF sing 40 n n C04 C05 9LF doub 41 e n C03 C53 9LF sing 42 n n O06 C05 9LF sing 43 n n O52 C50 9LF doub 44 n n C40 O41 9LF sing 45 n n C40 C42 9LF sing 46 n n C53 C48 9LF sing 47 n n C53 C54 9LF sing 48 n n C48 C46 9LF sing 49 n n C48 O49 9LF sing 50 n n C44 C42 9LF sing 51 n n C44 C46 9LF sing 52 n n C44 O45 9LF sing 53 n n C42 C43 9LF sing 54 n n C46 C47 9LF sing 55 n n C50 O49 9LF sing 56 n n C50 C51 9LF sing 57 n n C01 H1 9LF sing 58 n n C01 H2 9LF sing 59 n n C01 H3 9LF sing 60 n n C03 H4 9LF sing 61 n n C04 H5 9LF sing 62 n n C05 H6 9LF sing 63 n n C08 H7 9LF sing 64 n n C08 H8 9LF sing 65 n n C08 H9 9LF sing 66 n n C12 H10 9LF sing 67 n n C12 H11 9LF sing 68 n n C12 H12 9LF sing 69 n n O14 H13 9LF sing 70 n n O17 H14 9LF sing 71 n n C19 H15 9LF sing 72 n n C24 H16 9LF sing 73 n n C24 H17 9LF sing 74 n n O25 H18 9LF sing 75 n n N30 H19 9LF sing 76 n n C34 H20 9LF sing 77 n n C34 H21 9LF sing 78 n n C34 H22 9LF sing 79 n n C35 H23 9LF sing 80 n n C36 H24 9LF sing 81 n n C37 H25 9LF sing 82 n n C38 H26 9LF sing 83 n n C39 H27 9LF sing 84 n n C39 H28 9LF sing 85 n n C39 H29 9LF sing 86 n n C40 H30 9LF sing 87 n n O41 H31 9LF sing 88 n n C42 H32 9LF sing 89 n n C43 H33 9LF sing 90 n n C43 H34 9LF sing 91 n n C43 H35 9LF sing 92 n n C44 H36 9LF sing 93 n n O45 H37 9LF sing 94 n n C46 H38 9LF sing 95 n n C47 H39 9LF sing 96 n n C47 H40 9LF sing 97 n n C47 H41 9LF sing 98 n n C48 H42 9LF sing 99 n n C51 H43 9LF sing 100 n n C51 H44 9LF sing 101 n n C51 H45 9LF sing 102 n n C53 H46 9LF sing 103 n n C54 H47 9LF sing 104 n n C54 H48 9LF sing 105 n n C54 H49 9LF sing 106 n n # _atom_sites.entry_id 5YSW _atom_sites.fract_transf_matrix[1][1] 0.028505 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001994 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014142 _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] 0.01238 _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 HEM A 1 501 501 HEM HEM . C 3 9LF A 1 502 1 9LF L3 . D 4 HOH A 1 601 55 HOH HOH . D 4 HOH A 2 602 40 HOH HOH . D 4 HOH A 3 603 39 HOH HOH . D 4 HOH A 4 604 26 HOH HOH . D 4 HOH A 5 605 22 HOH HOH . D 4 HOH A 6 606 16 HOH HOH . D 4 HOH A 7 607 30 HOH HOH . D 4 HOH A 8 608 20 HOH HOH . D 4 HOH A 9 609 13 HOH HOH . D 4 HOH A 10 610 61 HOH HOH . D 4 HOH A 11 611 29 HOH HOH . D 4 HOH A 12 612 60 HOH HOH . D 4 HOH A 13 613 37 HOH HOH . D 4 HOH A 14 614 57 HOH HOH . D 4 HOH A 15 615 5 HOH HOH . D 4 HOH A 16 616 8 HOH HOH . D 4 HOH A 17 617 6 HOH HOH . D 4 HOH A 18 618 45 HOH HOH . D 4 HOH A 19 619 38 HOH HOH . D 4 HOH A 20 620 47 HOH HOH . D 4 HOH A 21 621 51 HOH HOH . D 4 HOH A 22 622 58 HOH HOH . D 4 HOH A 23 623 28 HOH HOH . D 4 HOH A 24 624 62 HOH HOH . D 4 HOH A 25 625 12 HOH HOH . D 4 HOH A 26 626 15 HOH HOH . D 4 HOH A 27 627 42 HOH HOH . D 4 HOH A 28 628 1 HOH HOH . D 4 HOH A 29 629 33 HOH HOH . D 4 HOH A 30 630 52 HOH HOH . D 4 HOH A 31 631 32 HOH HOH . D 4 HOH A 32 632 35 HOH HOH . D 4 HOH A 33 633 19 HOH HOH . D 4 HOH A 34 634 36 HOH HOH . D 4 HOH A 35 635 21 HOH HOH . D 4 HOH A 36 636 54 HOH HOH . D 4 HOH A 37 637 17 HOH HOH . D 4 HOH A 38 638 18 HOH HOH . D 4 HOH A 39 639 56 HOH HOH . D 4 HOH A 40 640 48 HOH HOH . D 4 HOH A 41 641 10 HOH HOH . D 4 HOH A 42 642 43 HOH HOH . D 4 HOH A 43 643 46 HOH HOH . D 4 HOH A 44 644 41 HOH HOH . D 4 HOH A 45 645 67 HOH HOH . D 4 HOH A 46 646 44 HOH HOH . D 4 HOH A 47 647 34 HOH HOH . D 4 HOH A 48 648 7 HOH HOH . D 4 HOH A 49 649 65 HOH HOH . D 4 HOH A 50 650 2 HOH HOH . D 4 HOH A 51 651 4 HOH HOH . D 4 HOH A 52 652 25 HOH HOH . D 4 HOH A 53 653 9 HOH HOH . D 4 HOH A 54 654 27 HOH HOH . D 4 HOH A 55 655 14 HOH HOH . D 4 HOH A 56 656 50 HOH HOH . D 4 HOH A 57 657 63 HOH HOH . D 4 HOH A 58 658 11 HOH HOH . D 4 HOH A 59 659 31 HOH HOH . D 4 HOH A 60 660 53 HOH HOH . D 4 HOH A 61 661 66 HOH HOH . D 4 HOH A 62 662 49 HOH HOH . D 4 HOH A 63 663 24 HOH HOH . D 4 HOH A 64 664 64 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 C01 9LF . . . C 3 97.006 61.14 271.318 1 73.52 ? C01 9LF 502 A 1 HETATM 2 O O02 9LF . . . C 3 96.918 61.261 272.714 1 78.39 ? O02 9LF 502 A 1 HETATM 3 C C03 9LF . . . C 3 96.33 62.449 273.201 1 86.7 ? C03 9LF 502 A 1 HETATM 4 C C04 9LF . . . C 3 94.786 62.489 272.99 1 85.29 ? C04 9LF 502 A 1 HETATM 5 C C05 9LF . . . C 3 94.018 63.27 273.818 1 87.31 ? C05 9LF 502 A 1 HETATM 6 O O06 9LF . . . C 3 92.593 63.351 273.734 1 92.96 ? O06 9LF 502 A 1 HETATM 7 C C07 9LF . . . C 3 92.03 64.127 272.643 1 106.4 ? C07 9LF 502 A 1 HETATM 8 C C08 9LF . . . C 3 90.574 63.76 272.483 1 107.43 ? C08 9LF 502 A 1 HETATM 9 O O09 9LF . . . C 3 92.099 65.574 272.977 1 107.3 ? O09 9LF 502 A 1 HETATM 10 C C10 9LF . . . C 3 93.392 66.03 272.257 1 105.01 ? C10 9LF 502 A 1 HETATM 11 C C11 9LF . . . C 3 94.175 67.166 272.463 1 108.61 ? C11 9LF 502 A 1 HETATM 12 C C12 9LF . . . C 3 93.733 68.124 273.531 1 95.46 ? C12 9LF 502 A 1 HETATM 13 C C13 9LF . . . C 3 95.315 67.393 271.712 1 110.38 ? C13 9LF 502 A 1 HETATM 14 O O14 9LF . . . C 3 96.144 68.53 271.873 1 109.61 ? O14 9LF 502 A 1 HETATM 15 C C15 9LF . . . C 3 95.653 66.411 270.722 1 110.52 ? C15 9LF 502 A 1 HETATM 16 C C16 9LF . . . C 3 96.809 66.71 269.996 1 112.81 ? C16 9LF 502 A 1 HETATM 17 O O17 9LF . . . C 3 97.554 67.889 270.249 1 105.5 ? O17 9LF 502 A 1 HETATM 18 C C18 9LF . . . C 3 97.235 65.816 269.018 1 113.87 ? C18 9LF 502 A 1 HETATM 19 C C19 9LF . . . C 3 96.502 64.626 268.752 1 112.21 ? C19 9LF 502 A 1 HETATM 20 C C20 9LF . . . C 3 95.326 64.315 269.474 1 108.11 ? C20 9LF 502 A 1 HETATM 21 O O21 9LF . . . C 3 94.574 63.124 269.178 1 102.72 ? O21 9LF 502 A 1 HETATM 22 C C22 9LF . . . C 3 93.515 63.275 268.178 1 98.23 ? C22 9LF 502 A 1 HETATM 23 O O23 9LF . . . C 3 92.593 63.996 268.347 1 89.88 ? O23 9LF 502 A 1 HETATM 24 C C24 9LF . . . C 3 93.465 62.529 266.818 1 94.57 ? C24 9LF 502 A 1 HETATM 25 O O25 9LF . . . C 3 92.781 63.35 265.892 1 78.65 ? O25 9LF 502 A 1 HETATM 26 C C26 9LF . . . C 3 94.9 65.249 270.5 1 110.69 ? C26 9LF 502 A 1 HETATM 27 C C27 9LF . . . C 3 93.716 65.049 271.269 1 108.9 ? C27 9LF 502 A 1 HETATM 28 C C28 9LF . . . C 3 92.72 64.029 271.41 1 111.93 ? C28 9LF 502 A 1 HETATM 29 O O29 9LF . . . C 3 92.497 63.13 270.676 1 112.34 ? O29 9LF 502 A 1 HETATM 30 N N30 9LF . . . C 3 98.464 66.238 268.342 1 107.43 ? N30 9LF 502 A 1 HETATM 31 C C31 9LF . . . C 3 99.806 65.75 268.705 1 101.68 ? C31 9LF 502 A 1 HETATM 32 O O32 9LF . . . C 3 100.719 66.182 268.091 1 98.85 ? O32 9LF 502 A 1 HETATM 33 C C33 9LF . . . C 3 100.094 64.654 269.78 1 97.26 ? C33 9LF 502 A 1 HETATM 34 C C34 9LF . . . C 3 101.501 64.079 269.728 1 96.5 ? C34 9LF 502 A 1 HETATM 35 C C35 9LF . . . C 3 99.21 64.209 270.707 1 93.62 ? C35 9LF 502 A 1 HETATM 36 C C36 9LF . . . C 3 99.637 63.057 271.698 1 93.86 ? C36 9LF 502 A 1 HETATM 37 C C37 9LF . . . C 3 100.893 62.929 272.217 1 97.2 ? C37 9LF 502 A 1 HETATM 38 C C38 9LF . . . C 3 101.397 61.794 273.132 1 93.87 ? C38 9LF 502 A 1 HETATM 39 C C39 9LF . . . C 3 100.938 60.438 272.614 1 89.33 ? C39 9LF 502 A 1 HETATM 40 C C40 9LF . . . C 3 101.032 62.046 274.616 1 91.46 ? C40 9LF 502 A 1 HETATM 41 O O41 9LF . . . C 3 102.047 62.816 275.126 1 90.73 ? O41 9LF 502 A 1 HETATM 42 C C42 9LF . . . C 3 100.911 60.772 275.457 1 94.18 ? C42 9LF 502 A 1 HETATM 43 C C43 9LF . . . C 3 100.96 61.134 276.933 1 99.51 ? C43 9LF 502 A 1 HETATM 44 C C44 9LF . . . C 3 99.567 60.082 275.113 1 100.93 ? C44 9LF 502 A 1 HETATM 45 O O45 9LF . . . C 3 99.527 58.785 275.642 1 101.22 ? O45 9LF 502 A 1 HETATM 46 C C46 9LF . . . C 3 98.3 60.873 275.54 1 99.07 ? C46 9LF 502 A 1 HETATM 47 C C47 9LF . . . C 3 98.09 60.87 277.066 1 101.45 ? C47 9LF 502 A 1 HETATM 48 C C48 9LF . . . C 3 98.14 62.303 274.909 1 97.63 ? C48 9LF 502 A 1 HETATM 49 O O49 9LF . . . C 3 98.76 63.392 275.587 1 94.79 ? O49 9LF 502 A 1 HETATM 50 C C50 9LF . . . C 3 98.401 64.747 275.261 1 86.87 ? C50 9LF 502 A 1 HETATM 51 C C51 9LF . . . C 3 97.621 65.57 276.296 1 81.11 ? C51 9LF 502 A 1 HETATM 52 O O52 9LF . . . C 3 98.717 65.253 274.22 1 78.63 ? O52 9LF 502 A 1 HETATM 53 C C53 9LF . . . C 3 96.64 62.611 274.703 1 93.09 ? C53 9LF 502 A 1 HETATM 54 C C54 9LF . . . C 3 95.698 61.795 275.611 1 88.98 ? C54 9LF 502 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 54 #