data_2YGA # _model_server_result.job_id UCqgEs1LkqeePahncANoww _model_server_result.datetime_utc '2024-10-19 02:31:58' _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 2yga # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1215}' # _entry.id 2YGA # _exptl.entry_id 2YGA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 560.636 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GELDANAMYCIN _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 2YGA _cell.length_a 74.34 _cell.length_b 74.34 _cell.length_c 110.07 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YGA _symmetry.cell_setting ? _symmetry.Int_Tables_number 95 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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 'C29 H40 N2 O9' _chem_comp.formula_weight 560.636 _chem_comp.id GDM _chem_comp.mon_nstd_flag . _chem_comp.name GELDANAMYCIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O1 C1 GDM doub 70 n n O2 C6 GDM sing 71 n n O2 C23 GDM sing 72 n n O3 C7 GDM sing 73 n n O3 C24 GDM sing 74 n n O4 C24 GDM doub 75 n n O5 C11 GDM sing 76 n n O5 HO5 GDM sing 77 n n O6 C12 GDM sing 78 n n O6 C27 GDM sing 79 n n O7 C17 GDM sing 80 n n O7 C29 GDM sing 81 n n O8 C18 GDM doub 82 n n O9 C21 GDM doub 83 n n N1 C1 GDM sing 84 n n N1 C20 GDM sing 85 n n N1 HN1 GDM sing 86 n n N2 C24 GDM sing 87 n n N2 HN21 GDM sing 88 n n N2 HN22 GDM sing 89 n n C1 C2 GDM sing 90 n n C2 C3 GDM doub 91 e n C2 C22 GDM sing 92 n n C3 C4 GDM sing 93 n n C3 H3 GDM sing 94 n n C4 C5 GDM doub 95 z n C4 H4 GDM sing 96 n n C5 C6 GDM sing 97 n n C5 H5 GDM sing 98 n n C6 C7 GDM sing 99 n n C6 H6 GDM sing 100 n n C7 C8 GDM sing 101 n n C7 H7 GDM sing 102 n n C8 C9 GDM doub 103 e n C8 C25 GDM sing 104 n n C9 C10 GDM sing 105 n n C9 H9 GDM sing 106 n n C10 C11 GDM sing 107 n n C10 C26 GDM sing 108 n n C10 H10 GDM sing 109 n n C11 C12 GDM sing 110 n n C11 H11 GDM sing 111 n n C12 C13 GDM sing 112 n n C12 H12 GDM sing 113 n n C13 C14 GDM sing 114 n n C13 H131 GDM sing 115 n n C13 H132 GDM sing 116 n n C14 C15 GDM sing 117 n n C14 C28 GDM sing 118 n n C14 H14 GDM sing 119 n n C15 C16 GDM sing 120 n n C15 H151 GDM sing 121 n n C15 H152 GDM sing 122 n n C16 C17 GDM doub 123 n n C16 C21 GDM sing 124 n n C17 C18 GDM sing 125 n n C18 C19 GDM sing 126 n n C19 C20 GDM doub 127 n n C19 H19 GDM sing 128 n n C20 C21 GDM sing 129 n n C22 H221 GDM sing 130 n n C22 H222 GDM sing 131 n n C22 H223 GDM sing 132 n n C23 H231 GDM sing 133 n n C23 H232 GDM sing 134 n n C23 H233 GDM sing 135 n n C25 H251 GDM sing 136 n n C25 H252 GDM sing 137 n n C25 H253 GDM sing 138 n n C26 H261 GDM sing 139 n n C26 H262 GDM sing 140 n n C26 H263 GDM sing 141 n n C27 H271 GDM sing 142 n n C27 H272 GDM sing 143 n n C27 H273 GDM sing 144 n n C28 H281 GDM sing 145 n n C28 H282 GDM sing 146 n n C28 H283 GDM sing 147 n n C29 H291 GDM sing 148 n n C29 H292 GDM sing 149 n n C29 H293 GDM sing 150 n n # _atom_sites.entry_id 2YGA _atom_sites.fract_transf_matrix[1][1] 0.013452 _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] 0.013452 _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] 0.009085 _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 GDM A 1 1215 1215 GDM GDM . C 3 HOH A 1 2001 2001 HOH HOH . C 3 HOH A 2 2002 2002 HOH HOH . C 3 HOH A 3 2003 2003 HOH HOH . C 3 HOH A 4 2004 2004 HOH HOH . C 3 HOH A 5 2005 2005 HOH HOH . C 3 HOH A 6 2006 2006 HOH HOH . C 3 HOH A 7 2007 2007 HOH HOH . C 3 HOH A 8 2008 2008 HOH HOH . C 3 HOH A 9 2009 2009 HOH HOH . C 3 HOH A 10 2010 2010 HOH HOH . C 3 HOH A 11 2011 2011 HOH HOH . C 3 HOH A 12 2012 2012 HOH HOH . C 3 HOH A 13 2013 2013 HOH HOH . C 3 HOH A 14 2014 2014 HOH HOH . C 3 HOH A 15 2015 2015 HOH HOH . C 3 HOH A 16 2016 2016 HOH HOH . C 3 HOH A 17 2017 2017 HOH HOH . C 3 HOH A 18 2018 2018 HOH HOH . C 3 HOH A 19 2019 2019 HOH HOH . C 3 HOH A 20 2020 2020 HOH HOH . C 3 HOH A 21 2021 2021 HOH HOH . C 3 HOH A 22 2022 2022 HOH HOH . C 3 HOH A 23 2023 2023 HOH HOH . C 3 HOH A 24 2024 2024 HOH HOH . C 3 HOH A 25 2025 2025 HOH HOH . C 3 HOH A 26 2026 2026 HOH HOH . C 3 HOH A 27 2027 2027 HOH HOH . C 3 HOH A 28 2028 2028 HOH HOH . C 3 HOH A 29 2029 2029 HOH HOH . C 3 HOH A 30 2030 2030 HOH HOH . C 3 HOH A 31 2031 2031 HOH HOH . C 3 HOH A 32 2032 2032 HOH HOH . C 3 HOH A 33 2033 2033 HOH HOH . C 3 HOH A 34 2034 2034 HOH HOH . C 3 HOH A 35 2035 2035 HOH HOH . C 3 HOH A 36 2036 2036 HOH HOH . C 3 HOH A 37 2037 2037 HOH HOH . C 3 HOH A 38 2038 2038 HOH HOH . C 3 HOH A 39 2039 2039 HOH HOH . C 3 HOH A 40 2040 2040 HOH HOH . C 3 HOH A 41 2041 2041 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 O1 GDM . . . B 2 25.572 -32.948 0.285 1 53.62 ? O1 GDM 1215 A 1 HETATM 2 O O2 GDM . . . B 2 19.925 -33.899 -1.617 1 54.84 ? O2 GDM 1215 A 1 HETATM 3 O O3 GDM . . . B 2 18.978 -32.81 -3.818 1 43.83 ? O3 GDM 1215 A 1 HETATM 4 O O4 GDM . . . B 2 17.068 -31.751 -4.457 1 45.6 ? O4 GDM 1215 A 1 HETATM 5 O O5 GDM . . . B 2 22.756 -36.297 -9.032 1 52.25 ? O5 GDM 1215 A 1 HETATM 6 O O6 GDM . . . B 2 22.827 -38.419 -6.819 1 57.04 ? O6 GDM 1215 A 1 HETATM 7 O O7 GDM . . . B 2 25.397 -33.289 -7.662 1 56 ? O7 GDM 1215 A 1 HETATM 8 O O8 GDM . . . B 2 24.235 -31.106 -6.382 1 54.58 ? O8 GDM 1215 A 1 HETATM 9 O O9 GDM . . . B 2 26.819 -34.572 -3.174 1 53.63 ? O9 GDM 1215 A 1 HETATM 10 N N1 GDM . . . B 2 25.621 -32.255 -1.883 1 46.94 ? N1 GDM 1215 A 1 HETATM 11 N N2 GDM . . . B 2 17.466 -33.725 -5.576 1 27.16 ? N2 GDM 1215 A 1 HETATM 12 C C1 GDM . . . B 2 25.305 -33.217 -0.847 1 45.31 ? C1 GDM 1215 A 1 HETATM 13 C C2 GDM . . . B 2 24.637 -34.544 -1.214 1 49.13 ? C2 GDM 1215 A 1 HETATM 14 C C3 GDM . . . B 2 23.351 -34.437 -1.917 1 42.71 ? C3 GDM 1215 A 1 HETATM 15 C C4 GDM . . . B 2 22.484 -35.687 -2.098 1 48.02 ? C4 GDM 1215 A 1 HETATM 16 C C5 GDM . . . B 2 21.248 -35.533 -2.85 1 45.76 ? C5 GDM 1215 A 1 HETATM 17 C C6 GDM . . . B 2 20.633 -34.134 -2.845 1 52.34 ? C6 GDM 1215 A 1 HETATM 18 C C7 GDM . . . B 2 19.661 -34.038 -4.017 1 47.68 ? C7 GDM 1215 A 1 HETATM 19 C C8 GDM . . . B 2 20.438 -34.008 -5.337 1 36.41 ? C8 GDM 1215 A 1 HETATM 20 C C9 GDM . . . B 2 20.473 -35.196 -6.194 1 41.83 ? C9 GDM 1215 A 1 HETATM 21 C C10 GDM . . . B 2 21.225 -35.151 -7.539 1 53.25 ? C10 GDM 1215 A 1 HETATM 22 C C11 GDM . . . B 2 21.884 -36.496 -7.91 1 52.15 ? C11 GDM 1215 A 1 HETATM 23 C C12 GDM . . . B 2 22.759 -36.983 -6.757 1 50.05 ? C12 GDM 1215 A 1 HETATM 24 C C13 GDM . . . B 2 24.137 -36.336 -6.974 1 48.08 ? C13 GDM 1215 A 1 HETATM 25 C C14 GDM . . . B 2 24.836 -36.1 -5.625 1 53.99 ? C14 GDM 1215 A 1 HETATM 26 C C15 GDM . . . B 2 26.247 -35.549 -5.865 1 45.99 ? C15 GDM 1215 A 1 HETATM 27 C C16 GDM . . . B 2 26.192 -34.076 -5.405 1 49.2 ? C16 GDM 1215 A 1 HETATM 28 C C17 GDM . . . B 2 25.477 -33.112 -6.254 1 45.81 ? C17 GDM 1215 A 1 HETATM 29 C C18 GDM . . . B 2 24.813 -31.872 -5.669 1 48.92 ? C18 GDM 1215 A 1 HETATM 30 C C19 GDM . . . B 2 24.871 -31.624 -4.17 1 50.64 ? C19 GDM 1215 A 1 HETATM 31 C C20 GDM . . . B 2 25.578 -32.561 -3.309 1 41.96 ? C20 GDM 1215 A 1 HETATM 32 C C21 GDM . . . B 2 26.258 -33.801 -3.895 1 45.57 ? C21 GDM 1215 A 1 HETATM 33 C C22 GDM . . . B 2 24.956 -35.796 -0.366 1 39.93 ? C22 GDM 1215 A 1 HETATM 34 C C23 GDM . . . B 2 18.751 -34.716 -1.489 1 42.27 ? C23 GDM 1215 A 1 HETATM 35 C C24 GDM . . . B 2 17.794 -32.703 -4.596 1 35.22 ? C24 GDM 1215 A 1 HETATM 36 C C25 GDM . . . B 2 21.183 -32.735 -5.76 1 39.69 ? C25 GDM 1215 A 1 HETATM 37 C C26 GDM . . . B 2 20.161 -34.87 -8.616 1 53.37 ? C26 GDM 1215 A 1 HETATM 38 C C27 GDM . . . B 2 23.67 -38.824 -7.901 1 65.78 ? C27 GDM 1215 A 1 HETATM 39 C C28 GDM . . . B 2 24.937 -37.395 -4.811 1 61.44 ? C28 GDM 1215 A 1 HETATM 40 C C29 GDM . . . B 2 26.484 -32.56 -8.244 1 50.63 ? C29 GDM 1215 A 1 HETATM 41 H HO5 GDM . . . B 2 22.22 -36.3 -9.876 1 52.25 ? HO5 GDM 1215 A 1 HETATM 42 H HN1 GDM . . . B 2 25.883 -31.331 -1.606 1 46.94 ? HN1 GDM 1215 A 1 HETATM 43 H HN21 GDM . . . B 2 16.632 -33.645 -6.121 1 27.16 ? HN21 GDM 1215 A 1 HETATM 44 H HN22 GDM . . . B 2 18.075 -34.508 -5.705 1 27.16 ? HN22 GDM 1215 A 1 HETATM 45 H H3 GDM . . . B 2 23.013 -33.467 -2.31 1 42.71 ? H3 GDM 1215 A 1 HETATM 46 H H4 GDM . . . B 2 22.783 -36.659 -1.678 1 48.02 ? H4 GDM 1215 A 1 HETATM 47 H H5 GDM . . . B 2 20.785 -36.372 -3.389 1 45.76 ? H5 GDM 1215 A 1 HETATM 48 H H6 GDM . . . B 2 21.429 -33.38 -2.936 1 52.34 ? H6 GDM 1215 A 1 HETATM 49 H H7 GDM . . . B 2 18.971 -34.893 -4.066 1 47.68 ? H7 GDM 1215 A 1 HETATM 50 H H9 GDM . . . B 2 19.964 -36.118 -5.878 1 41.83 ? H9 GDM 1215 A 1 HETATM 51 H H10 GDM . . . B 2 22.019 -34.393 -7.468 1 53.25 ? H10 GDM 1215 A 1 HETATM 52 H H11 GDM . . . B 2 21.091 -37.224 -8.135 1 52.15 ? H11 GDM 1215 A 1 HETATM 53 H H12 GDM . . . B 2 22.368 -36.71 -5.766 1 50.05 ? H12 GDM 1215 A 1 HETATM 54 H H131 GDM . . . B 2 24.021 -35.381 -7.507 1 48.08 ? H131 GDM 1215 A 1 HETATM 55 H H132 GDM . . . B 2 24.759 -36.985 -7.608 1 48.08 ? H132 GDM 1215 A 1 HETATM 56 H H14 GDM . . . B 2 24.234 -35.376 -5.056 1 53.99 ? H14 GDM 1215 A 1 HETATM 57 H H151 GDM . . . B 2 26.527 -35.623 -6.926 1 45.99 ? H151 GDM 1215 A 1 HETATM 58 H H152 GDM . . . B 2 26.997 -36.116 -5.294 1 45.99 ? H152 GDM 1215 A 1 HETATM 59 H H19 GDM . . . B 2 24.38 -30.74 -3.738 1 50.64 ? H19 GDM 1215 A 1 HETATM 60 H H221 GDM . . . B 2 24.208 -35.898 0.434 1 39.93 ? H221 GDM 1215 A 1 HETATM 61 H H222 GDM . . . B 2 24.93 -36.69 -1.007 1 39.93 ? H222 GDM 1215 A 1 HETATM 62 H H223 GDM . . . B 2 25.957 -35.693 0.079 1 39.93 ? H223 GDM 1215 A 1 HETATM 63 H H231 GDM . . . B 2 18.063 -34.503 -2.32 1 42.27 ? H231 GDM 1215 A 1 HETATM 64 H H232 GDM . . . B 2 19.038 -35.778 -1.514 1 42.27 ? H232 GDM 1215 A 1 HETATM 65 H H233 GDM . . . B 2 18.252 -34.494 -0.534 1 42.27 ? H233 GDM 1215 A 1 HETATM 66 H H251 GDM . . . B 2 22.256 -32.955 -5.865 1 39.69 ? H251 GDM 1215 A 1 HETATM 67 H H252 GDM . . . B 2 20.786 -32.38 -6.722 1 39.69 ? H252 GDM 1215 A 1 HETATM 68 H H253 GDM . . . B 2 21.042 -31.956 -4.996 1 39.69 ? H253 GDM 1215 A 1 HETATM 69 H H261 GDM . . . B 2 20.644 -34.811 -9.603 1 53.37 ? H261 GDM 1215 A 1 HETATM 70 H H262 GDM . . . B 2 19.419 -35.682 -8.62 1 53.37 ? H262 GDM 1215 A 1 HETATM 71 H H263 GDM . . . B 2 19.659 -33.916 -8.396 1 53.37 ? H263 GDM 1215 A 1 HETATM 72 H H271 GDM . . . B 2 23.262 -38.441 -8.848 1 65.78 ? H271 GDM 1215 A 1 HETATM 73 H H272 GDM . . . B 2 24.682 -38.421 -7.749 1 65.78 ? H272 GDM 1215 A 1 HETATM 74 H H273 GDM . . . B 2 23.715 -39.922 -7.94 1 65.78 ? H273 GDM 1215 A 1 HETATM 75 H H281 GDM . . . B 2 25.533 -38.133 -5.368 1 61.44 ? H281 GDM 1215 A 1 HETATM 76 H H282 GDM . . . B 2 25.422 -37.185 -3.846 1 61.44 ? H282 GDM 1215 A 1 HETATM 77 H H283 GDM . . . B 2 23.929 -37.797 -4.634 1 61.44 ? H283 GDM 1215 A 1 HETATM 78 H H291 GDM . . . B 2 26.394 -31.495 -7.983 1 50.63 ? H291 GDM 1215 A 1 HETATM 79 H H292 GDM . . . B 2 27.437 -32.952 -7.859 1 50.63 ? H292 GDM 1215 A 1 HETATM 80 H H293 GDM . . . B 2 26.457 -32.672 -9.338 1 50.63 ? H293 GDM 1215 A 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 80 #