data_1D67 # _model_server_result.job_id 0UBacWy5QsthivZ2rwU9lA _model_server_result.datetime_utc '2024-10-15 08:25:40' _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 1d67 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 1D67 # _exptl.entry_id 1D67 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 497.494 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description IDARUBICIN _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 1D67 _cell.length_a 28.19 _cell.length_b 28.19 _cell.length_c 52.77 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D67 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 26.385 # _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 hydrog WATSON-CRICK hydrog1 A N3 DT 1 A DT 1 1_555 A N1 DA 6 A DA 6 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A O4 DT 1 A DT 1 1_555 A N6 DA 6 A DA 6 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 DG 2 A DG 2 1_555 A N3 DC 5 A DC 5 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N2 DG 2 A DG 2 1_555 A O2 DC 5 A DC 5 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O6 DG 2 A DG 2 1_555 A N4 DC 5 A DC 5 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DA 3 A DA 3 1_555 A N3 DT 4 A DT 4 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N6 DA 3 A DA 3 1_555 A O4 DT 4 A DT 4 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N3 DT 4 A DT 4 1_555 A N1 DA 3 A DA 3 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O4 DT 4 A DT 4 1_555 A N6 DA 3 A DA 3 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N3 DC 5 A DC 5 1_555 A N1 DG 2 A DG 2 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N4 DC 5 A DC 5 1_555 A O6 DG 2 A DG 2 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O2 DC 5 A DC 5 1_555 A N2 DG 2 A DG 2 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DA 6 A DA 6 1_555 A N3 DT 1 A DT 1 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 DA 6 A DA 6 1_555 A O4 DT 1 A DT 1 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C26 H27 N O9' _chem_comp.formula_weight 497.494 _chem_comp.id DM5 _chem_comp.mon_nstd_flag . _chem_comp.name IDARUBICIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 4-DEMETHOXY-DAUNORUBICIN # 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 DM5 doub 113 n y C1 C20 DM5 sing 114 n y C1 H1 DM5 sing 115 n n C2 C3 DM5 sing 116 n y C2 H2 DM5 sing 117 n n C3 C4 DM5 doub 118 n y C3 H3 DM5 sing 119 n n C4 C5 DM5 sing 120 n y C4 H4 DM5 sing 121 n n C5 C6 DM5 sing 122 n n C5 C20 DM5 doub 123 n y C6 O6 DM5 doub 124 n n C6 C7 DM5 sing 125 n n C7 C8 DM5 doub 126 n y C7 C18 DM5 sing 127 n y C8 O8 DM5 sing 128 n n C8 C9 DM5 sing 129 n y O8 HO8 DM5 sing 130 n n C9 C10 DM5 sing 131 n n C9 C16 DM5 doub 132 n y C10 O10 DM5 sing 133 n n C10 C11 DM5 sing 134 n n C10 H10 DM5 sing 135 n n O10 C1' DM5 sing 136 n n C11 C12 DM5 sing 137 n n C11 H111 DM5 sing 138 n n C11 H112 DM5 sing 139 n n C12 O12 DM5 sing 140 n n C12 C13 DM5 sing 141 n n C12 C15 DM5 sing 142 n n O12 HO12 DM5 sing 143 n n C13 O13 DM5 doub 144 n n C13 C14 DM5 sing 145 n n C14 H141 DM5 sing 146 n n C14 H142 DM5 sing 147 n n C14 H143 DM5 sing 148 n n C15 C16 DM5 sing 149 n n C15 H151 DM5 sing 150 n n C15 H152 DM5 sing 151 n n C16 C17 DM5 sing 152 n y C17 O17 DM5 sing 153 n n C17 C18 DM5 doub 154 n y O17 HO17 DM5 sing 155 n n C18 C19 DM5 sing 156 n n C19 O19 DM5 doub 157 n n C19 C20 DM5 sing 158 n n C1' C2' DM5 sing 159 n n C1' O5' DM5 sing 160 n n C1' H1' DM5 sing 161 n n C2' C3' DM5 sing 162 n n C2' "H2'1" DM5 sing 163 n n C2' "H2'2" DM5 sing 164 n n C3' N3' DM5 sing 165 n n C3' C4' DM5 sing 166 n n C3' H3' DM5 sing 167 n n N3' "HN'1" DM5 sing 168 n n N3' "HN'2" DM5 sing 169 n n C4' O4' DM5 sing 170 n n C4' C5' DM5 sing 171 n n C4' H4' DM5 sing 172 n n O4' HO4' DM5 sing 173 n n C5' O5' DM5 sing 174 n n C5' C6' DM5 sing 175 n n C5' H5' DM5 sing 176 n n C6' "H6'1" DM5 sing 177 n n C6' "H6'2" DM5 sing 178 n n C6' "H6'3" DM5 sing 179 n n # _atom_sites.entry_id 1D67 _atom_sites.fract_transf_matrix[1][1] 0.035474 _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] 0.035474 _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] 0.01895 _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 DM5 A 1 7 7 DM5 DM5 . C 3 HOH A 1 8 8 HOH HOH . C 3 HOH A 2 9 9 HOH HOH . C 3 HOH A 3 10 10 HOH HOH . C 3 HOH A 4 11 11 HOH HOH . C 3 HOH A 5 12 12 HOH HOH . C 3 HOH A 6 13 13 HOH HOH . C 3 HOH A 7 14 14 HOH HOH . C 3 HOH A 8 15 15 HOH HOH . C 3 HOH A 9 16 16 HOH HOH . C 3 HOH A 10 17 17 HOH HOH . C 3 HOH A 11 18 18 HOH HOH . C 3 HOH A 12 19 19 HOH HOH . C 3 HOH A 13 20 20 HOH HOH . C 3 HOH A 14 21 21 HOH HOH . C 3 HOH A 15 22 22 HOH HOH . C 3 HOH A 16 23 23 HOH HOH . C 3 HOH A 17 24 24 HOH HOH . C 3 HOH A 18 25 25 HOH HOH . C 3 HOH A 19 26 26 HOH HOH . C 3 HOH A 20 27 27 HOH HOH . C 3 HOH A 21 28 28 HOH HOH . C 3 HOH A 22 29 29 HOH HOH . C 3 HOH A 23 30 30 HOH HOH . C 3 HOH A 24 31 31 HOH HOH . C 3 HOH A 25 32 32 HOH HOH . C 3 HOH A 26 33 33 HOH HOH . C 3 HOH A 27 34 34 HOH HOH . C 3 HOH A 28 35 35 HOH HOH . C 3 HOH A 29 36 36 HOH HOH . C 3 HOH A 30 37 37 HOH HOH . C 3 HOH A 31 38 38 HOH HOH . C 3 HOH A 32 39 39 HOH HOH . C 3 HOH A 33 40 40 HOH HOH . C 3 HOH A 34 41 41 HOH HOH . C 3 HOH A 35 42 42 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 DM5 . . . B 2 -12.748 18.56 4.966 1 16.39 ? C1 DM5 7 A 1 HETATM 2 C C2 DM5 . . . B 2 -11.592 19.243 4.982 1 16.1 ? C2 DM5 7 A 1 HETATM 3 C C3 DM5 . . . B 2 -10.447 18.619 4.913 1 16.61 ? C3 DM5 7 A 1 HETATM 4 C C4 DM5 . . . B 2 -10.278 17.295 4.828 1 12.99 ? C4 DM5 7 A 1 HETATM 5 C C5 DM5 . . . B 2 -11.456 16.522 4.865 1 15.05 ? C5 DM5 7 A 1 HETATM 6 C C6 DM5 . . . B 2 -11.392 14.986 4.813 1 11.6 ? C6 DM5 7 A 1 HETATM 7 O O6 DM5 . . . B 2 -10.354 14.385 4.723 1 15.45 ? O6 DM5 7 A 1 HETATM 8 C C7 DM5 . . . B 2 -12.717 14.29 4.834 1 8.69 ? C7 DM5 7 A 1 HETATM 9 C C8 DM5 . . . B 2 -12.674 12.891 4.781 1 9.41 ? C8 DM5 7 A 1 HETATM 10 O O8 DM5 . . . B 2 -11.516 12.167 4.781 1 12.05 ? O8 DM5 7 A 1 HETATM 11 C C9 DM5 . . . B 2 -13.889 12.147 4.77 1 12.09 ? C9 DM5 7 A 1 HETATM 12 C C10 DM5 . . . B 2 -13.827 10.65 4.886 1 16.39 ? C10 DM5 7 A 1 HETATM 13 O O10 DM5 . . . B 2 -13.215 10.419 6.121 1 17.52 ? O10 DM5 7 A 1 HETATM 14 C C11 DM5 . . . B 2 -15.183 10.033 4.649 1 13.38 ? C11 DM5 7 A 1 HETATM 15 C C12 DM5 . . . B 2 -16.316 10.721 5.467 1 16.26 ? C12 DM5 7 A 1 HETATM 16 O O12 DM5 . . . B 2 -16.133 10.74 6.876 1 14.12 ? O12 DM5 7 A 1 HETATM 17 C C13 DM5 . . . B 2 -17.613 10.044 5.04 1 17.39 ? C13 DM5 7 A 1 HETATM 18 O O13 DM5 . . . B 2 -18.301 10.292 3.995 1 19.31 ? O13 DM5 7 A 1 HETATM 19 C C14 DM5 . . . B 2 -18.036 8.857 5.747 1 17.28 ? C14 DM5 7 A 1 HETATM 20 C C15 DM5 . . . B 2 -16.412 12.122 4.897 1 12.35 ? C15 DM5 7 A 1 HETATM 21 C C16 DM5 . . . B 2 -15.099 12.829 4.818 1 12.23 ? C16 DM5 7 A 1 HETATM 22 C C17 DM5 . . . B 2 -15.082 14.273 4.886 1 10.53 ? C17 DM5 7 A 1 HETATM 23 O O17 DM5 . . . B 2 -16.297 14.98 4.781 1 13.06 ? O17 DM5 7 A 1 HETATM 24 C C18 DM5 . . . B 2 -13.881 14.966 4.876 1 9.3 ? C18 DM5 7 A 1 HETATM 25 C C19 DM5 . . . B 2 -13.917 16.392 4.923 1 10.27 ? C19 DM5 7 A 1 HETATM 26 O O19 DM5 . . . B 2 -14.991 17.075 4.934 1 13.77 ? O19 DM5 7 A 1 HETATM 27 C C20 DM5 . . . B 2 -12.708 17.148 4.918 1 10.7 ? C20 DM5 7 A 1 HETATM 28 C C1' DM5 . . . B 2 -12.336 9.28 6.459 1 19.8 ? C1' DM5 7 A 1 HETATM 29 C C2' DM5 . . . B 2 -11.149 9.678 7.377 1 19.78 ? C2' DM5 7 A 1 HETATM 30 C C3' DM5 . . . B 2 -11.674 9.81 8.844 1 25.64 ? C3' DM5 7 A 1 HETATM 31 N N3' DM5 . . . B 2 -10.659 10.591 9.583 1 23.88 ? N3' DM5 7 A 1 HETATM 32 C C4' DM5 . . . B 2 -12.533 8.626 9.282 1 22.51 ? C4' DM5 7 A 1 HETATM 33 O O4' DM5 . . . B 2 -11.476 7.547 9.134 1 26.72 ? O4' DM5 7 A 1 HETATM 34 C C5' DM5 . . . B 2 -13.627 8.511 8.348 1 21.62 ? C5' DM5 7 A 1 HETATM 35 O O5' DM5 . . . B 2 -13.193 8.268 7.018 1 22.81 ? O5' DM5 7 A 1 HETATM 36 C C6' DM5 . . . B 2 -14.462 7.49 8.876 1 23.34 ? C6' DM5 7 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #