data_1D58 # _model_server_result.job_id n-PwDkPvvS325txN3w71Rg _model_server_result.datetime_utc '2025-03-01 10:29:25' _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 1d58 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 1D58 # _exptl.entry_id 1D58 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 544.527 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "4'-EPIDOXORUBICIN" _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 1D58 _cell.length_a 28.014 _cell.length_b 28.014 _cell.length_c 52.947 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D58 _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_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 28.014 28.014 26.4735 # _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_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A O4 DT 1 A DT 1 1_555 A N6 DA 6 A DA 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 DG 2 A DG 2 1_555 A N3 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N2 DG 2 A DG 2 1_555 A O2 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O6 DG 2 A DG 2 1_555 A N4 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DA 3 A DA 3 1_555 A N3 DT 4 A DT 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N6 DA 3 A DA 3 1_555 A O4 DT 4 A DT 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N3 DT 4 A DT 4 1_555 A N1 DA 3 A DA 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O4 DT 4 A DT 4 1_555 A N6 DA 3 A DA 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N3 DC 5 A DC 5 1_555 A N1 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N4 DC 5 A DC 5 1_555 A O6 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O2 DC 5 A DC 5 1_555 A N2 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DA 6 A DA 6 1_555 A N3 DT 1 A DT 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 DA 6 A DA 6 1_555 A O4 DT 1 A DT 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C27 H30 N O11 1' _chem_comp.formula_weight 544.527 _chem_comp.id DM6 _chem_comp.mon_nstd_flag . _chem_comp.name "4'-EPIDOXORUBICIN" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "4'-EPIADRIAMYCIN" # 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 DM6 doub 113 n y C1 C15 DM6 sing 114 n y C1 H1 DM6 sing 115 n n C2 C3 DM6 sing 116 n y C2 H2 DM6 sing 117 n n C3 C4 DM6 doub 118 n y C3 H3 DM6 sing 119 n n C4 C16 DM6 sing 120 n y C4 O4 DM6 sing 121 n n C5 C16 DM6 sing 122 n n C5 C17 DM6 sing 123 n n C5 O5 DM6 doub 124 n n C6 C17 DM6 doub 125 n y C6 C20 DM6 sing 126 n y C6 O6 DM6 sing 127 n n C7 C8 DM6 sing 128 n n C7 C20 DM6 sing 129 n n C7 O7 DM6 sing 130 n n C7 H7 DM6 sing 131 n n C8 C9 DM6 sing 132 n n C8 H81 DM6 sing 133 n n C8 H82 DM6 sing 134 n n C9 C10 DM6 sing 135 n n C9 C13 DM6 sing 136 n n C9 O9 DM6 sing 137 n n C10 C19 DM6 sing 138 n n C10 H101 DM6 sing 139 n n C10 H102 DM6 sing 140 n n C11 C18 DM6 doub 141 n y C11 C19 DM6 sing 142 n y C11 O11 DM6 sing 143 n n C12 C15 DM6 sing 144 n n C12 C18 DM6 sing 145 n n C12 O12 DM6 doub 146 n n C13 C14 DM6 sing 147 n n C13 O13 DM6 doub 148 n n C14 O14 DM6 sing 149 n n C14 H141 DM6 sing 150 n n C14 H142 DM6 sing 151 n n C15 C16 DM6 doub 152 n y C17 C18 DM6 sing 153 n y C19 C20 DM6 doub 154 n y C21 O4 DM6 sing 155 n n C21 H211 DM6 sing 156 n n C21 H212 DM6 sing 157 n n C21 H213 DM6 sing 158 n n O6 HO6 DM6 sing 159 n n O7 C1' DM6 sing 160 n n O9 HO9 DM6 sing 161 n n O11 HO11 DM6 sing 162 n n O14 HO14 DM6 sing 163 n n C1' C2' DM6 sing 164 n n C1' O5' DM6 sing 165 n n C1' H1' DM6 sing 166 n n C2' C3' DM6 sing 167 n n C2' "H2'1" DM6 sing 168 n n C2' "H2'2" DM6 sing 169 n n C3' C4' DM6 sing 170 n n C3' N3' DM6 sing 171 n n C3' H3' DM6 sing 172 n n C4' C5' DM6 sing 173 n n C4' O4' DM6 sing 174 n n C4' H4' DM6 sing 175 n n C5' C6' DM6 sing 176 n n C5' O5' DM6 sing 177 n n C5' H5' DM6 sing 178 n n C6' "H6'1" DM6 sing 179 n n C6' "H6'2" DM6 sing 180 n n C6' "H6'3" DM6 sing 181 n n O4' "HO'4" DM6 sing 182 n n N3' "HN'1" DM6 sing 183 n n N3' "HN'2" DM6 sing 184 n n N3' "HN'3" DM6 sing 185 n n # _atom_sites.entry_id 1D58 _atom_sites.fract_transf_matrix[1][1] 0.035696 _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] 0.035696 _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] 0.018887 _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 DM6 A 1 7 7 DM6 DM6 . 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 . # 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 DM6 . . . B 2 15.581 18.38 5.168 1 8.62 ? C1 DM6 7 A 1 HETATM 2 C C2 DM6 . . . B 2 16.657 19.089 5.189 1 9.93 ? C2 DM6 7 A 1 HETATM 3 C C3 DM6 . . . B 2 17.82 18.419 5.078 1 10.26 ? C3 DM6 7 A 1 HETATM 4 C C4 DM6 . . . B 2 17.878 17.153 4.961 1 8.03 ? C4 DM6 7 A 1 HETATM 5 C C5 DM6 . . . B 2 16.789 14.85 4.834 1 6.18 ? C5 DM6 7 A 1 HETATM 6 C C6 DM6 . . . B 2 15.509 12.783 4.771 1 7.43 ? C6 DM6 7 A 1 HETATM 7 C C7 DM6 . . . B 2 14.24 10.595 4.797 1 9.59 ? C7 DM6 7 A 1 HETATM 8 C C8 DM6 . . . B 2 12.861 10.035 4.596 1 9.11 ? C8 DM6 7 A 1 HETATM 9 C C9 DM6 . . . B 2 11.853 10.724 5.385 1 10.41 ? C9 DM6 7 A 1 HETATM 10 C C10 DM6 . . . B 2 11.788 12.046 4.781 1 9.04 ? C10 DM6 7 A 1 HETATM 11 C C11 DM6 . . . B 2 13.127 14.153 4.924 1 8.04 ? C11 DM6 7 A 1 HETATM 12 C C12 DM6 . . . B 2 14.256 16.271 5.025 1 6.71 ? C12 DM6 7 A 1 HETATM 13 C C13 DM6 . . . B 2 10.567 9.953 4.876 1 11.8 ? C13 DM6 7 A 1 HETATM 14 C C14 DM6 . . . B 2 10.141 8.653 5.422 1 13.13 ? C14 DM6 7 A 1 HETATM 15 C C15 DM6 . . . B 2 15.531 16.988 5.046 1 6.62 ? C15 DM6 7 A 1 HETATM 16 C C16 DM6 . . . B 2 16.752 16.369 4.94 1 8.14 ? C16 DM6 7 A 1 HETATM 17 C C17 DM6 . . . B 2 15.478 14.181 4.892 1 6.89 ? C17 DM6 7 A 1 HETATM 18 C C18 DM6 . . . B 2 14.273 14.884 4.903 1 6.19 ? C18 DM6 7 A 1 HETATM 19 C C19 DM6 . . . B 2 13.032 12.76 4.829 1 8.9 ? C19 DM6 7 A 1 HETATM 20 C C20 DM6 . . . B 2 14.214 12.105 4.755 1 7.24 ? C20 DM6 7 A 1 HETATM 21 C C21 DM6 . . . B 2 20.394 17.36 4.802 1 10.43 ? C21 DM6 7 A 1 HETATM 22 O O4 DM6 . . . B 2 19.114 16.576 4.829 1 9.67 ? O4 DM6 7 A 1 HETATM 23 O O5 DM6 . . . B 2 17.901 14.189 4.564 1 9.9 ? O5 DM6 7 A 1 HETATM 24 O O6 DM6 . . . B 2 16.657 12.099 4.691 1 9.11 ? O6 DM6 7 A 1 HETATM 25 O O7 DM6 . . . B 2 14.808 10.043 5.951 1 11.86 ? O7 DM6 7 A 1 HETATM 26 O O9 DM6 . . . B 2 11.979 10.648 6.724 1 7.9 ? O9 DM6 7 A 1 HETATM 27 O O11 DM6 . . . B 2 11.97 14.943 4.871 1 9.44 ? O11 DM6 7 A 1 HETATM 28 O O12 DM6 . . . B 2 13.228 16.937 4.972 1 11.57 ? O12 DM6 7 A 1 HETATM 29 O O13 DM6 . . . B 2 9.883 10.175 3.828 1 14.72 ? O13 DM6 7 A 1 HETATM 30 O O14 DM6 . . . B 2 8.847 8.474 5.798 1 19.81 ? O14 DM6 7 A 1 HETATM 31 C C1' DM6 . . . B 2 15.733 8.903 6.295 1 13.18 ? C1' DM6 7 A 1 HETATM 32 C C2' DM6 . . . B 2 16.797 9.46 7.238 1 14.34 ? C2' DM6 7 A 1 HETATM 33 C C3' DM6 . . . B 2 16.341 9.463 8.651 1 16.36 ? C3' DM6 7 A 1 HETATM 34 C C4' DM6 . . . B 2 15.576 8.261 9.128 1 16.16 ? C4' DM6 7 A 1 HETATM 35 C C5' DM6 . . . B 2 14.503 8.146 8.127 1 17.45 ? C5' DM6 7 A 1 HETATM 36 C C6' DM6 . . . B 2 13.483 7.298 8.752 1 15.28 ? C6' DM6 7 A 1 HETATM 37 O O4' DM6 . . . B 2 15.167 8.466 10.404 1 19.93 ? O4' DM6 7 A 1 HETATM 38 O O5' DM6 . . . B 2 14.861 7.942 6.767 1 16.46 ? O5' DM6 7 A 1 HETATM 39 N N3' DM6 . . . B 2 17.447 9.939 9.589 1 14.01 ? N3' DM6 7 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #