data_1DA9 # _model_server_result.job_id xxYBvHbw2rNQT2be5XeVRg _model_server_result.datetime_utc '2024-10-12 11:16:09' _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 1da9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 1DA9 # _exptl.entry_id 1DA9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 543.519 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description DOXORUBICIN _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 1DA9 _cell.length_a 28.01 _cell.length_b 28.01 _cell.length_c 52.99 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DA9 _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 26.495 # _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 DG 3 A DG 3 1_555 A N3 DC 4 A DC 4 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 DG 3 A DG 3 1_555 A O2 DC 4 A DC 4 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 DG 3 A DG 3 1_555 A N4 DC 4 A DC 4 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 DC 4 A DC 4 1_555 A N1 DG 3 A DG 3 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N4 DC 4 A DC 4 1_555 A O6 DG 3 A DG 3 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O2 DC 4 A DC 4 1_555 A N2 DG 3 A DG 3 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 DC 5 A DC 5 1_555 A N1 DG 2 A DG 2 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N4 DC 5 A DC 5 1_555 A O6 DG 2 A DG 2 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O2 DC 5 A DC 5 1_555 A N2 DG 2 A DG 2 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 DA 6 A DA 6 1_555 A N3 DT 1 A DT 1 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N6 DA 6 A DA 6 1_555 A O4 DT 1 A DT 1 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C27 H29 N O11' _chem_comp.formula_weight 543.519 _chem_comp.id DM2 _chem_comp.mon_nstd_flag . _chem_comp.name DOXORUBICIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ADRIAMYCIN # 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 DM2 doub 113 n y C1 C20 DM2 sing 114 n y C1 H1 DM2 sing 115 n n C2 C3 DM2 sing 116 n y C2 H2 DM2 sing 117 n n C3 C4 DM2 doub 118 n y C3 H3 DM2 sing 119 n n C4 O4 DM2 sing 120 n n C4 C5 DM2 sing 121 n y O4 C21 DM2 sing 122 n n C5 C6 DM2 sing 123 n n C5 C20 DM2 doub 124 n y C6 O6 DM2 doub 125 n n C6 C7 DM2 sing 126 n n C7 C8 DM2 doub 127 n y C7 C18 DM2 sing 128 n y C8 O8 DM2 sing 129 n n C8 C9 DM2 sing 130 n y O8 HO8 DM2 sing 131 n n C9 C10 DM2 sing 132 n n C9 C16 DM2 doub 133 n y C10 O10 DM2 sing 134 n n C10 C11 DM2 sing 135 n n C10 H10 DM2 sing 136 n n O10 C1' DM2 sing 137 n n C11 C12 DM2 sing 138 n n C11 H111 DM2 sing 139 n n C11 H112 DM2 sing 140 n n C12 O12 DM2 sing 141 n n C12 C13 DM2 sing 142 n n C12 C15 DM2 sing 143 n n O12 HO12 DM2 sing 144 n n C13 O13 DM2 doub 145 n n C13 C14 DM2 sing 146 n n C14 O14 DM2 sing 147 n n C14 H141 DM2 sing 148 n n C14 H142 DM2 sing 149 n n O14 HO14 DM2 sing 150 n n C15 C16 DM2 sing 151 n n C15 H151 DM2 sing 152 n n C15 H152 DM2 sing 153 n n C16 C17 DM2 sing 154 n y C17 O17 DM2 sing 155 n n C17 C18 DM2 doub 156 n y O17 HO17 DM2 sing 157 n n C18 C19 DM2 sing 158 n n C19 O19 DM2 doub 159 n n C19 C20 DM2 sing 160 n n C21 H211 DM2 sing 161 n n C21 H212 DM2 sing 162 n n C21 H213 DM2 sing 163 n n C1' C2' DM2 sing 164 n n C1' O5' DM2 sing 165 n n C1' H1' DM2 sing 166 n n C2' C3' DM2 sing 167 n n C2' "H2'1" DM2 sing 168 n n C2' "H2'2" DM2 sing 169 n n C3' N3' DM2 sing 170 n n C3' C4' DM2 sing 171 n n C3' H3' DM2 sing 172 n n N3' "HN'1" DM2 sing 173 n n N3' "HN'2" DM2 sing 174 n n C4' O4' DM2 sing 175 n n C4' C5' DM2 sing 176 n n C4' H4' DM2 sing 177 n n O4' HO4' DM2 sing 178 n n C5' O5' DM2 sing 179 n n C5' C6' DM2 sing 180 n n C5' H5' DM2 sing 181 n n C6' "H6'1" DM2 sing 182 n n C6' "H6'2" DM2 sing 183 n n C6' "H6'3" DM2 sing 184 n n # _atom_sites.entry_id 1DA9 _atom_sites.fract_transf_matrix[1][1] 0.035701 _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] 0.035701 _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] 0.018871 _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 DM2 A 1 7 7 DM2 DM2 . 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 . C 3 HOH A 36 43 43 HOH HOH . C 3 HOH A 37 44 44 HOH HOH . C 3 HOH A 38 45 45 HOH HOH . C 3 HOH A 39 46 46 HOH HOH . C 3 HOH A 40 47 47 HOH HOH . C 3 HOH A 41 48 48 HOH HOH . C 3 HOH A 42 49 49 HOH HOH . C 3 HOH A 43 50 50 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 DM2 . . . B 2 -12.358 18.75 5.31 1 2.93 ? C1 DM2 7 A 1 HETATM 2 C C2 DM2 . . . B 2 -11.204 19.523 5.325 1 8.87 ? C2 DM2 7 A 1 HETATM 3 C C3 DM2 . . . B 2 -9.986 19.005 5.167 1 15.3 ? C3 DM2 7 A 1 HETATM 4 C C4 DM2 . . . B 2 -9.809 17.621 4.992 1 9.22 ? C4 DM2 7 A 1 HETATM 5 O O4 DM2 . . . B 2 -8.613 16.96 4.88 1 9.2 ? O4 DM2 7 A 1 HETATM 6 C C5 DM2 . . . B 2 -10.98 16.77 4.981 1 3.2 ? C5 DM2 7 A 1 HETATM 7 C C6 DM2 . . . B 2 -10.885 15.305 4.827 1 6.82 ? C6 DM2 7 A 1 HETATM 8 O O6 DM2 . . . B 2 -9.789 14.75 4.631 1 13.73 ? O6 DM2 7 A 1 HETATM 9 C C7 DM2 . . . B 2 -12.134 14.557 4.838 1 5.93 ? C7 DM2 7 A 1 HETATM 10 C C8 DM2 . . . B 2 -12.095 13.182 4.69 1 7.52 ? C8 DM2 7 A 1 HETATM 11 O O8 DM2 . . . B 2 -10.921 12.476 4.668 1 15.03 ? O8 DM2 7 A 1 HETATM 12 C C9 DM2 . . . B 2 -13.35 12.459 4.695 1 13.12 ? C9 DM2 7 A 1 HETATM 13 C C10 DM2 . . . B 2 -13.305 10.952 4.695 1 15.1 ? C10 DM2 7 A 1 HETATM 14 O O10 DM2 . . . B 2 -12.585 10.481 5.834 1 18.99 ? O10 DM2 7 A 1 HETATM 15 C C11 DM2 . . . B 2 -14.714 10.353 4.557 1 10.53 ? C11 DM2 7 A 1 HETATM 16 C C12 DM2 . . . B 2 -15.697 10.966 5.537 1 11.48 ? C12 DM2 7 A 1 HETATM 17 O O12 DM2 . . . B 2 -15.372 10.907 6.926 1 28.08 ? O12 DM2 7 A 1 HETATM 18 C C13 DM2 . . . B 2 -16.84 9.983 5.31 1 25.57 ? C13 DM2 7 A 1 HETATM 19 O O13 DM2 . . . B 2 -17.383 10.008 4.25 1 27.28 ? O13 DM2 7 A 1 HETATM 20 C C14 DM2 . . . B 2 -17.425 9.173 6.433 1 32.75 ? C14 DM2 7 A 1 HETATM 21 O O14 DM2 . . . B 2 -17.842 7.969 5.85 1 50.33 ? O14 DM2 7 A 1 HETATM 22 C C15 DM2 . . . B 2 -15.884 12.386 5.045 1 19.29 ? C15 DM2 7 A 1 HETATM 23 C C16 DM2 . . . B 2 -14.56 13.109 4.827 1 6.56 ? C16 DM2 7 A 1 HETATM 24 C C17 DM2 . . . B 2 -14.557 14.495 4.986 1 2 ? C17 DM2 7 A 1 HETATM 25 O O17 DM2 . . . B 2 -15.711 15.184 5.151 1 7.98 ? O17 DM2 7 A 1 HETATM 26 C C18 DM2 . . . B 2 -13.35 15.195 4.986 1 6.46 ? C18 DM2 7 A 1 HETATM 27 C C19 DM2 . . . B 2 -13.436 16.632 5.135 1 2 ? C19 DM2 7 A 1 HETATM 28 O O19 DM2 . . . B 2 -14.523 17.195 5.278 1 16.31 ? O19 DM2 7 A 1 HETATM 29 C C20 DM2 . . . B 2 -12.207 17.377 5.14 1 5.78 ? C20 DM2 7 A 1 HETATM 30 C C21 DM2 . . . B 2 -7.4 17.772 4.854 1 8.54 ? C21 DM2 7 A 1 HETATM 31 C C1' DM2 . . . B 2 -11.834 9.35 5.813 1 17.51 ? C1' DM2 7 A 1 HETATM 32 C C2' DM2 . . . B 2 -11.358 9.33 7.223 1 39.12 ? C2' DM2 7 A 1 HETATM 33 C C3' DM2 . . . B 2 -12.212 8.54 8.224 1 30.41 ? C3' DM2 7 A 1 HETATM 34 N N3' DM2 . . . B 2 -11.28 8.061 9.289 1 46.08 ? N3' DM2 7 A 1 HETATM 35 C C4' DM2 . . . B 2 -12.899 7.347 7.657 1 34.76 ? C4' DM2 7 A 1 HETATM 36 O O4' DM2 . . . B 2 -11.882 6.431 7.366 1 43.52 ? O4' DM2 7 A 1 HETATM 37 C C5' DM2 . . . B 2 -13.431 7.518 6.279 1 24.17 ? C5' DM2 7 A 1 HETATM 38 O O5' DM2 . . . B 2 -12.476 8.154 5.421 1 13.01 ? O5' DM2 7 A 1 HETATM 39 C C6' DM2 . . . B 2 -13.632 6.123 5.585 1 20.93 ? C6' DM2 7 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 39 #