data_1D12 # _model_server_result.job_id fCk_3eyHIwk1aOB-TQSEyg _model_server_result.datetime_utc '2025-03-06 00:14:48' _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 1d12 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 1D12 # _exptl.entry_id 1D12 _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 1D12 _cell.length_a 28.21 _cell.length_b 28.21 _cell.length_c 53.19 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D12 _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,D,E _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 28.21 28.21 26.595 # _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 metalc ? metalc1 A N7 DG 6 A DG 6 1_555 D NA NA . A NA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? metalc ? metalc2 D NA NA . A NA 9 1_555 E O HOH . A HOH 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 A N1 DG 6 A DG 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 A O6 DG 6 A DG 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 A N2 DG 6 A DG 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 A N3 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 A O2 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 A N4 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DA 3 A DA 3 1_555 A N3 DT 4 A DT 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N6 DA 3 A DA 3 1_555 A O4 DT 4 A DT 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 DT 4 A DT 4 1_555 A N1 DA 3 A DA 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O4 DT 4 A DT 4 1_555 A N6 DA 3 A DA 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 DC 5 A DC 5 1_555 A N1 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N4 DC 5 A DC 5 1_555 A O6 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O2 DC 5 A DC 5 1_555 A N2 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 DG 6 A DG 6 1_555 A N3 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N2 DG 6 A DG 6 1_555 A O2 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O6 DG 6 A DG 6 1_555 A N4 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 1D12 _atom_sites.fract_transf_matrix[1][1] 0.035448 _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] 0.035448 _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] 0.018801 _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 SPM A 1 8 8 SPM SPM . D 4 NA A 1 9 9 NA NA . E 5 HOH A 1 10 10 HOH HOH . E 5 HOH A 2 11 11 HOH HOH . E 5 HOH A 3 12 12 HOH HOH . E 5 HOH A 4 13 13 HOH HOH . E 5 HOH A 5 14 14 HOH HOH . E 5 HOH A 6 15 15 HOH HOH . E 5 HOH A 7 16 16 HOH HOH . E 5 HOH A 8 17 17 HOH HOH . E 5 HOH A 9 18 18 HOH HOH . E 5 HOH A 10 19 19 HOH HOH . E 5 HOH A 11 20 20 HOH HOH . E 5 HOH A 12 21 21 HOH HOH . E 5 HOH A 13 22 22 HOH HOH . E 5 HOH A 14 23 23 HOH HOH . E 5 HOH A 15 24 24 HOH HOH . E 5 HOH A 16 25 25 HOH HOH . E 5 HOH A 17 26 26 HOH HOH . E 5 HOH A 18 27 27 HOH HOH . E 5 HOH A 19 28 28 HOH HOH . E 5 HOH A 20 29 29 HOH HOH . E 5 HOH A 21 30 30 HOH HOH . E 5 HOH A 22 31 31 HOH HOH . E 5 HOH A 23 32 32 HOH HOH . E 5 HOH A 24 33 33 HOH HOH . E 5 HOH A 25 34 34 HOH HOH . E 5 HOH A 26 35 35 HOH HOH . E 5 HOH A 27 36 36 HOH HOH . E 5 HOH A 28 37 37 HOH HOH . E 5 HOH A 29 38 38 HOH HOH . E 5 HOH A 30 39 39 HOH HOH . E 5 HOH A 31 40 40 HOH HOH . E 5 HOH A 32 41 41 HOH HOH . E 5 HOH A 33 42 42 HOH HOH . E 5 HOH A 34 43 43 HOH HOH . E 5 HOH A 35 44 44 HOH HOH . E 5 HOH A 36 45 45 HOH HOH . E 5 HOH A 37 46 46 HOH HOH . E 5 HOH A 38 47 47 HOH HOH . E 5 HOH A 39 48 48 HOH HOH . E 5 HOH A 40 49 49 HOH HOH . E 5 HOH A 41 50 50 HOH HOH . E 5 HOH A 42 51 51 HOH HOH . E 5 HOH A 43 52 52 HOH HOH . E 5 HOH A 44 53 53 HOH HOH . E 5 HOH A 45 54 54 HOH HOH . E 5 HOH A 46 55 55 HOH HOH . E 5 HOH A 47 56 56 HOH HOH . E 5 HOH A 48 57 57 HOH HOH . E 5 HOH A 49 58 58 HOH HOH . E 5 HOH A 50 59 59 HOH HOH . E 5 HOH A 51 60 60 HOH HOH . E 5 HOH A 52 61 61 HOH HOH . E 5 HOH A 53 62 62 HOH HOH . E 5 HOH A 54 63 63 HOH HOH . E 5 HOH A 55 64 64 HOH HOH . E 5 HOH A 56 65 65 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 15.442 18.526 5.022 1 7.78 ? C1 DM2 7 A 1 HETATM 2 C C2 DM2 . . . B 2 16.603 19.313 4.985 1 7.97 ? C2 DM2 7 A 1 HETATM 3 C C3 DM2 . . . B 2 17.845 18.621 4.952 1 8.5 ? C3 DM2 7 A 1 HETATM 4 C C4 DM2 . . . B 2 17.931 17.232 4.912 1 7.31 ? C4 DM2 7 A 1 HETATM 5 O O4 DM2 . . . B 2 19.177 16.609 4.903 1 7.91 ? O4 DM2 7 A 1 HETATM 6 C C5 DM2 . . . B 2 16.767 16.473 4.909 1 7.55 ? C5 DM2 7 A 1 HETATM 7 C C6 DM2 . . . B 2 16.742 15.089 4.931 1 7.25 ? C6 DM2 7 A 1 HETATM 8 O O6 DM2 . . . B 2 17.917 14.369 4.832 1 8.86 ? O6 DM2 7 A 1 HETATM 9 C C7 DM2 . . . B 2 15.567 14.365 4.948 1 7.35 ? C7 DM2 7 A 1 HETATM 10 C C8 DM2 . . . B 2 15.541 12.986 4.906 1 8.55 ? C8 DM2 7 A 1 HETATM 11 O O8 DM2 . . . B 2 16.694 12.204 4.891 1 8.13 ? O8 DM2 7 A 1 HETATM 12 C C9 DM2 . . . B 2 14.305 12.305 4.907 1 10.14 ? C9 DM2 7 A 1 HETATM 13 C C10 DM2 . . . B 2 14.369 10.839 4.897 1 11.5 ? C10 DM2 7 A 1 HETATM 14 O O10 DM2 . . . B 2 15.098 10.503 6.024 1 13.9 ? O10 DM2 7 A 1 HETATM 15 C C11 DM2 . . . B 2 13.077 10.066 4.736 1 11.95 ? C11 DM2 7 A 1 HETATM 16 C C12 DM2 . . . B 2 11.963 10.795 5.583 1 11.32 ? C12 DM2 7 A 1 HETATM 17 O O12 DM2 . . . B 2 11.915 10.977 7.079 1 12.1 ? O12 DM2 7 A 1 HETATM 18 C C13 DM2 . . . B 2 10.661 10.013 5.269 1 11.82 ? C13 DM2 7 A 1 HETATM 19 O O13 DM2 . . . B 2 9.985 10.356 4.063 1 12.51 ? O13 DM2 7 A 1 HETATM 20 C C14 DM2 . . . B 2 10.141 8.992 6.167 1 11.37 ? C14 DM2 7 A 1 HETATM 21 O O14 DM2 . . . B 2 9.071 8.13 5.806 1 10.91 ? O14 DM2 7 A 1 HETATM 22 C C15 DM2 . . . B 2 11.841 12.244 4.982 1 10.66 ? C15 DM2 7 A 1 HETATM 23 C C16 DM2 . . . B 2 13.08 12.991 4.957 1 9.42 ? C16 DM2 7 A 1 HETATM 24 C C17 DM2 . . . B 2 13.144 14.382 4.987 1 8.78 ? C17 DM2 7 A 1 HETATM 25 O O17 DM2 . . . B 2 11.929 15.114 4.95 1 9.45 ? O17 DM2 7 A 1 HETATM 26 C C18 DM2 . . . B 2 14.361 15.063 4.987 1 7.02 ? C18 DM2 7 A 1 HETATM 27 C C19 DM2 . . . B 2 14.373 16.446 4.981 1 6.72 ? C19 DM2 7 A 1 HETATM 28 O O19 DM2 . . . B 2 13.206 17.134 5.057 1 7.2 ? O19 DM2 7 A 1 HETATM 29 C C20 DM2 . . . B 2 15.551 17.14 4.997 1 6.39 ? C20 DM2 7 A 1 HETATM 30 C C21 DM2 . . . B 2 20.424 17.346 4.89 1 7.78 ? C21 DM2 7 A 1 HETATM 31 C C1' DM2 . . . B 2 15.805 9.414 6.47 1 15.85 ? C1' DM2 7 A 1 HETATM 32 C C2' DM2 . . . B 2 16.996 9.831 7.353 1 16.87 ? C2' DM2 7 A 1 HETATM 33 C C3' DM2 . . . B 2 16.601 10.144 8.797 1 17.66 ? C3' DM2 7 A 1 HETATM 34 N N3' DM2 . . . B 2 17.715 10.467 9.744 1 17.04 ? N3' DM2 7 A 1 HETATM 35 C C4' DM2 . . . B 2 15.554 9.119 9.272 1 18.05 ? C4' DM2 7 A 1 HETATM 36 O O4' DM2 . . . B 2 16.354 7.951 9.468 1 19.79 ? O4' DM2 7 A 1 HETATM 37 C C5' DM2 . . . B 2 14.472 8.686 8.216 1 17.92 ? C5' DM2 7 A 1 HETATM 38 O O5' DM2 . . . B 2 15.009 8.297 6.917 1 17.15 ? O5' DM2 7 A 1 HETATM 39 C C6' DM2 . . . B 2 13.586 7.531 8.714 1 18.5 ? C6' DM2 7 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #