data_1D10 # _model_server_result.job_id I5yiyfk58uG-uFvKVEiY2A _model_server_result.datetime_utc '2024-10-18 13:16:05' _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 1d10 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 1D10 # _exptl.entry_id 1D10 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 527.52 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description DAUNOMYCIN _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 1D10 _cell.length_a 28.11 _cell.length_b 28.11 _cell.length_c 53.08 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D10 _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 28.11 28.11 26.54 # _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 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 O10' _chem_comp.formula_weight 527.52 _chem_comp.id DM1 _chem_comp.mon_nstd_flag . _chem_comp.name DAUNOMYCIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 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 DM1 doub 113 n y C1 C20 DM1 sing 114 n y C1 H1 DM1 sing 115 n n C2 C3 DM1 sing 116 n y C2 H2 DM1 sing 117 n n C3 C4 DM1 doub 118 n y C3 H3 DM1 sing 119 n n C4 O4 DM1 sing 120 n n C4 C5 DM1 sing 121 n y O4 C21 DM1 sing 122 n n C5 C6 DM1 sing 123 n n C5 C20 DM1 doub 124 n y C6 O6 DM1 doub 125 n n C6 C7 DM1 sing 126 n n C7 C8 DM1 doub 127 n y C7 C18 DM1 sing 128 n y C8 O8 DM1 sing 129 n n C8 C9 DM1 sing 130 n y O8 HO8 DM1 sing 131 n n C9 C10 DM1 sing 132 n n C9 C16 DM1 doub 133 n y C10 O10 DM1 sing 134 n n C10 C11 DM1 sing 135 n n C10 H10 DM1 sing 136 n n O10 C1' DM1 sing 137 n n C11 C12 DM1 sing 138 n n C11 H111 DM1 sing 139 n n C11 H112 DM1 sing 140 n n C12 O12 DM1 sing 141 n n C12 C13 DM1 sing 142 n n C12 C15 DM1 sing 143 n n O12 HO12 DM1 sing 144 n n C13 O13 DM1 doub 145 n n C13 C14 DM1 sing 146 n n C14 H141 DM1 sing 147 n n C14 H142 DM1 sing 148 n n C14 H143 DM1 sing 149 n n C15 C16 DM1 sing 150 n n C15 H151 DM1 sing 151 n n C15 H152 DM1 sing 152 n n C16 C17 DM1 sing 153 n y C17 O17 DM1 sing 154 n n C17 C18 DM1 doub 155 n y O17 HO17 DM1 sing 156 n n C18 C19 DM1 sing 157 n n C19 O19 DM1 doub 158 n n C19 C20 DM1 sing 159 n n C21 H211 DM1 sing 160 n n C21 H212 DM1 sing 161 n n C21 H213 DM1 sing 162 n n C1' C2' DM1 sing 163 n n C1' O5' DM1 sing 164 n n C1' H1' DM1 sing 165 n n C2' C3' DM1 sing 166 n n C2' "H2'1" DM1 sing 167 n n C2' "H2'2" DM1 sing 168 n n C3' N3' DM1 sing 169 n n C3' C4' DM1 sing 170 n n C3' H3' DM1 sing 171 n n N3' "HN'1" DM1 sing 172 n n N3' "HN'2" DM1 sing 173 n n C4' O4' DM1 sing 174 n n C4' C5' DM1 sing 175 n n C4' H4' DM1 sing 176 n n O4' HO4' DM1 sing 177 n n C5' O5' DM1 sing 178 n n C5' C6' DM1 sing 179 n n C5' H5' DM1 sing 180 n n C6' "H6'1" DM1 sing 181 n n C6' "H6'2" DM1 sing 182 n n C6' "H6'3" DM1 sing 183 n n # _atom_sites.entry_id 1D10 _atom_sites.fract_transf_matrix[1][1] 0.035575 _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] 0.035575 _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] 0.018839 _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 DM1 A 1 7 7 DM1 DM1 . 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 . E 5 HOH A 57 66 66 HOH HOH . E 5 HOH A 58 67 67 HOH HOH . E 5 HOH A 59 68 68 HOH HOH . E 5 HOH A 60 69 69 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 DM1 . . . B 2 15.442 18.471 5.008 1 9.85 ? C1 DM1 7 A 1 HETATM 2 C C2 DM1 . . . B 2 16.644 19.206 5.019 1 9.83 ? C2 DM1 7 A 1 HETATM 3 C C3 DM1 . . . B 2 17.868 18.531 4.932 1 10.66 ? C3 DM1 7 A 1 HETATM 4 C C4 DM1 . . . B 2 17.902 17.139 4.863 1 9.9 ? C4 DM1 7 A 1 HETATM 5 O O4 DM1 . . . B 2 19.102 16.529 4.795 1 11.23 ? O4 DM1 7 A 1 HETATM 6 C C5 DM1 . . . B 2 16.68 16.37 4.922 1 9.66 ? C5 DM1 7 A 1 HETATM 7 C C6 DM1 . . . B 2 16.65 14.983 4.905 1 8.17 ? C6 DM1 7 A 1 HETATM 8 O O6 DM1 . . . B 2 17.753 14.276 4.801 1 10.35 ? O6 DM1 7 A 1 HETATM 9 C C7 DM1 . . . B 2 15.414 14.267 4.885 1 7.98 ? C7 DM1 7 A 1 HETATM 10 C C8 DM1 . . . B 2 15.41 12.865 4.858 1 8.32 ? C8 DM1 7 A 1 HETATM 11 O O8 DM1 . . . B 2 16.557 12.136 4.829 1 8.95 ? O8 DM1 7 A 1 HETATM 12 C C9 DM1 . . . B 2 14.14 12.158 4.871 1 8.24 ? C9 DM1 7 A 1 HETATM 13 C C10 DM1 . . . B 2 14.243 10.678 4.868 1 10.08 ? C10 DM1 7 A 1 HETATM 14 O O10 DM1 . . . B 2 14.922 10.432 6.141 1 13.17 ? O10 DM1 7 A 1 HETATM 15 C C11 DM1 . . . B 2 12.938 9.859 4.696 1 10.64 ? C11 DM1 7 A 1 HETATM 16 C C12 DM1 . . . B 2 11.778 10.648 5.447 1 11.23 ? C12 DM1 7 A 1 HETATM 17 O O12 DM1 . . . B 2 11.79 10.821 6.951 1 12.2 ? O12 DM1 7 A 1 HETATM 18 C C13 DM1 . . . B 2 10.479 9.896 5.212 1 12.91 ? C13 DM1 7 A 1 HETATM 19 O O13 DM1 . . . B 2 9.733 10.313 4.183 1 14.09 ? O13 DM1 7 A 1 HETATM 20 C C14 DM1 . . . B 2 10.164 8.718 6.072 1 14.04 ? C14 DM1 7 A 1 HETATM 21 C C15 DM1 . . . B 2 11.649 12.119 4.913 1 8.97 ? C15 DM1 7 A 1 HETATM 22 C C16 DM1 . . . B 2 12.922 12.871 4.896 1 7.54 ? C16 DM1 7 A 1 HETATM 23 C C17 DM1 . . . B 2 13.003 14.273 4.913 1 7.85 ? C17 DM1 7 A 1 HETATM 24 O O17 DM1 . . . B 2 11.78 14.925 4.872 1 9.51 ? O17 DM1 7 A 1 HETATM 25 C C18 DM1 . . . B 2 14.208 14.982 4.905 1 7.63 ? C18 DM1 7 A 1 HETATM 26 C C19 DM1 . . . B 2 14.243 16.403 4.942 1 8.21 ? C19 DM1 7 A 1 HETATM 27 O O19 DM1 . . . B 2 13.117 17.15 4.983 1 9.91 ? O19 DM1 7 A 1 HETATM 28 C C20 DM1 . . . B 2 15.469 17.062 4.97 1 8.84 ? C20 DM1 7 A 1 HETATM 29 C C21 DM1 . . . B 2 20.409 17.249 4.926 1 12.19 ? C21 DM1 7 A 1 HETATM 30 C C1' DM1 . . . B 2 15.791 9.288 6.458 1 14.52 ? C1' DM1 7 A 1 HETATM 31 C C2' DM1 . . . B 2 16.934 9.797 7.419 1 15.26 ? C2' DM1 7 A 1 HETATM 32 C C3' DM1 . . . B 2 16.334 10.054 8.864 1 15.6 ? C3' DM1 7 A 1 HETATM 33 N N3' DM1 . . . B 2 17.456 10.46 9.771 1 13.77 ? N3' DM1 7 A 1 HETATM 34 C C4' DM1 . . . B 2 15.543 8.761 9.352 1 15.76 ? C4' DM1 7 A 1 HETATM 35 O O4' DM1 . . . B 2 16.567 7.719 9.356 1 18.22 ? O4' DM1 7 A 1 HETATM 36 C C5' DM1 . . . B 2 14.461 8.366 8.376 1 15.13 ? C5' DM1 7 A 1 HETATM 37 O O5' DM1 . . . B 2 14.971 8.21 7.027 1 15.54 ? O5' DM1 7 A 1 HETATM 38 C C6' DM1 . . . B 2 13.677 7.086 8.71 1 15.89 ? C6' DM1 7 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 38 #