data_1D11 # _model_server_result.job_id WicUAaC2Q7cjey7PDIAeDQ _model_server_result.datetime_utc '2024-12-04 20:31:48' _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 1d11 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 1D11 # _exptl.entry_id 1D11 _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 1D11 _cell.length_a 27.86 _cell.length_b 27.86 _cell.length_c 52.72 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D11 _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 _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 27.86 27.86 26.36 # _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 C NA NA . A NA 8 1_555 D O HOH . A HOH 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.895 ? metalc ? metalc2 C NA NA . A NA 8 1_555 D O HOH . A HOH 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.044 ? metalc ? metalc3 C NA NA . A NA 8 1_555 D O HOH . A HOH 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? 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 N3 DT 3 A DT 3 1_555 A N1 DA 4 A DA 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O4 DT 3 A DT 3 1_555 A N6 DA 4 A DA 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 DA 4 A DA 4 1_555 A N3 DT 3 A DT 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N6 DA 4 A DA 4 1_555 A O4 DT 3 A DT 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 1D11 _atom_sites.fract_transf_matrix[1][1] 0.035894 _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] 0.035894 _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] 0.018968 _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 NA A 1 8 8 NA NA . D 4 HOH A 1 9 9 HOH HOH . D 4 HOH A 2 10 10 HOH HOH . D 4 HOH A 3 11 11 HOH HOH . D 4 HOH A 4 12 12 HOH HOH . D 4 HOH A 5 13 13 HOH HOH . D 4 HOH A 6 14 14 HOH HOH . D 4 HOH A 7 15 15 HOH HOH . D 4 HOH A 8 16 16 HOH HOH . D 4 HOH A 9 17 17 HOH HOH . D 4 HOH A 10 18 18 HOH HOH . D 4 HOH A 11 19 19 HOH HOH . D 4 HOH A 12 20 20 HOH HOH . D 4 HOH A 13 21 21 HOH HOH . D 4 HOH A 14 22 22 HOH HOH . D 4 HOH A 15 23 23 HOH HOH . D 4 HOH A 16 24 24 HOH HOH . D 4 HOH A 17 25 25 HOH HOH . D 4 HOH A 18 26 26 HOH HOH . D 4 HOH A 19 27 27 HOH HOH . D 4 HOH A 20 28 28 HOH HOH . D 4 HOH A 21 29 29 HOH HOH . D 4 HOH A 22 30 30 HOH HOH . D 4 HOH A 23 31 31 HOH HOH . D 4 HOH A 24 32 32 HOH HOH . D 4 HOH A 25 33 33 HOH HOH . D 4 HOH A 26 34 34 HOH HOH . D 4 HOH A 27 35 35 HOH HOH . D 4 HOH A 28 36 36 HOH HOH . D 4 HOH A 29 37 37 HOH HOH . D 4 HOH A 30 38 38 HOH HOH . D 4 HOH A 31 39 39 HOH HOH . D 4 HOH A 32 40 40 HOH HOH . D 4 HOH A 33 41 41 HOH HOH . D 4 HOH A 34 42 42 HOH HOH . D 4 HOH A 35 43 43 HOH HOH . D 4 HOH A 36 44 44 HOH HOH . D 4 HOH A 37 45 45 HOH HOH . D 4 HOH A 38 46 46 HOH HOH . D 4 HOH A 39 47 47 HOH HOH . D 4 HOH A 40 48 48 HOH HOH . D 4 HOH A 41 49 49 HOH HOH . D 4 HOH A 42 50 50 HOH HOH . D 4 HOH A 43 51 51 HOH HOH . D 4 HOH A 44 52 52 HOH HOH . D 4 HOH A 45 53 53 HOH HOH . D 4 HOH A 46 54 54 HOH HOH . D 4 HOH A 47 55 55 HOH HOH . D 4 HOH A 48 56 56 HOH HOH . D 4 HOH A 49 57 57 HOH HOH . D 4 HOH A 50 58 58 HOH HOH . D 4 HOH A 51 59 59 HOH HOH . D 4 HOH A 52 60 60 HOH HOH . D 4 HOH A 53 61 61 HOH HOH . D 4 HOH A 54 62 62 HOH HOH . D 4 HOH A 55 63 63 HOH HOH . D 4 HOH A 56 64 64 HOH HOH . D 4 HOH A 57 65 65 HOH HOH . D 4 HOH A 58 66 66 HOH HOH . D 4 HOH A 59 67 67 HOH HOH . D 4 HOH A 60 68 68 HOH HOH . D 4 HOH A 61 69 69 HOH HOH . D 4 HOH A 62 70 70 HOH HOH . D 4 HOH A 63 71 71 HOH HOH . D 4 HOH A 64 72 72 HOH HOH . D 4 HOH A 65 73 73 HOH HOH . D 4 HOH A 66 74 74 HOH HOH . D 4 HOH A 67 75 75 HOH HOH . D 4 HOH A 68 76 76 HOH HOH . D 4 HOH A 69 77 77 HOH HOH . D 4 HOH A 70 78 78 HOH HOH . D 4 HOH A 71 79 79 HOH HOH . D 4 HOH A 72 80 80 HOH HOH . D 4 HOH A 73 81 81 HOH HOH . D 4 HOH A 74 82 82 HOH HOH . D 4 HOH A 75 83 83 HOH HOH . D 4 HOH A 76 84 84 HOH HOH . D 4 HOH A 77 85 85 HOH HOH . D 4 HOH A 78 86 86 HOH HOH . D 4 HOH A 79 87 87 HOH HOH . D 4 HOH A 80 88 88 HOH HOH . D 4 HOH A 81 89 89 HOH HOH . D 4 HOH A 82 90 90 HOH HOH . D 4 HOH A 83 91 91 HOH HOH . D 4 HOH A 84 92 92 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 15.076 18.21 5.093 1 9.66 ? C1 DM1 7 A 1 HETATM 2 C C2 DM1 . . . B 2 16.284 18.936 5.143 1 10.52 ? C2 DM1 7 A 1 HETATM 3 C C3 DM1 . . . B 2 17.527 18.293 5.081 1 10.79 ? C3 DM1 7 A 1 HETATM 4 C C4 DM1 . . . B 2 17.52 16.91 5.002 1 9.04 ? C4 DM1 7 A 1 HETATM 5 O O4 DM1 . . . B 2 18.754 16.294 4.969 1 10.59 ? O4 DM1 7 A 1 HETATM 6 C C5 DM1 . . . B 2 16.334 16.176 4.98 1 7.88 ? C5 DM1 7 A 1 HETATM 7 C C6 DM1 . . . B 2 16.306 14.768 4.911 1 7.15 ? C6 DM1 7 A 1 HETATM 8 O O6 DM1 . . . B 2 17.462 14.041 4.823 1 7.7 ? O6 DM1 7 A 1 HETATM 9 C C7 DM1 . . . B 2 15.089 14.049 4.912 1 6.38 ? C7 DM1 7 A 1 HETATM 10 C C8 DM1 . . . B 2 15.065 12.635 4.85 1 6.09 ? C8 DM1 7 A 1 HETATM 11 O O8 DM1 . . . B 2 16.272 11.915 4.864 1 6.51 ? O8 DM1 7 A 1 HETATM 12 C C9 DM1 . . . B 2 13.847 11.929 4.81 1 6.04 ? C9 DM1 7 A 1 HETATM 13 C C10 DM1 . . . B 2 13.931 10.456 4.819 1 7.37 ? C10 DM1 7 A 1 HETATM 14 O O10 DM1 . . . B 2 14.546 10.208 6.171 1 9.19 ? O10 DM1 7 A 1 HETATM 15 C C11 DM1 . . . B 2 12.603 9.711 4.699 1 7.99 ? C11 DM1 7 A 1 HETATM 16 C C12 DM1 . . . B 2 11.442 10.539 5.37 1 7.93 ? C12 DM1 7 A 1 HETATM 17 O O12 DM1 . . . B 2 11.531 10.603 6.805 1 7.15 ? O12 DM1 7 A 1 HETATM 18 C C13 DM1 . . . B 2 10.153 9.725 5.149 1 9.3 ? C13 DM1 7 A 1 HETATM 19 O O13 DM1 . . . B 2 9.415 10.008 4.095 1 10.77 ? O13 DM1 7 A 1 HETATM 20 C C14 DM1 . . . B 2 9.798 8.587 6.083 1 9.75 ? C14 DM1 7 A 1 HETATM 21 C C15 DM1 . . . B 2 11.346 11.979 4.813 1 6.34 ? C15 DM1 7 A 1 HETATM 22 C C16 DM1 . . . B 2 12.679 12.633 4.852 1 5.56 ? C16 DM1 7 A 1 HETATM 23 C C17 DM1 . . . B 2 12.674 14.045 4.878 1 5.4 ? C17 DM1 7 A 1 HETATM 24 O O17 DM1 . . . B 2 11.428 14.623 4.847 1 6.12 ? O17 DM1 7 A 1 HETATM 25 C C18 DM1 . . . B 2 13.866 14.761 4.931 1 5.99 ? C18 DM1 7 A 1 HETATM 26 C C19 DM1 . . . B 2 13.865 16.186 4.984 1 6.99 ? C19 DM1 7 A 1 HETATM 27 O O19 DM1 . . . B 2 12.738 16.887 5.004 1 8.12 ? O19 DM1 7 A 1 HETATM 28 C C20 DM1 . . . B 2 15.112 16.834 4.999 1 7.72 ? C20 DM1 7 A 1 HETATM 29 C C21 DM1 . . . B 2 19.976 17.161 5.15 1 11.44 ? C21 DM1 7 A 1 HETATM 30 C C1' DM1 . . . B 2 15.484 9.139 6.38 1 10.36 ? C1' DM1 7 A 1 HETATM 31 C C2' DM1 . . . B 2 16.539 9.605 7.374 1 10.9 ? C2' DM1 7 A 1 HETATM 32 C C3' DM1 . . . B 2 15.948 9.604 8.804 1 12.13 ? C3' DM1 7 A 1 HETATM 33 N N3' DM1 . . . B 2 16.975 9.929 9.802 1 12.08 ? N3' DM1 7 A 1 HETATM 34 C C4' DM1 . . . B 2 15.066 8.368 9.128 1 12.84 ? C4' DM1 7 A 1 HETATM 35 O O4' DM1 . . . B 2 16.035 7.236 9.128 1 13.97 ? O4' DM1 7 A 1 HETATM 36 C C5' DM1 . . . B 2 14.045 8.04 7.988 1 12.67 ? C5' DM1 7 A 1 HETATM 37 O O5' DM1 . . . B 2 14.723 7.953 6.669 1 11.52 ? O5' DM1 7 A 1 HETATM 38 C C6' DM1 . . . B 2 13.253 6.745 8.148 1 12.9 ? C6' DM1 7 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 249 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 38 #