data_1QDA # _model_server_result.job_id fy_Z67Pbh8ObBWlCev0lyg _model_server_result.datetime_utc '2024-10-18 15:24:25' _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 1qda # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":100}' # _entry.id 1QDA # _exptl.entry_id 1QDA _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 1QDA _cell.length_a 28.11 _cell.length_b 28.11 _cell.length_c 52.54 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1QDA _symmetry.cell_setting tetragonal _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 28.11 28.11 26.27 # _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 covale ? covale1 A O3' DC 3 A DC 3 1_555 A P G49 4 A G49 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.575 ? covale ? covale2 A O3' G49 4 A G49 4 1_555 A P DC 5 A DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? covale ? covale3 A CM2 G49 4 A G49 4 1_555 B N3' DM6 . A DM6 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.516 ? 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 DC 3 A DC 3 1_555 A N1 G49 4 A G49 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 A O6 G49 4 A G49 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 A N2 G49 4 A G49 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 G49 4 A G49 4 1_555 A N3 DC 3 A DC 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 G49 4 A G49 4 1_555 A O2 DC 3 A DC 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 G49 4 A G49 4 1_555 A N4 DC 3 A DC 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 DC 5 A DC 5 1_555 A N1 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N4 DC 5 A DC 5 1_555 A O6 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O2 DC 5 A DC 5 1_555 A N2 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 DG 6 A DG 6 1_555 A N3 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N2 DG 6 A DG 6 1_555 A O2 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O6 DG 6 A DG 6 1_555 A N4 DC 1 A DC 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 75 n y C1 C15 DM6 sing 76 n y C1 H1 DM6 sing 77 n n C2 C3 DM6 sing 78 n y C2 H2 DM6 sing 79 n n C3 C4 DM6 doub 80 n y C3 H3 DM6 sing 81 n n C4 C16 DM6 sing 82 n y C4 O4 DM6 sing 83 n n C5 C16 DM6 sing 84 n n C5 C17 DM6 sing 85 n n C5 O5 DM6 doub 86 n n C6 C17 DM6 doub 87 n y C6 C20 DM6 sing 88 n y C6 O6 DM6 sing 89 n n C7 C8 DM6 sing 90 n n C7 C20 DM6 sing 91 n n C7 O7 DM6 sing 92 n n C7 H7 DM6 sing 93 n n C8 C9 DM6 sing 94 n n C8 H81 DM6 sing 95 n n C8 H82 DM6 sing 96 n n C9 C10 DM6 sing 97 n n C9 C13 DM6 sing 98 n n C9 O9 DM6 sing 99 n n C10 C19 DM6 sing 100 n n C10 H101 DM6 sing 101 n n C10 H102 DM6 sing 102 n n C11 C18 DM6 doub 103 n y C11 C19 DM6 sing 104 n y C11 O11 DM6 sing 105 n n C12 C15 DM6 sing 106 n n C12 C18 DM6 sing 107 n n C12 O12 DM6 doub 108 n n C13 C14 DM6 sing 109 n n C13 O13 DM6 doub 110 n n C14 O14 DM6 sing 111 n n C14 H141 DM6 sing 112 n n C14 H142 DM6 sing 113 n n C15 C16 DM6 doub 114 n y C17 C18 DM6 sing 115 n y C19 C20 DM6 doub 116 n y C21 O4 DM6 sing 117 n n C21 H211 DM6 sing 118 n n C21 H212 DM6 sing 119 n n C21 H213 DM6 sing 120 n n O6 HO6 DM6 sing 121 n n O7 C1' DM6 sing 122 n n O9 HO9 DM6 sing 123 n n O11 HO11 DM6 sing 124 n n O14 HO14 DM6 sing 125 n n C1' C2' DM6 sing 126 n n C1' O5' DM6 sing 127 n n C1' H1' DM6 sing 128 n n C2' C3' DM6 sing 129 n n C2' "H2'1" DM6 sing 130 n n C2' "H2'2" DM6 sing 131 n n C3' C4' DM6 sing 132 n n C3' N3' DM6 sing 133 n n C3' H3' DM6 sing 134 n n C4' C5' DM6 sing 135 n n C4' O4' DM6 sing 136 n n C4' H4' DM6 sing 137 n n C5' C6' DM6 sing 138 n n C5' O5' DM6 sing 139 n n C5' H5' DM6 sing 140 n n C6' "H6'1" DM6 sing 141 n n C6' "H6'2" DM6 sing 142 n n C6' "H6'3" DM6 sing 143 n n O4' "HO'4" DM6 sing 144 n n N3' "HN'1" DM6 sing 145 n n N3' "HN'2" DM6 sing 146 n n N3' "HN'3" DM6 sing 147 n n # _atom_sites.entry_id 1QDA _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] 0.019033 _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 1 100 100 DM6 DM2 . C 3 HOH A 1 101 1 HOH WAT . C 3 HOH A 2 102 2 HOH WAT . C 3 HOH A 3 103 3 HOH WAT . C 3 HOH A 4 104 4 HOH WAT . C 3 HOH A 5 105 5 HOH WAT . C 3 HOH A 6 106 6 HOH WAT . C 3 HOH A 7 107 7 HOH WAT . C 3 HOH A 8 108 8 HOH WAT . C 3 HOH A 9 109 9 HOH WAT . C 3 HOH A 10 110 10 HOH WAT . C 3 HOH A 11 111 11 HOH WAT . C 3 HOH A 12 112 12 HOH WAT . C 3 HOH A 13 113 13 HOH WAT . C 3 HOH A 14 114 14 HOH WAT . C 3 HOH A 15 115 15 HOH WAT . C 3 HOH A 16 116 16 HOH WAT . C 3 HOH A 17 117 17 HOH WAT . C 3 HOH A 18 118 18 HOH WAT . C 3 HOH A 19 119 19 HOH WAT . C 3 HOH A 20 120 20 HOH WAT . C 3 HOH A 21 121 21 HOH WAT . C 3 HOH A 22 122 22 HOH WAT . C 3 HOH A 23 123 23 HOH WAT . C 3 HOH A 24 124 24 HOH WAT . C 3 HOH A 25 125 25 HOH WAT . C 3 HOH A 26 126 26 HOH WAT . C 3 HOH A 27 127 27 HOH WAT . C 3 HOH A 28 128 28 HOH WAT . C 3 HOH A 29 129 29 HOH WAT . C 3 HOH A 30 130 30 HOH WAT . # 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 15.768 18.679 5.125 1 16.61 ? C1 DM6 100 A 1 HETATM 2 C C2 DM6 . . . B 2 17.034 19.342 5.145 1 17.69 ? C2 DM6 100 A 1 HETATM 3 C C3 DM6 . . . B 2 18.206 18.732 5.073 1 17.14 ? C3 DM6 100 A 1 HETATM 4 C C4 DM6 . . . B 2 18.274 17.326 4.97 1 15.98 ? C4 DM6 100 A 1 HETATM 5 C C5 DM6 . . . B 2 16.994 15.059 4.873 1 14.15 ? C5 DM6 100 A 1 HETATM 6 C C6 DM6 . . . B 2 15.723 13.014 4.852 1 13.56 ? C6 DM6 100 A 1 HETATM 7 C C7 DM6 . . . B 2 14.485 10.81 4.861 1 14.53 ? C7 DM6 100 A 1 HETATM 8 C C8 DM6 . . . B 2 13.14 10.136 4.548 1 14.33 ? C8 DM6 100 A 1 HETATM 9 C C9 DM6 . . . B 2 11.942 10.79 5.332 1 16.18 ? C9 DM6 100 A 1 HETATM 10 C C10 DM6 . . . B 2 11.825 12.291 4.92 1 14.85 ? C10 DM6 100 A 1 HETATM 11 C C11 DM6 . . . B 2 13.194 14.439 4.943 1 13.3 ? C11 DM6 100 A 1 HETATM 12 C C12 DM6 . . . B 2 14.465 16.583 5.025 1 14.86 ? C12 DM6 100 A 1 HETATM 13 C C13 DM6 . . . B 2 10.637 9.998 4.945 1 18.26 ? C13 DM6 100 A 1 HETATM 14 C C14 DM6 . . . B 2 9.993 9.209 6.132 1 20.01 ? C14 DM6 100 A 1 HETATM 15 C C15 DM6 . . . B 2 15.8 17.272 5.034 1 15.23 ? C15 DM6 100 A 1 HETATM 16 C C16 DM6 . . . B 2 17.013 16.567 4.959 1 15.73 ? C16 DM6 100 A 1 HETATM 17 C C17 DM6 . . . B 2 15.722 14.422 4.892 1 13.47 ? C17 DM6 100 A 1 HETATM 18 C C18 DM6 . . . B 2 14.465 15.141 4.952 1 13.5 ? C18 DM6 100 A 1 HETATM 19 C C19 DM6 . . . B 2 13.192 13.004 4.915 1 14.42 ? C19 DM6 100 A 1 HETATM 20 C C20 DM6 . . . B 2 14.411 12.304 4.879 1 13.69 ? C20 DM6 100 A 1 HETATM 21 C C21 DM6 . . . B 2 20.724 17.259 4.915 1 17.74 ? C21 DM6 100 A 1 HETATM 22 O O4 DM6 . . . B 2 19.386 16.622 4.89 1 18.64 ? O4 DM6 100 A 1 HETATM 23 O O5 DM6 . . . B 2 17.997 14.405 4.79 1 15.68 ? O5 DM6 100 A 1 HETATM 24 O O6 DM6 . . . B 2 16.867 12.239 4.787 1 13.27 ? O6 DM6 100 A 1 HETATM 25 O O7 DM6 . . . B 2 15.069 10.538 6.213 1 14.74 ? O7 DM6 100 A 1 HETATM 26 O O9 DM6 . . . B 2 12.15 10.758 6.721 1 15.07 ? O9 DM6 100 A 1 HETATM 27 O O11 DM6 . . . B 2 11.977 15.039 4.959 1 14.76 ? O11 DM6 100 A 1 HETATM 28 O O12 DM6 . . . B 2 13.38 17.205 5.095 1 16.24 ? O12 DM6 100 A 1 HETATM 29 O O13 DM6 . . . B 2 10.234 10.338 3.86 1 20.18 ? O13 DM6 100 A 1 HETATM 30 O O14 DM6 . . . B 2 8.807 8.523 5.616 1 21.82 ? O14 DM6 100 A 1 HETATM 31 C C1' DM6 . . . B 2 16.065 9.511 6.206 1 14.67 ? C1' DM6 100 A 1 HETATM 32 C C2' DM6 . . . B 2 17.088 9.853 7.24 1 15.1 ? C2' DM6 100 A 1 HETATM 33 C C3' DM6 . . . B 2 16.468 9.793 8.658 1 15.44 ? C3' DM6 100 A 1 HETATM 34 C C4' DM6 . . . B 2 15.854 8.434 8.886 1 15.67 ? C4' DM6 100 A 1 HETATM 35 C C5' DM6 . . . B 2 14.791 8.202 7.818 1 15.07 ? C5' DM6 100 A 1 HETATM 36 C C6' DM6 . . . B 2 14.1 6.824 7.922 1 16.84 ? C6' DM6 100 A 1 HETATM 37 O O4' DM6 . . . B 2 15.28 8.358 10.19 1 17.73 ? O4' DM6 100 A 1 HETATM 38 O O5' DM6 . . . B 2 15.393 8.265 6.496 1 15.3 ? O5' DM6 100 A 1 HETATM 39 N N3' DM6 . . . B 2 17.585 10.119 9.602 1 15.54 ? N3' DM6 100 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 39 #