data_482D # _model_server_result.job_id tMxIjm1A-C5qyWblAa0jtA _model_server_result.datetime_utc '2024-10-18 13:18:37' _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 482d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 482D # _exptl.entry_id 482D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 617.641 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-HYDROXYMETHYL-N-(2-METHOXYETHYL)-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 482D _cell.length_a 28.16 _cell.length_b 28.16 _cell.length_c 53.4 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 482D _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 28.16 28.16 26.7 # _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 'C31 H39 N O12' _chem_comp.formula_weight 617.641 _chem_comp.id DM9 _chem_comp.mon_nstd_flag . _chem_comp.name N-HYDROXYMETHYL-N-(2-METHOXYETHYL)-DAUNOMYCIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 DM9 doub 113 n y C1 C15 DM9 sing 114 n y C1 H1 DM9 sing 115 n n C2 C3 DM9 sing 116 n y C2 H2 DM9 sing 117 n n C3 C4 DM9 doub 118 n y C3 H3 DM9 sing 119 n n C4 O4 DM9 sing 120 n n C4 C16 DM9 sing 121 n y O4 C21 DM9 sing 122 n n C5 O5 DM9 sing 123 n n C5 C16 DM9 doub 124 n y C5 C17 DM9 sing 125 n y O5 HO5 DM9 sing 126 n n C6 O6 DM9 sing 127 n n C6 C17 DM9 doub 128 n y C6 C20 DM9 sing 129 n y O6 HO6 DM9 sing 130 n n C7 O7 DM9 sing 131 n n C7 C8 DM9 sing 132 n n C7 C20 DM9 sing 133 n n C7 H7 DM9 sing 134 n n O7 C1' DM9 sing 135 n n C8 C9 DM9 sing 136 n n C8 H81 DM9 sing 137 n n C8 H82 DM9 sing 138 n n C9 O9 DM9 sing 139 n n C9 C10 DM9 sing 140 n n C9 C13 DM9 sing 141 n n O9 HO9 DM9 sing 142 n n C10 C19 DM9 sing 143 n n C10 H101 DM9 sing 144 n n C10 H102 DM9 sing 145 n n C11 O11 DM9 sing 146 n n C11 C18 DM9 doub 147 n y C11 C19 DM9 sing 148 n y O11 HO11 DM9 sing 149 n n C12 O12 DM9 sing 150 n n C12 C15 DM9 doub 151 n y C12 C18 DM9 sing 152 n y O12 HO12 DM9 sing 153 n n C13 O13 DM9 doub 154 n n C13 C14 DM9 sing 155 n n C14 H141 DM9 sing 156 n n C14 H142 DM9 sing 157 n n C14 H143 DM9 sing 158 n n C15 C16 DM9 sing 159 n y C17 C18 DM9 sing 160 n y C19 C20 DM9 doub 161 n y C21 H211 DM9 sing 162 n n C21 H212 DM9 sing 163 n n C21 H213 DM9 sing 164 n n C1' C2' DM9 sing 165 n n C1' O5' DM9 sing 166 n n C1' H1' DM9 sing 167 n n C2' C3' DM9 sing 168 n n C2' "H2'1" DM9 sing 169 n n C2' "H2'2" DM9 sing 170 n n C3' C4' DM9 sing 171 n n C3' N3' DM9 sing 172 n n C3' H3' DM9 sing 173 n n C4' O4' DM9 sing 174 n n C4' C5' DM9 sing 175 n n C4' H4' DM9 sing 176 n n O4' HO4' DM9 sing 177 n n C5' O5' DM9 sing 178 n n C5' C6' DM9 sing 179 n n C5' H5' DM9 sing 180 n n C6' "H6'1" DM9 sing 181 n n C6' "H6'2" DM9 sing 182 n n C6' "H6'3" DM9 sing 183 n n N3' C31 DM9 sing 184 n n N3' C41 DM9 sing 185 n n C31 O31 DM9 sing 186 n n C31 H311 DM9 sing 187 n n C31 H312 DM9 sing 188 n n O31 HO31 DM9 sing 189 n n C41 C42 DM9 sing 190 n n C41 H411 DM9 sing 191 n n C41 H412 DM9 sing 192 n n C42 O42 DM9 sing 193 n n C42 H421 DM9 sing 194 n n C42 H422 DM9 sing 195 n n O42 C43 DM9 sing 196 n n C43 H431 DM9 sing 197 n n C43 H432 DM9 sing 198 n n C43 H433 DM9 sing 199 n n # _atom_sites.entry_id 482D _atom_sites.fract_transf_matrix[1][1] 0.035511 _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] 0.035511 _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] 0.018726 _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 DM9 A 1 7 7 DM9 DM9 . 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 . # 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 DM9 . . . B 2 15.566 18.348 5.136 1 13.91 ? C1 DM9 7 A 1 HETATM 2 C C2 DM9 . . . B 2 16.77 19.075 5.151 1 13.94 ? C2 DM9 7 A 1 HETATM 3 C C3 DM9 . . . B 2 18.02 18.424 5.05 1 14.58 ? C3 DM9 7 A 1 HETATM 4 C C4 DM9 . . . B 2 18.011 17.033 4.94 1 14.29 ? C4 DM9 7 A 1 HETATM 5 O O4 DM9 . . . B 2 19.235 16.401 4.836 1 15.08 ? O4 DM9 7 A 1 HETATM 6 C C5 DM9 . . . B 2 16.763 14.875 4.847 1 13.61 ? C5 DM9 7 A 1 HETATM 7 O O5 DM9 . . . B 2 17.916 14.159 4.753 1 14.45 ? O5 DM9 7 A 1 HETATM 8 C C6 DM9 . . . B 2 15.422 12.725 4.783 1 13.21 ? C6 DM9 7 A 1 HETATM 9 O O6 DM9 . . . B 2 16.593 11.963 4.706 1 13.31 ? O6 DM9 7 A 1 HETATM 10 C C7 DM9 . . . B 2 14.157 10.573 4.716 1 14.93 ? C7 DM9 7 A 1 HETATM 11 O O7 DM9 . . . B 2 14.761 10.203 6.077 1 16.66 ? O7 DM9 7 A 1 HETATM 12 C C8 DM9 . . . B 2 12.806 9.899 4.53 1 14.16 ? C8 DM9 7 A 1 HETATM 13 C C9 DM9 . . . B 2 11.695 10.716 5.294 1 14.4 ? C9 DM9 7 A 1 HETATM 14 O O9 DM9 . . . B 2 11.831 10.661 6.722 1 14.08 ? O9 DM9 7 A 1 HETATM 15 C C10 DM9 . . . B 2 11.623 12.217 4.872 1 14.22 ? C10 DM9 7 A 1 HETATM 16 C C11 DM9 . . . B 2 13.073 14.229 4.944 1 13.05 ? C11 DM9 7 A 1 HETATM 17 O O11 DM9 . . . B 2 11.864 14.87 5.026 1 14.26 ? O11 DM9 7 A 1 HETATM 18 C C12 DM9 . . . B 2 14.326 16.304 5.028 1 13.25 ? C12 DM9 7 A 1 HETATM 19 O O12 DM9 . . . B 2 13.199 16.976 5.103 1 13.91 ? O12 DM9 7 A 1 HETATM 20 C C13 DM9 . . . B 2 10.408 9.987 5.067 1 14.67 ? C13 DM9 7 A 1 HETATM 21 O O13 DM9 . . . B 2 9.668 10.374 4.059 1 15.34 ? O13 DM9 7 A 1 HETATM 22 C C14 DM9 . . . B 2 9.977 8.858 5.991 1 14.46 ? C14 DM9 7 A 1 HETATM 23 C C15 DM9 . . . B 2 15.593 16.965 5.031 1 13.59 ? C15 DM9 7 A 1 HETATM 24 C C16 DM9 . . . B 2 16.81 16.299 4.942 1 14.03 ? C16 DM9 7 A 1 HETATM 25 C C17 DM9 . . . B 2 15.499 14.146 4.857 1 13.41 ? C17 DM9 7 A 1 HETATM 26 C C18 DM9 . . . B 2 14.293 14.892 4.943 1 13 ? C18 DM9 7 A 1 HETATM 27 C C19 DM9 . . . B 2 13.003 12.826 4.867 1 13.82 ? C19 DM9 7 A 1 HETATM 28 C C20 DM9 . . . B 2 14.151 12.061 4.791 1 13.88 ? C20 DM9 7 A 1 HETATM 29 C C21 DM9 . . . B 2 20.516 17.202 4.836 1 15.61 ? C21 DM9 7 A 1 HETATM 30 C C1' DM9 . . . B 2 15.679 9.022 6.19 1 18.82 ? C1' DM9 7 A 1 HETATM 31 C C2' DM9 . . . B 2 16.526 9.188 7.433 1 20.34 ? C2' DM9 7 A 1 HETATM 32 C C3' DM9 . . . B 2 15.647 8.88 8.676 1 21.58 ? C3' DM9 7 A 1 HETATM 33 C C4' DM9 . . . B 2 14.768 7.623 8.553 1 21.18 ? C4' DM9 7 A 1 HETATM 34 O O4' DM9 . . . B 2 15.779 6.531 8.392 1 21.26 ? O4' DM9 7 A 1 HETATM 35 C C5' DM9 . . . B 2 13.94 7.661 7.218 1 21.01 ? C5' DM9 7 A 1 HETATM 36 O O5' DM9 . . . B 2 14.849 7.861 6.058 1 19.93 ? O5' DM9 7 A 1 HETATM 37 C C6' DM9 . . . B 2 13.113 6.376 7.039 1 21.26 ? C6' DM9 7 A 1 HETATM 38 N N3' DM9 . . . B 2 16.299 9.159 9.98 1 23.35 ? N3' DM9 7 A 1 HETATM 39 C C31 DM9 . . . B 2 17.752 9.461 9.816 1 23.31 ? C31 DM9 7 A 1 HETATM 40 O O31 DM9 . . . B 2 18.017 10.926 10.096 1 23.02 ? O31 DM9 7 A 1 HETATM 41 C C41 DM9 . . . B 2 15.998 8.105 11.049 1 24.39 ? C41 DM9 7 A 1 HETATM 42 C C42 DM9 . . . B 2 16.857 8.315 12.307 1 25.52 ? C42 DM9 7 A 1 HETATM 43 O O42 DM9 . . . B 2 17.444 6.968 12.767 1 26.72 ? O42 DM9 7 A 1 HETATM 44 C C43 DM9 . . . B 2 17.449 5.736 11.9 1 26.34 ? C43 DM9 7 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 44 #