data_288D # _model_server_result.job_id pVmixHe6VZIWn0mcKszMSA _model_server_result.datetime_utc '2024-10-18 15:22:41' _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 288d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 288D # _exptl.entry_id 288D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 606.416 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-BROMO-4'-EPIDAUNORUBICIN" _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 288D _cell.length_a 28.042 _cell.length_b 28.042 _cell.length_c 53.363 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 288D _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 _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 28.042 28.042 26.6815 # _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 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 H28 Br N O10' _chem_comp.formula_weight 606.416 _chem_comp.id DM8 _chem_comp.mon_nstd_flag . _chem_comp.name "2'-BROMO-4'-EPIDAUNORUBICIN" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'WP401;DAUNOMYCIN DERIVATIVE;DAUNORUBICIN DERIVATIVE' # 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 DM8 doub 113 n y C1 C15 DM8 sing 114 n y C1 H1 DM8 sing 115 n n C2 C3 DM8 sing 116 n y C2 H2 DM8 sing 117 n n C3 C4 DM8 doub 118 n y C3 H3 DM8 sing 119 n n C4 C16 DM8 sing 120 n y C4 O4 DM8 sing 121 n n C5 C16 DM8 sing 122 n n C5 C17 DM8 sing 123 n n C5 O5 DM8 doub 124 n n C6 C17 DM8 doub 125 n y C6 C20 DM8 sing 126 n y C6 O6 DM8 sing 127 n n C7 C8 DM8 sing 128 n n C7 C20 DM8 sing 129 n n C7 O7 DM8 sing 130 n n C7 H7 DM8 sing 131 n n C8 C9 DM8 sing 132 n n C8 H81 DM8 sing 133 n n C8 H82 DM8 sing 134 n n C9 C10 DM8 sing 135 n n C9 C13 DM8 sing 136 n n C9 O9 DM8 sing 137 n n C10 C19 DM8 sing 138 n n C10 H101 DM8 sing 139 n n C10 H102 DM8 sing 140 n n C11 C18 DM8 doub 141 n y C11 C19 DM8 sing 142 n y C11 O11 DM8 sing 143 n n C12 C15 DM8 sing 144 n n C12 C18 DM8 sing 145 n n C12 O12 DM8 doub 146 n n C13 C14 DM8 sing 147 n n C13 O13 DM8 doub 148 n n C14 H141 DM8 sing 149 n n C14 H142 DM8 sing 150 n n C14 H143 DM8 sing 151 n n C15 C16 DM8 doub 152 n y C17 C18 DM8 sing 153 n y C19 C20 DM8 doub 154 n y C21 O4 DM8 sing 155 n n C21 H211 DM8 sing 156 n n C21 H212 DM8 sing 157 n n C21 H213 DM8 sing 158 n n O6 H6 DM8 sing 159 n n O7 C1' DM8 sing 160 n n O9 H9 DM8 sing 161 n n O11 H11 DM8 sing 162 n n C1' C2' DM8 sing 163 n n C1' O5' DM8 sing 164 n n C1' H1' DM8 sing 165 n n C2' C3' DM8 sing 166 n n C2' BR DM8 sing 167 n n C2' H2' DM8 sing 168 n n C3' C4' DM8 sing 169 n n C3' N3' DM8 sing 170 n n C3' H3' DM8 sing 171 n n C4' C5' DM8 sing 172 n n C4' O4' DM8 sing 173 n n C4' H4' DM8 sing 174 n n C5' C6' DM8 sing 175 n n C5' O5' DM8 sing 176 n n C5' H5' DM8 sing 177 n n C6' "H6'1" DM8 sing 178 n n C6' "H6'2" DM8 sing 179 n n C6' "H6'3" DM8 sing 180 n n O4' HO4' DM8 sing 181 n n N3' "HN'1" DM8 sing 182 n n N3' "HN'2" DM8 sing 183 n n # _atom_sites.entry_id 288D _atom_sites.fract_transf_matrix[1][1] 0.035661 _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] 0.035661 _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] 0.01874 _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 DM8 A 1 7 7 DM8 DM8 . 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 . C 3 HOH A 26 33 33 HOH HOH . C 3 HOH A 27 34 34 HOH HOH . C 3 HOH A 28 35 35 HOH HOH . C 3 HOH A 29 36 36 HOH HOH . C 3 HOH A 30 37 37 HOH HOH . C 3 HOH A 31 38 38 HOH HOH . C 3 HOH A 32 39 39 HOH HOH . C 3 HOH A 33 40 40 HOH HOH . C 3 HOH A 34 41 41 HOH HOH . C 3 HOH A 35 42 42 HOH HOH . C 3 HOH A 36 43 43 HOH HOH . C 3 HOH A 37 44 44 HOH HOH . C 3 HOH A 38 45 45 HOH HOH . C 3 HOH A 39 46 46 HOH HOH . C 3 HOH A 40 47 47 HOH HOH . C 3 HOH A 41 48 48 HOH HOH . C 3 HOH A 42 49 49 HOH HOH . C 3 HOH A 43 50 50 HOH HOH . C 3 HOH A 44 51 51 HOH HOH . C 3 HOH A 45 52 52 HOH HOH . C 3 HOH A 46 53 53 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 DM8 . . . B 2 15.274 18.233 5.16 1 17.12 ? C1 DM8 7 A 1 HETATM 2 C C2 DM8 . . . B 2 16.433 18.99 5.192 1 17.48 ? C2 DM8 7 A 1 HETATM 3 C C3 DM8 . . . B 2 17.77 18.382 5.139 1 17.54 ? C3 DM8 7 A 1 HETATM 4 C C4 DM8 . . . B 2 17.843 16.929 5.032 1 17.31 ? C4 DM8 7 A 1 HETATM 5 C C5 DM8 . . . B 2 16.674 14.73 4.915 1 16.57 ? C5 DM8 7 A 1 HETATM 6 C C6 DM8 . . . B 2 15.426 12.608 4.888 1 16.56 ? C6 DM8 7 A 1 HETATM 7 C C7 DM8 . . . B 2 14.139 10.412 4.808 1 17.93 ? C7 DM8 7 A 1 HETATM 8 C C8 DM8 . . . B 2 12.801 9.789 4.728 1 17.79 ? C8 DM8 7 A 1 HETATM 9 C C9 DM8 . . . B 2 11.663 10.538 5.336 1 17.98 ? C9 DM8 7 A 1 HETATM 10 C C10 DM8 . . . B 2 11.604 12.036 4.877 1 17.21 ? C10 DM8 7 A 1 HETATM 11 C C11 DM8 . . . B 2 12.975 14.015 4.941 1 16.48 ? C11 DM8 7 A 1 HETATM 12 C C12 DM8 . . . B 2 14.125 16.183 5.059 1 16.38 ? C12 DM8 7 A 1 HETATM 13 C C13 DM8 . . . B 2 10.342 9.899 4.963 1 18.43 ? C13 DM8 7 A 1 HETATM 14 C C14 DM8 . . . B 2 10.005 8.931 5.801 1 18.72 ? C14 DM8 7 A 1 HETATM 15 C C15 DM8 . . . B 2 15.409 16.834 5.075 1 16.74 ? C15 DM8 7 A 1 HETATM 16 C C16 DM8 . . . B 2 16.626 16.234 5 1 16.95 ? C16 DM8 7 A 1 HETATM 17 C C17 DM8 . . . B 2 15.398 14.004 4.947 1 16.47 ? C17 DM8 7 A 1 HETATM 18 C C18 DM8 . . . B 2 14.122 14.753 4.963 1 16.23 ? C18 DM8 7 A 1 HETATM 19 C C19 DM8 . . . B 2 12.913 12.616 4.899 1 16.77 ? C19 DM8 7 A 1 HETATM 20 C C20 DM8 . . . B 2 14.147 11.988 4.851 1 16.97 ? C20 DM8 7 A 1 HETATM 21 C C21 DM8 . . . B 2 20.319 16.808 5.011 1 17.97 ? C21 DM8 7 A 1 HETATM 22 O O4 DM8 . . . B 2 19.021 16.304 4.995 1 17.73 ? O4 DM8 7 A 1 HETATM 23 O O5 DM8 . . . B 2 17.711 14.049 4.856 1 16.99 ? O5 DM8 7 A 1 HETATM 24 O O6 DM8 . . . B 2 16.522 11.918 4.845 1 16.77 ? O6 DM8 7 A 1 HETATM 25 O O7 DM8 . . . B 2 14.812 10.154 6.083 1 19.44 ? O7 DM8 7 A 1 HETATM 26 O O9 DM8 . . . B 2 11.685 10.527 6.814 1 17.9 ? O9 DM8 7 A 1 HETATM 27 O O11 DM8 . . . B 2 11.778 14.756 5 1 16.87 ? O11 DM8 7 A 1 HETATM 28 O O12 DM8 . . . B 2 13.09 16.892 5.08 1 16.78 ? O12 DM8 7 A 1 HETATM 29 O O13 DM8 . . . B 2 9.358 10.261 3.922 1 20.1 ? O13 DM8 7 A 1 HETATM 30 C C1' DM8 . . . B 2 15.734 9.125 6.217 1 21.67 ? C1' DM8 7 A 1 HETATM 31 C C2' DM8 . . . B 2 16.374 9.178 7.631 1 22.22 ? C2' DM8 7 A 1 HETATM 32 C C3' DM8 . . . B 2 15.317 8.898 8.65 1 22.86 ? C3' DM8 7 A 1 HETATM 33 C C4' DM8 . . . B 2 14.669 7.49 8.437 1 22.5 ? C4' DM8 7 A 1 HETATM 34 C C5' DM8 . . . B 2 13.895 7.563 7.065 1 22.39 ? C5' DM8 7 A 1 HETATM 35 C C6' DM8 . . . B 2 13.306 6.228 6.622 1 22.38 ? C6' DM8 7 A 1 HETATM 36 O O5' DM8 . . . B 2 14.958 7.857 6.03 1 21.87 ? O5' DM8 7 A 1 HETATM 37 O O4' DM8 . . . B 2 13.738 7.215 9.515 1 22.88 ? O4' DM8 7 A 1 HETATM 38 N N3' DM8 . . . B 2 15.872 8.945 10.107 1 22.68 ? N3' DM8 7 A 1 HETATM 39 BR BR DM8 . . . B 2 17.849 8.11 7.61 1 25.34 ? BR DM8 7 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #