data_1D33 # _model_server_result.job_id zLnZ9y-oKNFv--zMo5f6fQ _model_server_result.datetime_utc '2024-10-18 13:21:55' _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 1d33 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 1D33 # _exptl.entry_id 1D33 _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 1D33 _cell.length_a 27.943 _cell.length_b 27.943 _cell.length_c 52.243 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D33 _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 PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_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 27.943 27.943 26.1215 # _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? covale ? covale2 A O3' G49 4 A G49 4 1_555 A P DC 5 A DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.633 ? covale ? covale3 A CM2 G49 4 A G49 4 1_555 B N3' DM1 . A DM1 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.532 ? 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 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 75 n y C1 C20 DM1 sing 76 n y C1 H1 DM1 sing 77 n n C2 C3 DM1 sing 78 n y C2 H2 DM1 sing 79 n n C3 C4 DM1 doub 80 n y C3 H3 DM1 sing 81 n n C4 O4 DM1 sing 82 n n C4 C5 DM1 sing 83 n y O4 C21 DM1 sing 84 n n C5 C6 DM1 sing 85 n n C5 C20 DM1 doub 86 n y C6 O6 DM1 doub 87 n n C6 C7 DM1 sing 88 n n C7 C8 DM1 doub 89 n y C7 C18 DM1 sing 90 n y C8 O8 DM1 sing 91 n n C8 C9 DM1 sing 92 n y O8 HO8 DM1 sing 93 n n C9 C10 DM1 sing 94 n n C9 C16 DM1 doub 95 n y C10 O10 DM1 sing 96 n n C10 C11 DM1 sing 97 n n C10 H10 DM1 sing 98 n n O10 C1' DM1 sing 99 n n C11 C12 DM1 sing 100 n n C11 H111 DM1 sing 101 n n C11 H112 DM1 sing 102 n n C12 O12 DM1 sing 103 n n C12 C13 DM1 sing 104 n n C12 C15 DM1 sing 105 n n O12 HO12 DM1 sing 106 n n C13 O13 DM1 doub 107 n n C13 C14 DM1 sing 108 n n C14 H141 DM1 sing 109 n n C14 H142 DM1 sing 110 n n C14 H143 DM1 sing 111 n n C15 C16 DM1 sing 112 n n C15 H151 DM1 sing 113 n n C15 H152 DM1 sing 114 n n C16 C17 DM1 sing 115 n y C17 O17 DM1 sing 116 n n C17 C18 DM1 doub 117 n y O17 HO17 DM1 sing 118 n n C18 C19 DM1 sing 119 n n C19 O19 DM1 doub 120 n n C19 C20 DM1 sing 121 n n C21 H211 DM1 sing 122 n n C21 H212 DM1 sing 123 n n C21 H213 DM1 sing 124 n n C1' C2' DM1 sing 125 n n C1' O5' DM1 sing 126 n n C1' H1' DM1 sing 127 n n C2' C3' DM1 sing 128 n n C2' "H2'1" DM1 sing 129 n n C2' "H2'2" DM1 sing 130 n n C3' N3' DM1 sing 131 n n C3' C4' DM1 sing 132 n n C3' H3' DM1 sing 133 n n N3' "HN'1" DM1 sing 134 n n N3' "HN'2" DM1 sing 135 n n C4' O4' DM1 sing 136 n n C4' C5' DM1 sing 137 n n C4' H4' DM1 sing 138 n n O4' HO4' DM1 sing 139 n n C5' O5' DM1 sing 140 n n C5' C6' DM1 sing 141 n n C5' H5' DM1 sing 142 n n C6' "H6'1" DM1 sing 143 n n C6' "H6'2" DM1 sing 144 n n C6' "H6'3" DM1 sing 145 n n # _atom_sites.entry_id 1D33 _atom_sites.fract_transf_matrix[1][1] 0.035787 _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] 0.035787 _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] 0.019141 _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 4 DM1 DM1 . C 3 MG A 1 8 8 MG MG . 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 . # 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 15.263 18.283 5.005 1 9.43 ? C1 DM1 7 A 1 HETATM 2 C C2 DM1 . . . B 2 16.419 19.018 5.052 1 9.78 ? C2 DM1 7 A 1 HETATM 3 C C3 DM1 . . . B 2 17.747 18.367 5.057 1 10.12 ? C3 DM1 7 A 1 HETATM 4 C C4 DM1 . . . B 2 17.786 16.911 5.015 1 9.62 ? C4 DM1 7 A 1 HETATM 5 O O4 DM1 . . . B 2 18.87 16.174 4.979 1 10.17 ? O4 DM1 7 A 1 HETATM 6 C C5 DM1 . . . B 2 16.512 16.263 4.979 1 9.33 ? C5 DM1 7 A 1 HETATM 7 C C6 DM1 . . . B 2 16.537 14.768 4.916 1 8.69 ? C6 DM1 7 A 1 HETATM 8 O O6 DM1 . . . B 2 17.532 14.039 4.895 1 9.32 ? O6 DM1 7 A 1 HETATM 9 C C7 DM1 . . . B 2 15.243 14.069 4.911 1 8.47 ? C7 DM1 7 A 1 HETATM 10 C C8 DM1 . . . B 2 15.26 12.681 4.885 1 8.31 ? C8 DM1 7 A 1 HETATM 11 O O8 DM1 . . . B 2 16.35 11.921 4.906 1 8.57 ? O8 DM1 7 A 1 HETATM 12 C C9 DM1 . . . B 2 14.022 12.016 4.827 1 8.52 ? C9 DM1 7 A 1 HETATM 13 C C10 DM1 . . . B 2 14.067 10.442 4.869 1 9.15 ? C10 DM1 7 A 1 HETATM 14 O O10 DM1 . . . B 2 14.681 10.23 6.217 1 9.85 ? O10 DM1 7 A 1 HETATM 15 C C11 DM1 . . . B 2 12.731 9.822 4.744 1 9.39 ? C11 DM1 7 A 1 HETATM 16 C C12 DM1 . . . B 2 11.56 10.565 5.303 1 9.58 ? C12 DM1 7 A 1 HETATM 17 O O12 DM1 . . . B 2 11.644 10.655 6.776 1 9.84 ? O12 DM1 7 A 1 HETATM 18 C C13 DM1 . . . B 2 10.247 9.864 5.068 1 9.92 ? C13 DM1 7 A 1 HETATM 19 O O13 DM1 . . . B 2 9.649 10.141 4.023 1 11.07 ? O13 DM1 7 A 1 HETATM 20 C C14 DM1 . . . B 2 9.598 8.858 6.045 1 10.53 ? C14 DM1 7 A 1 HETATM 21 C C15 DM1 . . . B 2 11.462 12.044 4.796 1 9.05 ? C15 DM1 7 A 1 HETATM 22 C C16 DM1 . . . B 2 12.778 12.65 4.832 1 8.51 ? C16 DM1 7 A 1 HETATM 23 C C17 DM1 . . . B 2 12.812 14.067 4.848 1 8.16 ? C17 DM1 7 A 1 HETATM 24 O O17 DM1 . . . B 2 11.636 14.782 4.812 1 8.52 ? O17 DM1 7 A 1 HETATM 25 C C18 DM1 . . . B 2 13.96 14.838 4.895 1 8.4 ? C18 DM1 7 A 1 HETATM 26 C C19 DM1 . . . B 2 13.994 16.288 4.921 1 8.59 ? C19 DM1 7 A 1 HETATM 27 O O19 DM1 . . . B 2 12.994 17.006 4.911 1 9.07 ? O19 DM1 7 A 1 HETATM 28 C C20 DM1 . . . B 2 15.304 16.9 4.953 1 8.93 ? C20 DM1 7 A 1 HETATM 29 C C21 DM1 . . . B 2 20.214 16.819 5.141 1 10.64 ? C21 DM1 7 A 1 HETATM 30 C C1' DM1 . . . B 2 15.654 9.249 6.405 1 10.2 ? C1' DM1 7 A 1 HETATM 31 C C2' DM1 . . . B 2 16.674 9.615 7.45 1 10.21 ? C2' DM1 7 A 1 HETATM 32 C C3' DM1 . . . B 2 15.981 9.777 8.813 1 10.49 ? C3' DM1 7 A 1 HETATM 33 N N3' DM1 . . . B 2 17.093 10.034 9.848 1 10.43 ? N3' DM1 7 A 1 HETATM 34 C C4' DM1 . . . B 2 15.196 8.489 9.132 1 10.65 ? C4' DM1 7 A 1 HETATM 35 O O4' DM1 . . . B 2 16.176 7.399 9.284 1 11.32 ? O4' DM1 7 A 1 HETATM 36 C C5' DM1 . . . B 2 14.139 8.257 8.066 1 10.59 ? C5' DM1 7 A 1 HETATM 37 O O5' DM1 . . . B 2 14.922 7.995 6.765 1 10.38 ? O5' DM1 7 A 1 HETATM 38 C C6' DM1 . . . B 2 13.301 6.975 8.166 1 10.62 ? C6' DM1 7 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 38 #