data_1AGL # _model_server_result.job_id 3G0iV5Qjiqvqcsuvgq0p8A _model_server_result.datetime_utc '2024-10-18 16:22:48' _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 1agl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 1AGL # _exptl.entry_id 1AGL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 1159.189 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-METHYLBENZYL-N-BIS[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 1AGL _cell.length_a 28.27 _cell.length_b 28.27 _cell.length_c 53.77 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1AGL _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 28.27 28.27 26.885 # _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 B C9A BDA . A BDA 7 1_555 B C9A BDA . A BDA 7 8_665 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale2 B C9B BDA . A BDA 7 1_555 B C9B BDA . A BDA 7 8_665 ? ? ? ? ? ? ? ? ? ? ? ? 1.36 ? 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 'C62 H66 N2 O20 2' _chem_comp.formula_weight 1159.189 _chem_comp.id BDA _chem_comp.mon_nstd_flag . _chem_comp.name 4-METHYLBENZYL-N-BIS[DAUNOMYCIN] _chem_comp.type non-polymer _chem_comp.pdbx_synonyms WP631 # 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 BDA doub 1 n y C1 C20 BDA sing 2 n y C1 H1 BDA sing 3 n n C2 C3 BDA sing 4 n y C2 H2 BDA sing 5 n n C3 C4 BDA doub 6 n y C3 H3 BDA sing 7 n n C4 O4 BDA sing 8 n n C4 C5 BDA sing 9 n y O4 C21 BDA sing 10 n n C5 C6 BDA sing 11 n n C5 C20 BDA doub 12 n y C6 O6 BDA doub 13 n n C6 C7 BDA sing 14 n n C7 C8 BDA sing 15 n y C7 C18 BDA doub 16 n y C8 O8 BDA sing 17 n n C8 C9 BDA doub 18 n y O8 HO8 BDA sing 19 n n C9 C10 BDA sing 20 n n C9 C16 BDA sing 21 n y C10 O10 BDA sing 22 n n C10 C11 BDA sing 23 n n C10 H10 BDA sing 24 n n O10 C1' BDA sing 25 n n C11 C12 BDA sing 26 n n C11 H111 BDA sing 27 n n C11 H112 BDA sing 28 n n C12 O12 BDA sing 29 n n C12 C13 BDA sing 30 n n C12 C15 BDA sing 31 n n O12 H12 BDA sing 32 n n C13 O13 BDA doub 33 n n C13 C14 BDA sing 34 n n C14 H141 BDA sing 35 n n C14 H142 BDA sing 36 n n C14 H143 BDA sing 37 n n C15 C16 BDA sing 38 n n C15 H151 BDA sing 39 n n C15 H152 BDA sing 40 n n C16 C17 BDA doub 41 n y C17 O17 BDA sing 42 n n C17 C18 BDA sing 43 n y O17 H17 BDA sing 44 n n C18 C19 BDA sing 45 n n C19 O19 BDA doub 46 n n C19 C20 BDA sing 47 n n C21 H211 BDA sing 48 n n C21 H212 BDA sing 49 n n C21 H213 BDA sing 50 n n C1' C2' BDA sing 51 n n C1' O5' BDA sing 52 n n C1' H1B BDA sing 53 n n C2' C3' BDA sing 54 n n C2' "H2'1" BDA sing 55 n n C2' "H2'2" BDA sing 56 n n C3' N3' BDA sing 57 n n C3' C4' BDA sing 58 n n C3' H3B BDA sing 59 n n N3' C7' BDA sing 60 n n N3' "HN'1" BDA sing 61 n n N3' "HN'2" BDA sing 62 n n C4' O4' BDA sing 63 n n C4' C5' BDA sing 64 n n C4' H4' BDA sing 65 n n O4' HO4' BDA sing 66 n n C5' O5' BDA sing 67 n n C5' C6' BDA sing 68 n n C5' H5' BDA sing 69 n n C6' "H6'1" BDA sing 70 n n C6' "H6'2" BDA sing 71 n n C6' "H6'3" BDA sing 72 n n C7' C8' BDA sing 73 n n C7' "H7'1" BDA sing 74 n n C7' "H7'2" BDA sing 75 n n C8' C9A BDA doub 76 n y C8' C9B BDA sing 77 n y C9A C1A BDA sing 78 n y C9A H9A BDA sing 79 n n C9B C1C BDA doub 80 n y C9B H9B BDA sing 81 n n C1B C2B BDA doub 82 n y C1B CK' BDA sing 83 n y C1B H1' BDA sing 84 n n C2B C3B BDA sing 85 n y C2B H2' BDA sing 86 n n C3B C4B BDA doub 87 n y C3B H3' BDA sing 88 n n C4B O4B BDA sing 89 n n C4B C5B BDA sing 90 n y O4B CL' BDA sing 91 n n C5B C6B BDA sing 92 n n C5B CK' BDA doub 93 n y C6B O6' BDA doub 94 n n C6B C7B BDA sing 95 n n C7B C8B BDA sing 96 n y C7B CI' BDA doub 97 n y C8B O8' BDA sing 98 n n C8B C9' BDA doub 99 n y O8' HO8' BDA sing 100 n n C9' CA' BDA sing 101 n n C9' CG' BDA sing 102 n y CA' OA' BDA sing 103 n n CA' CB' BDA sing 104 n n CA' H10' BDA sing 105 n n OA' C1D BDA sing 106 n n CB' CC' BDA sing 107 n n CB' "HL'1" BDA sing 108 n n CB' "HL'2" BDA sing 109 n n CC' OC' BDA sing 110 n n CC' CD' BDA sing 111 n n CC' CF' BDA sing 112 n n OC' H12' BDA sing 113 n n CD' OD' BDA doub 114 n n CD' CE' BDA sing 115 n n CE' "HK'1" BDA sing 116 n n CE' "HK'2" BDA sing 117 n n CE' "HK'3" BDA sing 118 n n CF' CG' BDA sing 119 n n CF' "HJ'1" BDA sing 120 n n CF' "HJ'2" BDA sing 121 n n CG' CH' BDA doub 122 n y CH' OH' BDA sing 123 n n CH' CI' BDA sing 124 n y OH' H17' BDA sing 125 n n CI' CJ' BDA sing 126 n n CJ' OJ' BDA doub 127 n n CJ' CK' BDA sing 128 n n CL' "HI'1" BDA sing 129 n n CL' "HI'2" BDA sing 130 n n CL' "HI'3" BDA sing 131 n n C1D C2D BDA sing 132 n n C1D O5D BDA sing 133 n n C1D H1D BDA sing 134 n n C2D C3D BDA sing 135 n n C2D H2B BDA sing 136 n n C2D H2D BDA sing 137 n n C3D N3D BDA sing 138 n n C3D C4D BDA sing 139 n n C3D H3D BDA sing 140 n n N3D C7D BDA sing 141 n n N3D HNB BDA sing 142 n n N3D HND BDA sing 143 n n C4D O4D BDA sing 144 n n C4D C5D BDA sing 145 n n C4D H4D BDA sing 146 n n O4D HO4A BDA sing 147 n n C5D O5D BDA sing 148 n n C5D C6D BDA sing 149 n n C5D H5D BDA sing 150 n n C6D H6B BDA sing 151 n n C6D H6D BDA sing 152 n n C6D H6E BDA sing 153 n n C7D C8D BDA sing 154 n n C7D H7B BDA sing 155 n n C7D H7D BDA sing 156 n n C8D C1A BDA doub 157 n y C8D C1C BDA sing 158 n y C1A H9A' BDA sing 159 n n C1C H9B' BDA sing 160 n n # _atom_sites.entry_id 1AGL _atom_sites.fract_transf_matrix[1][1] 0.035373 _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] 0.035373 _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] 0.018598 _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 BDA A 1 7 7 BDA BDA . 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 . # 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 BDA . . . B 2 16 19.065 5.115 1 12.71 ? C1 BDA 7 A 1 HETATM 2 C C2 BDA . . . B 2 17.112 19.838 5.052 1 15.25 ? C2 BDA 7 A 1 HETATM 3 C C3 BDA . . . B 2 18.336 19.275 4.895 1 17.32 ? C3 BDA 7 A 1 HETATM 4 C C4 BDA . . . B 2 18.456 17.816 4.793 1 20.92 ? C4 BDA 7 A 1 HETATM 5 O O4 BDA . . . B 2 19.707 17.103 4.674 1 21.47 ? O4 BDA 7 A 1 HETATM 6 C C5 BDA . . . B 2 17.265 16.997 4.876 1 12.54 ? C5 BDA 7 A 1 HETATM 7 C C6 BDA . . . B 2 17.333 15.56 4.813 1 11.38 ? C6 BDA 7 A 1 HETATM 8 O O6 BDA . . . B 2 18.405 15.003 4.688 1 12.12 ? O6 BDA 7 A 1 HETATM 9 C C7 BDA . . . B 2 16.094 14.841 4.913 1 9.33 ? C7 BDA 7 A 1 HETATM 10 C C8 BDA . . . B 2 16.114 13.411 4.856 1 8.26 ? C8 BDA 7 A 1 HETATM 11 O O8 BDA . . . B 2 17.285 12.74 4.689 1 11.07 ? O8 BDA 7 A 1 HETATM 12 C C9 BDA . . . B 2 14.899 12.677 4.896 1 7.22 ? C9 BDA 7 A 1 HETATM 13 C C10 BDA . . . B 2 14.996 11.195 4.902 1 7.42 ? C10 BDA 7 A 1 HETATM 14 O O10 BDA . . . B 2 15.549 10.849 6.191 1 14.24 ? O10 BDA 7 A 1 HETATM 15 C C11 BDA . . . B 2 13.63 10.484 4.709 1 2.78 ? C11 BDA 7 A 1 HETATM 16 C C12 BDA . . . B 2 12.565 11.145 5.57 1 5.1 ? C12 BDA 7 A 1 HETATM 17 O O12 BDA . . . B 2 12.934 11.091 6.959 1 12.28 ? O12 BDA 7 A 1 HETATM 18 C C13 BDA . . . B 2 11.238 10.429 5.35 1 12.64 ? C13 BDA 7 A 1 HETATM 19 O O13 BDA . . . B 2 10.52 10.676 4.375 1 23.18 ? O13 BDA 7 A 1 HETATM 20 C C14 BDA . . . B 2 10.832 9.347 6.34 1 11.57 ? C14 BDA 7 A 1 HETATM 21 C C15 BDA . . . B 2 12.396 12.579 5.106 1 2.8 ? C15 BDA 7 A 1 HETATM 22 C C16 BDA . . . B 2 13.694 13.347 5.041 1 8.24 ? C16 BDA 7 A 1 HETATM 23 C C17 BDA . . . B 2 13.675 14.777 5.11 1 9.04 ? C17 BDA 7 A 1 HETATM 24 O O17 BDA . . . B 2 12.519 15.48 5.236 1 16.01 ? O17 BDA 7 A 1 HETATM 25 C C18 BDA . . . B 2 14.89 15.509 5.044 1 10.93 ? C18 BDA 7 A 1 HETATM 26 C C19 BDA . . . B 2 14.819 16.94 5.11 1 13.27 ? C19 BDA 7 A 1 HETATM 27 O O19 BDA . . . B 2 13.77 17.572 5.229 1 15.89 ? O19 BDA 7 A 1 HETATM 28 C C20 BDA . . . B 2 16.051 17.654 5.03 1 13.16 ? C20 BDA 7 A 1 HETATM 29 C C21 BDA . . . B 2 20.942 17.717 4.588 1 28.12 ? C21 BDA 7 A 1 HETATM 30 C C1' BDA . . . B 2 16.743 10.049 6.188 1 12.83 ? C1' BDA 7 A 1 HETATM 31 C C2' BDA . . . B 2 17.456 10.099 7.549 1 15.3 ? C2' BDA 7 A 1 HETATM 32 C C3' BDA . . . B 2 16.628 9.429 8.658 1 17.84 ? C3' BDA 7 A 1 HETATM 33 N N3' BDA . . . B 2 17.478 9.558 9.84 1 22.41 ? N3' BDA 7 A 1 HETATM 34 C C4' BDA . . . B 2 16.28 7.96 8.26 1 17.28 ? C4' BDA 7 A 1 HETATM 35 O O4' BDA . . . B 2 17.413 7.036 8.227 1 18.11 ? O4' BDA 7 A 1 HETATM 36 C C5' BDA . . . B 2 15.604 8.009 6.873 1 15.91 ? C5' BDA 7 A 1 HETATM 37 O O5' BDA . . . B 2 16.399 8.693 5.853 1 13.96 ? O5' BDA 7 A 1 HETATM 38 C C6' BDA . . . B 2 15.321 6.584 6.422 1 16.41 ? C6' BDA 7 A 1 HETATM 39 C C7' BDA . . . B 2 16.806 9.081 11.034 1 30.9 ? C7' BDA 7 A 1 HETATM 40 C C8' BDA . . . B 2 17.458 9.663 12.277 1 37.32 ? C8' BDA 7 A 1 HETATM 41 C C9A BDA . . . B 2 16.88 10.84 12.888 0.5 38.09 ? C9A BDA 7 A 1 HETATM 42 C C9B BDA . . . B 2 18.65 9.076 12.882 0.5 43.55 ? C9B BDA 7 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 42 #