data_1DNE # _model_server_result.job_id 8Rh8bUoVJlKRFM4QzNQDWg _model_server_result.datetime_utc '2025-03-01 10:33:23' _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 1dne # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":25}' # _entry.id 1DNE # _exptl.entry_id 1DNE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 430.464 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NETROPSIN _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 1DNE _cell.length_a 25.48 _cell.length_b 41.26 _cell.length_c 66.88 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DNE _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _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 B N1 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DA 5 A DA 5 1_555 B N3 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 DA 5 A DA 5 1_555 B O4 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N3 DT 6 A DT 6 1_555 B N1 DA 7 B DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O4 DT 6 A DT 6 1_555 B N6 DA 7 B DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 DA 7 A DA 7 1_555 B N3 DT 6 B DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N6 DA 7 A DA 7 1_555 B O4 DT 6 B DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N3 DT 8 A DT 8 1_555 B N1 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O4 DT 8 A DT 8 1_555 B N6 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N3 DC 9 A DC 9 1_555 B N1 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N4 DC 9 A DC 9 1_555 B O6 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O2 DC 9 A DC 9 1_555 B N2 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N1 DG 10 A DG 10 1_555 B N3 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N2 DG 10 A DG 10 1_555 B O2 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O6 DG 10 A DG 10 1_555 B N4 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N3 DC 11 A DC 11 1_555 B N1 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N4 DC 11 A DC 11 1_555 B O6 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A O2 DC 11 A DC 11 1_555 B N2 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N1 DG 12 A DG 12 1_555 B N3 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N2 DG 12 A DG 12 1_555 B O2 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A O6 DG 12 A DG 12 1_555 B N4 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C18 H26 N10 O3' _chem_comp.formula_weight 430.464 _chem_comp.id NT _chem_comp.mon_nstd_flag . _chem_comp.name NETROPSIN _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 N1 NT doub 152 n n C1 N2 NT sing 153 n n C1 N3 NT sing 154 n n N1 HN1 NT sing 155 n n N2 HN21 NT sing 156 n n N2 HN22 NT sing 157 n n N3 C2 NT sing 158 n n N3 HN3 NT sing 159 n n C2 C3 NT sing 160 n n C2 H21 NT sing 161 n n C2 H22 NT sing 162 n n C3 O1 NT doub 163 n n C3 N4 NT sing 164 n n N4 C4 NT sing 165 n n N4 HN4 NT sing 166 n n C4 C5 NT sing 167 n y C4 C7 NT doub 168 n y C5 C6 NT doub 169 n y C5 H5 NT sing 170 n n C6 N5 NT sing 171 n y C6 C9 NT sing 172 n n N5 C8 NT sing 173 n n N5 C7 NT sing 174 n y C8 H81 NT sing 175 n n C8 H82 NT sing 176 n n C8 H83 NT sing 177 n n C7 H7 NT sing 178 n n C9 O2 NT doub 179 n n C9 N6 NT sing 180 n n N6 C10 NT sing 181 n n N6 HN6 NT sing 182 n n C10 C11 NT sing 183 n y C10 C13 NT doub 184 n y C11 C12 NT doub 185 n y C11 H11 NT sing 186 n n C12 N7 NT sing 187 n y C12 C15 NT sing 188 n n N7 C14 NT sing 189 n n N7 C13 NT sing 190 n y C14 H141 NT sing 191 n n C14 H142 NT sing 192 n n C14 H143 NT sing 193 n n C13 H13 NT sing 194 n n C15 O3 NT doub 195 n n C15 N8 NT sing 196 n n N8 C16 NT sing 197 n n N8 HN8 NT sing 198 n n C16 C17 NT sing 199 n n C16 H161 NT sing 200 n n C16 H162 NT sing 201 n n C17 C18 NT sing 202 n n C17 H171 NT sing 203 n n C17 H172 NT sing 204 n n C18 N9 NT doub 205 n n C18 N10 NT sing 206 n n N9 HN9 NT sing 207 n n N10 HN01 NT sing 208 n n N10 HN02 NT sing 209 n n # _atom_sites.entry_id 1DNE _atom_sites.fract_transf_matrix[1][1] 0.039246 _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] 0.024237 _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] 0.014952 _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 C 2 NT A 1 25 25 NT NT . D 3 HOH A 1 29 29 HOH HOH . D 3 HOH A 2 30 30 HOH HOH . D 3 HOH A 3 33 33 HOH HOH . D 3 HOH A 4 36 36 HOH HOH . D 3 HOH A 5 37 37 HOH HOH . D 3 HOH A 6 40 40 HOH HOH . D 3 HOH A 7 42 42 HOH HOH . D 3 HOH A 8 45 45 HOH HOH . D 3 HOH A 9 46 46 HOH HOH . D 3 HOH A 10 47 47 HOH HOH . D 3 HOH A 11 48 48 HOH HOH . D 3 HOH A 12 49 49 HOH HOH . D 3 HOH A 13 50 50 HOH HOH . D 3 HOH A 14 52 52 HOH HOH . D 3 HOH A 15 53 53 HOH HOH . D 3 HOH A 16 57 57 HOH HOH . D 3 HOH A 17 60 60 HOH HOH . D 3 HOH A 18 61 61 HOH HOH . D 3 HOH A 19 62 62 HOH HOH . D 3 HOH A 20 63 63 HOH HOH . D 3 HOH A 21 65 65 HOH HOH . D 3 HOH A 22 66 66 HOH HOH . D 3 HOH A 23 69 69 HOH HOH . D 3 HOH A 24 77 77 HOH HOH . D 3 HOH A 25 82 82 HOH HOH . D 3 HOH A 26 83 83 HOH HOH . D 3 HOH A 27 85 85 HOH HOH . E 3 HOH B 1 26 26 HOH HOH . E 3 HOH B 2 27 27 HOH HOH . E 3 HOH B 3 28 28 HOH HOH . E 3 HOH B 4 31 31 HOH HOH . E 3 HOH B 5 32 32 HOH HOH . E 3 HOH B 6 34 34 HOH HOH . E 3 HOH B 7 35 35 HOH HOH . E 3 HOH B 8 38 38 HOH HOH . E 3 HOH B 9 39 39 HOH HOH . E 3 HOH B 10 41 41 HOH HOH . E 3 HOH B 11 43 43 HOH HOH . E 3 HOH B 12 44 44 HOH HOH . E 3 HOH B 13 51 51 HOH HOH . E 3 HOH B 14 54 54 HOH HOH . E 3 HOH B 15 55 55 HOH HOH . E 3 HOH B 16 56 56 HOH HOH . E 3 HOH B 17 58 58 HOH HOH . E 3 HOH B 18 59 59 HOH HOH . E 3 HOH B 19 64 64 HOH HOH . E 3 HOH B 20 67 67 HOH HOH . E 3 HOH B 21 68 68 HOH HOH . E 3 HOH B 22 70 70 HOH HOH . E 3 HOH B 23 71 71 HOH HOH . E 3 HOH B 24 72 72 HOH HOH . E 3 HOH B 25 73 73 HOH HOH . E 3 HOH B 26 74 74 HOH HOH . E 3 HOH B 27 75 75 HOH HOH . E 3 HOH B 28 76 76 HOH HOH . E 3 HOH B 29 78 78 HOH HOH . E 3 HOH B 30 79 79 HOH HOH . E 3 HOH B 31 80 80 HOH HOH . E 3 HOH B 32 81 81 HOH HOH . E 3 HOH B 33 84 84 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 NT . . . C 2 12.778 25.09 69.997 1 45.36 ? C1 NT 25 A 1 HETATM 2 N N1 NT . . . C 2 12.564 23.865 69.582 1 45.24 ? N1 NT 25 A 1 HETATM 3 N N2 NT . . . C 2 13.724 25.87 69.495 1 45.24 ? N2 NT 25 A 1 HETATM 4 N N3 NT . . . C 2 11.932 25.495 70.926 1 45.27 ? N3 NT 25 A 1 HETATM 5 C C2 NT . . . C 2 11.942 26.559 71.802 1 45.21 ? C2 NT 25 A 1 HETATM 6 C C3 NT . . . C 2 10.694 26.076 72.652 1 44.68 ? C3 NT 25 A 1 HETATM 7 O O1 NT . . . C 2 9.764 26.699 72.217 1 45.12 ? O1 NT 25 A 1 HETATM 8 N N4 NT . . . C 2 10.763 24.979 73.3 1 44.43 ? N4 NT 25 A 1 HETATM 9 C C4 NT . . . C 2 9.797 24.401 74.177 1 44.76 ? C4 NT 25 A 1 HETATM 10 C C5 NT . . . C 2 10.169 23.638 75.26 1 44.77 ? C5 NT 25 A 1 HETATM 11 C C6 NT . . . C 2 9.058 23.32 75.956 1 44.92 ? C6 NT 25 A 1 HETATM 12 N N5 NT . . . C 2 7.991 23.902 75.327 1 44.59 ? N5 NT 25 A 1 HETATM 13 C C8 NT . . . C 2 6.546 23.869 75.661 1 44.05 ? C8 NT 25 A 1 HETATM 14 C C7 NT . . . C 2 8.464 24.62 74.25 1 44.54 ? C7 NT 25 A 1 HETATM 15 C C9 NT . . . C 2 8.757 22.437 77.093 1 45.63 ? C9 NT 25 A 1 HETATM 16 O O2 NT . . . C 2 7.555 22.157 77.313 1 46.76 ? O2 NT 25 A 1 HETATM 17 N N6 NT . . . C 2 9.698 21.901 77.868 1 46.12 ? N6 NT 25 A 1 HETATM 18 C C10 NT . . . C 2 9.308 20.948 78.918 1 45.66 ? C10 NT 25 A 1 HETATM 19 C C11 NT . . . C 2 10.189 20.461 79.908 1 45.57 ? C11 NT 25 A 1 HETATM 20 C C12 NT . . . C 2 9.491 19.561 80.697 1 45.19 ? C12 NT 25 A 1 HETATM 21 N N7 NT . . . C 2 8.199 19.491 80.122 1 45.4 ? N7 NT 25 A 1 HETATM 22 C C14 NT . . . C 2 7.071 18.674 80.537 1 45.57 ? C14 NT 25 A 1 HETATM 23 C C13 NT . . . C 2 8.118 20.316 79.072 1 45.4 ? C13 NT 25 A 1 HETATM 24 C C15 NT . . . C 2 9.843 18.641 81.727 1 45.1 ? C15 NT 25 A 1 HETATM 25 O O3 NT . . . C 2 9.053 17.837 82.249 1 45.22 ? O3 NT 25 A 1 HETATM 26 N N8 NT . . . C 2 11.191 18.352 81.915 1 45.14 ? N8 NT 25 A 1 HETATM 27 C C16 NT . . . C 2 11.39 17.251 82.965 1 44.89 ? C16 NT 25 A 1 HETATM 28 C C17 NT . . . C 2 12.707 17.156 83.587 1 44.97 ? C17 NT 25 A 1 HETATM 29 C C18 NT . . . C 2 12.822 16.987 85.085 1 45.07 ? C18 NT 25 A 1 HETATM 30 N N9 NT . . . C 2 11.79 17.016 85.907 1 44.82 ? N9 NT 25 A 1 HETATM 31 N N10 NT . . . C 2 14.011 16.822 85.653 1 45.21 ? N10 NT 25 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #