data_5YUN # _model_server_result.job_id 7KtQ7hNIa3c8cb9A5QLSqw _model_server_result.datetime_utc '2024-11-22 14:28:05' _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 5yun # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5YUN # _exptl.entry_id 5YUN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 318.235 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 5YUN _cell.length_a 60.11 _cell.length_b 60.11 _cell.length_c 130.868 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YUN _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,E,F,G,H,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N # _chem_comp.formula 'C15 H10 O8' _chem_comp.formula_weight 318.235 _chem_comp.id MYC _chem_comp.mon_nstd_flag . _chem_comp.name 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE;3,3',4',5,5',7-HEXAHYDROXYFLAVONE;MYRICETIN;CANNABISCETIN" # 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 MYC doub 224 n y C1 C6 MYC sing 225 n y C1 H1 MYC sing 226 n n C2 C3 MYC sing 227 n y C2 O30 MYC sing 228 n n C3 C4 MYC doub 229 n y C3 C9 MYC sing 230 n y C4 C5 MYC sing 231 n y C4 O12 MYC sing 232 n y C5 C6 MYC doub 233 n y C5 H5 MYC sing 234 n n C6 O29 MYC sing 235 n n C9 C10 MYC sing 236 n y C9 O13 MYC doub 237 n n C10 C11 MYC doub 238 n y C10 O27 MYC sing 239 n n C11 C14 MYC sing 240 n y C11 O12 MYC sing 241 n y C14 C15 MYC doub 242 n y C14 C19 MYC sing 243 n y C15 C16 MYC sing 244 n y C15 H15 MYC sing 245 n n C16 C17 MYC doub 246 n y C16 O25 MYC sing 247 n n C17 C18 MYC sing 248 n y C17 O24 MYC sing 249 n n C18 C19 MYC doub 250 n y C18 O23 MYC sing 251 n n C19 H19 MYC sing 252 n n O23 HO3 MYC sing 253 n n O24 HO4 MYC sing 254 n n O25 HO5 MYC sing 255 n n O27 HO7 MYC sing 256 n n O29 HO9 MYC sing 257 n n O30 HO0 MYC sing 258 n n # _atom_sites.entry_id 5YUN _atom_sites.fract_transf_matrix[1][1] 0.016636 _atom_sites.fract_transf_matrix[1][2] 0.009605 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01921 _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] 0.007641 _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 E 2 MYC B 1 201 2 MYC MYC . F 2 MYC D 1 201 1 MYC MYC . G 3 HOH A 1 201 45 HOH HOH . G 3 HOH A 2 202 31 HOH HOH . G 3 HOH A 3 203 1 HOH HOH . G 3 HOH A 4 204 4 HOH HOH . G 3 HOH A 5 205 38 HOH HOH . G 3 HOH A 6 206 32 HOH HOH . G 3 HOH A 7 207 30 HOH HOH . G 3 HOH A 8 208 40 HOH HOH . G 3 HOH A 9 209 17 HOH HOH . G 3 HOH A 10 210 42 HOH HOH . H 3 HOH B 1 301 46 HOH HOH . H 3 HOH B 2 302 3 HOH HOH . H 3 HOH B 3 303 15 HOH HOH . H 3 HOH B 4 304 29 HOH HOH . H 3 HOH B 5 305 37 HOH HOH . I 3 HOH C 1 201 16 HOH HOH . J 3 HOH D 1 301 13 HOH HOH . J 3 HOH D 2 302 27 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 MYC . . . E 2 -24.282 -2.687 -14.535 1 150.09 ? C1 MYC 201 B 1 HETATM 2 C C2 MYC . . . E 2 -24.269 -1.307 -14.4 1 150.44 ? C2 MYC 201 B 1 HETATM 3 C C3 MYC . . . E 2 -24.498 -0.492 -15.599 1 154.67 ? C3 MYC 201 B 1 HETATM 4 C C4 MYC . . . E 2 -24.728 -1.169 -16.889 1 166.43 ? C4 MYC 201 B 1 HETATM 5 C C5 MYC . . . E 2 -24.718 -2.543 -16.918 1 156.28 ? C5 MYC 201 B 1 HETATM 6 C C6 MYC . . . E 2 -24.503 -3.286 -15.78 1 149.38 ? C6 MYC 201 B 1 HETATM 7 C C9 MYC . . . E 2 -24.502 0.977 -15.535 1 146.71 ? C9 MYC 201 B 1 HETATM 8 C C10 MYC . . . E 2 -24.744 1.692 -16.804 1 150.52 ? C10 MYC 201 B 1 HETATM 9 C C11 MYC . . . E 2 -24.952 0.905 -18.05 1 164.09 ? C11 MYC 201 B 1 HETATM 10 C C14 MYC . . . E 2 -25.213 1.576 -19.34 1 157.1 ? C14 MYC 201 B 1 HETATM 11 C C15 MYC . . . E 2 -26.217 1.038 -20.136 1 146.67 ? C15 MYC 201 B 1 HETATM 12 C C16 MYC . . . E 2 -26.55 1.586 -21.359 1 136.21 ? C16 MYC 201 B 1 HETATM 13 C C17 MYC . . . E 2 -25.814 2.776 -21.804 1 135.16 ? C17 MYC 201 B 1 HETATM 14 C C18 MYC . . . E 2 -24.752 3.321 -20.913 1 135.59 ? C18 MYC 201 B 1 HETATM 15 C C19 MYC . . . E 2 -24.488 2.693 -19.711 1 144.34 ? C19 MYC 201 B 1 HETATM 16 O O12 MYC . . . E 2 -24.95 -0.465 -18.045 1 174.6 ? O12 MYC 201 B 1 HETATM 17 O O13 MYC . . . E 2 -24.305 1.556 -14.456 1 128.62 ? O13 MYC 201 B 1 HETATM 18 O O23 MYC . . . E 2 -24.021 4.413 -21.246 1 119.83 ? O23 MYC 201 B 1 HETATM 19 O O24 MYC . . . E 2 -26.134 3.319 -23.011 1 137.4 ? O24 MYC 201 B 1 HETATM 20 O O25 MYC . . . E 2 -27.528 1.047 -22.133 1 122.03 ? O25 MYC 201 B 1 HETATM 21 O O27 MYC . . . E 2 -24.763 3.039 -16.845 1 143.56 ? O27 MYC 201 B 1 HETATM 22 O O29 MYC . . . E 2 -24.51 -4.635 -15.937 1 135.8 ? O29 MYC 201 B 1 HETATM 23 O O30 MYC . . . E 2 -24.05 -0.686 -13.216 1 134.87 ? O30 MYC 201 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #