data_5YUN # _model_server_result.job_id m311hAhkZI6a2aBOBrmpfA _model_server_result.datetime_utc '2024-11-22 14:29:01' _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":"F","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 . . . F 2 -18.696 3.548 8.266 1 114.27 ? C1 MYC 201 D 1 HETATM 2 C C2 MYC . . . F 2 -18.69 3.782 6.909 1 112.53 ? C2 MYC 201 D 1 HETATM 3 C C3 MYC . . . F 2 -18.147 5.062 6.387 1 118.22 ? C3 MYC 201 D 1 HETATM 4 C C4 MYC . . . F 2 -17.639 6.06 7.34 1 127.48 ? C4 MYC 201 D 1 HETATM 5 C C5 MYC . . . F 2 -17.7 5.73 8.69 1 131.36 ? C5 MYC 201 D 1 HETATM 6 C C6 MYC . . . F 2 -18.208 4.506 9.14 1 123.44 ? C6 MYC 201 D 1 HETATM 7 C C9 MYC . . . F 2 -18.116 5.387 4.959 1 105.02 ? C9 MYC 201 D 1 HETATM 8 C C10 MYC . . . F 2 -17.571 6.698 4.568 1 102.88 ? C10 MYC 201 D 1 HETATM 9 C C11 MYC . . . F 2 -17.074 7.645 5.603 1 114.05 ? C11 MYC 201 D 1 HETATM 10 C C14 MYC . . . F 2 -16.521 8.993 5.236 1 113.79 ? C14 MYC 201 D 1 HETATM 11 C C15 MYC . . . F 2 -16.263 9.927 6.238 1 111.57 ? C15 MYC 201 D 1 HETATM 12 C C16 MYC . . . F 2 -15.755 11.201 5.955 1 114.35 ? C16 MYC 201 D 1 HETATM 13 C C17 MYC . . . F 2 -15.481 11.571 4.532 1 107.88 ? C17 MYC 201 D 1 HETATM 14 C C18 MYC . . . F 2 -15.775 10.548 3.505 1 106.22 ? C18 MYC 201 D 1 HETATM 15 C C19 MYC . . . F 2 -16.282 9.323 3.904 1 107.14 ? C19 MYC 201 D 1 HETATM 16 O O12 MYC . . . F 2 -17.137 7.268 6.921 1 119.58 ? O12 MYC 201 D 1 HETATM 17 O O13 MYC . . . F 2 -18.541 4.576 4.136 1 95.63 ? O13 MYC 201 D 1 HETATM 18 O O23 MYC . . . F 2 -15.553 10.784 2.191 1 89.68 ? O23 MYC 201 D 1 HETATM 19 O O24 MYC . . . F 2 -14.992 12.787 4.173 1 80.26 ? O24 MYC 201 D 1 HETATM 20 O O25 MYC . . . F 2 -15.523 12.085 6.971 1 98.19 ? O25 MYC 201 D 1 HETATM 21 O O27 MYC . . . F 2 -17.533 7.019 3.266 1 89.67 ? O27 MYC 201 D 1 HETATM 22 O O29 MYC . . . F 2 -18.225 4.247 10.474 1 118.88 ? O29 MYC 201 D 1 HETATM 23 O O30 MYC . . . F 2 -19.177 2.846 6.077 1 102.53 ? O30 MYC 201 D 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #