data_5YGV # _model_server_result.job_id 0Kxna3m89T1_v1Tx2XJEgg _model_server_result.datetime_utc '2025-03-05 18:29:49' _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 5ygv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":300}' # _entry.id 5YGV # _exptl.entry_id 5YGV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 394.503 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2Z,4E)-3-methyl-5-[(1S,4S)-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic acid' _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 90 _cell.entry_id 5YGV _cell.length_a 38.203 _cell.length_b 38.203 _cell.length_c 263.349 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YGV _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _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,E,F _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 C N N ? 2 D N N # _chem_comp.formula 'C25 H30 O4' _chem_comp.formula_weight 394.503 _chem_comp.id 8V6 _chem_comp.mon_nstd_flag . _chem_comp.name '(2Z,4E)-3-methyl-5-[(1S,4S)-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic acid' _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 CA5 CA6 8V6 doub 1 n y CA5 CA4 8V6 sing 2 n y CA6 CA7 8V6 sing 3 n y CA1 CA2 8V6 sing 4 n n CA1 O4' 8V6 sing 5 n n CA2 CA3 8V6 trip 6 n n CA3 CA4 8V6 sing 7 n n CA4 CA9 8V6 doub 8 n y CA7 CA0 8V6 sing 9 n n CA7 CA8 8V6 doub 10 n y CA9 CA8 8V6 sing 11 n y C3' C4' 8V6 sing 12 n n C3' C2' 8V6 doub 13 n n O4' C4' 8V6 sing 14 n n C4' C5' 8V6 sing 15 n n C7' C2' 8V6 sing 16 n n C2' C1' 8V6 sing 17 n n C8' C6' 8V6 sing 18 n n C5' C6' 8V6 sing 19 n n C6' C1' 8V6 sing 20 n n C6' C9' 8V6 sing 21 n n C1' O1 8V6 sing 22 n n C1' C5 8V6 sing 23 n n C5 C4 8V6 doub 24 e n C4 C3 8V6 sing 25 n n C6 C3 8V6 sing 26 n n C3 C2 8V6 doub 27 z n O11 C1 8V6 doub 28 n n C2 C1 8V6 sing 29 n n C1 O12 8V6 sing 30 n n C2 H1 8V6 sing 31 n n C4 H2 8V6 sing 32 n n C5 H3 8V6 sing 33 n n C6 H4 8V6 sing 34 n n C6 H5 8V6 sing 35 n n C6 H6 8V6 sing 36 n n O12 H7 8V6 sing 37 n n C9' H8 8V6 sing 38 n n C9' H9 8V6 sing 39 n n C9' H10 8V6 sing 40 n n C5' H11 8V6 sing 41 n n C5' H12 8V6 sing 42 n n C8' H13 8V6 sing 43 n n C8' H14 8V6 sing 44 n n C8' H15 8V6 sing 45 n n O1 H16 8V6 sing 46 n n C7' H17 8V6 sing 47 n n C7' H18 8V6 sing 48 n n C7' H19 8V6 sing 49 n n C3' H20 8V6 sing 50 n n C4' H21 8V6 sing 51 n n CA1 H22 8V6 sing 52 n n CA1 H23 8V6 sing 53 n n CA5 H24 8V6 sing 54 n n CA6 H25 8V6 sing 55 n n CA0 H26 8V6 sing 56 n n CA0 H27 8V6 sing 57 n n CA0 H28 8V6 sing 58 n n CA8 H29 8V6 sing 59 n n CA9 H30 8V6 sing 60 n n # _atom_sites.entry_id 5YGV _atom_sites.fract_transf_matrix[1][1] 0.026176 _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] 0.026176 _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] 0.003797 _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 8V6 A 1 300 300 8V6 A10 . D 2 8V6 B 1 301 301 8V6 A10 . E 3 HOH A 1 401 18 HOH HOH . E 3 HOH A 2 402 3 HOH HOH . E 3 HOH A 3 403 17 HOH HOH . E 3 HOH A 4 404 13 HOH HOH . E 3 HOH A 5 405 4 HOH HOH . E 3 HOH A 6 406 6 HOH HOH . E 3 HOH A 7 407 2 HOH HOH . E 3 HOH A 8 408 7 HOH HOH . F 3 HOH B 1 401 5 HOH HOH . F 3 HOH B 2 402 10 HOH HOH . F 3 HOH B 3 403 9 HOH HOH . F 3 HOH B 4 404 16 HOH HOH . F 3 HOH B 5 405 1 HOH HOH . F 3 HOH B 6 406 8 HOH HOH . F 3 HOH B 7 407 14 HOH HOH . F 3 HOH B 8 408 12 HOH HOH . F 3 HOH B 9 409 11 HOH HOH . F 3 HOH B 10 410 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 8V6 . . . C 2 11.606 2.772 9.274 1 43.43 ? C1 8V6 300 A 1 HETATM 2 C C2 8V6 . . . C 2 12.242 1.425 8.929 1 43.37 ? C2 8V6 300 A 1 HETATM 3 C C3 8V6 . . . C 2 12.14 0.796 7.532 1 44.47 ? C3 8V6 300 A 1 HETATM 4 C C4 8V6 . . . C 2 11.413 1.502 6.39 1 45.73 ? C4 8V6 300 A 1 HETATM 5 C C5 8V6 . . . C 2 11.35 0.901 4.992 1 46.27 ? C5 8V6 300 A 1 HETATM 6 C C6 8V6 . . . C 2 12.847 -0.529 7.254 1 43.91 ? C6 8V6 300 A 1 HETATM 7 O O11 8V6 . . . C 2 10.974 3.45 8.44 1 43.82 ? O11 8V6 300 A 1 HETATM 8 O O12 8V6 . . . C 2 11.703 3.207 10.439 1 44.11 ? O12 8V6 300 A 1 HETATM 9 C C1' 8V6 . . . C 2 10.635 1.559 3.98 1 49.1 ? C1' 8V6 300 A 1 HETATM 10 C C6' 8V6 . . . C 2 9.15 1.04 3.929 1 52.12 ? C6' 8V6 300 A 1 HETATM 11 C C9' 8V6 . . . C 2 8.438 1.205 5.3 1 53.67 ? C9' 8V6 300 A 1 HETATM 12 C C5' 8V6 . . . C 2 9.168 -0.439 3.586 1 53.87 ? C5' 8V6 300 A 1 HETATM 13 C C8' 8V6 . . . C 2 8.304 1.828 2.873 1 50.92 ? C8' 8V6 300 A 1 HETATM 14 O O1 8V6 . . . C 2 10.578 2.974 4.186 1 49.23 ? O1 8V6 300 A 1 HETATM 15 C C2' 8V6 . . . C 2 11.303 1.317 2.77 1 49.37 ? C2' 8V6 300 A 1 HETATM 16 C C7' 8V6 . . . C 2 12.372 2.111 2.349 1 49.13 ? C7' 8V6 300 A 1 HETATM 17 C C3' 8V6 . . . C 2 10.911 0.287 1.925 1 51.92 ? C3' 8V6 300 A 1 HETATM 18 C C4' 8V6 . . . C 2 9.85 -0.615 2.191 1 55.2 ? C4' 8V6 300 A 1 HETATM 19 O O4' 8V6 . . . C 2 10.325 -1.972 2.089 1 59.51 ? O4' 8V6 300 A 1 HETATM 20 C CA1 8V6 . . . C 2 10.793 -2.343 0.78 1 66.63 ? CA1 8V6 300 A 1 HETATM 21 C CA2 8V6 . . . C 2 12.222 -2.179 0.801 1 71.39 ? CA2 8V6 300 A 1 HETATM 22 C CA3 8V6 . . . C 2 13.349 -2.051 0.813 1 79.18 ? CA3 8V6 300 A 1 HETATM 23 C CA4 8V6 . . . C 2 14.713 -1.9 0.838 1 83.98 ? CA4 8V6 300 A 1 HETATM 24 C CA5 8V6 . . . C 2 15.509 -2.703 0.018 1 86.78 ? CA5 8V6 300 A 1 HETATM 25 C CA6 8V6 . . . C 2 16.893 -2.548 0.03 1 87.59 ? CA6 8V6 300 A 1 HETATM 26 C CA7 8V6 . . . C 2 17.468 -1.591 0.867 1 89.17 ? CA7 8V6 300 A 1 HETATM 27 C CA0 8V6 . . . C 2 18.829 -1.436 0.888 1 90.38 ? CA0 8V6 300 A 1 HETATM 28 C CA8 8V6 . . . C 2 16.674 -0.79 1.679 1 89.21 ? CA8 8V6 300 A 1 HETATM 29 C CA9 8V6 . . . C 2 15.292 -0.949 1.661 1 87.54 ? CA9 8V6 300 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #