data_5YGV
#
_model_server_result.job_id            nTMBeo35lwQqhisYdWB9Qw 
_model_server_result.datetime_utc      '2025-03-05 18:49:02' 
_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":"D","auth_seq_id":301}' 
#
_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 . . . D 2 26.577 2.801 -9.263 1 38.89 ? C1 8V6 301 B 1 
HETATM 2 C C2 8V6 . . . D 2 26.126 1.381 -8.94 1 39.56 ? C2 8V6 301 B 1 
HETATM 3 C C3 8V6 . . . D 2 26.331 0.705 -7.58 1 40.46 ? C3 8V6 301 B 1 
HETATM 4 C C4 8V6 . . . D 2 27.028 1.39 -6.399 1 41.48 ? C4 8V6 301 B 1 
HETATM 5 C C5 8V6 . . . D 2 27.176 0.672 -5.054 1 41.66 ? C5 8V6 301 B 1 
HETATM 6 C C6 8V6 . . . D 2 25.801 -0.714 -7.411 1 41.81 ? C6 8V6 301 B 1 
HETATM 7 O O11 8V6 . . . D 2 27.154 3.53 -8.439 1 37.51 ? O11 8V6 301 B 1 
HETATM 8 O O12 8V6 . . . D 2 26.37 3.239 -10.41 1 39.6 ? O12 8V6 301 B 1 
HETATM 9 C C1' 8V6 . . . D 2 27.827 1.283 -3.969 1 43.56 ? C1' 8V6 301 B 1 
HETATM 10 C C6' 8V6 . . . D 2 29.136 0.47 -3.57 1 45.9 ? C6' 8V6 301 B 1 
HETATM 11 C C9' 8V6 . . . D 2 30.027 0.19 -4.81 1 44.48 ? C9' 8V6 301 B 1 
HETATM 12 C C5' 8V6 . . . D 2 28.767 -0.876 -2.994 1 47.11 ? C5' 8V6 301 B 1 
HETATM 13 C C8' 8V6 . . . D 2 29.985 1.257 -2.513 1 45.08 ? C8' 8V6 301 B 1 
HETATM 14 O O1 8V6 . . . D 2 28.223 2.625 -4.278 1 41.66 ? O1 8V6 301 B 1 
HETATM 15 C C2' 8V6 . . . D 2 26.9 1.338 -2.909 1 43.98 ? C2' 8V6 301 B 1 
HETATM 16 C C7' 8V6 . . . D 2 25.92 2.351 -2.86 1 43.88 ? C7' 8V6 301 B 1 
HETATM 17 C C3' 8V6 . . . D 2 26.913 0.395 -1.875 1 45.6 ? C3' 8V6 301 B 1 
HETATM 18 C C4' 8V6 . . . D 2 27.849 -0.685 -1.763 1 48.67 ? C4' 8V6 301 B 1 
HETATM 19 O O4' 8V6 . . . D 2 27.278 -1.996 -1.504 1 54.16 ? O4' 8V6 301 B 1 
HETATM 20 C CA1 8V6 . . . D 2 25.924 -2.112 -1.894 1 62.72 ? CA1 8V6 301 B 1 
HETATM 21 C CA2 8V6 . . . D 2 25.384 -3.364 -1.725 1 70.61 ? CA2 8V6 301 B 1 
HETATM 22 C CA3 8V6 . . . D 2 24.908 -4.432 -1.472 1 78.95 ? CA3 8V6 301 B 1 
HETATM 23 C CA4 8V6 . . . D 2 24.164 -5.593 -1.119 1 81.63 ? CA4 8V6 301 B 1 
HETATM 24 C CA5 8V6 . . . D 2 24.416 -6.846 -1.678 1 82.88 ? CA5 8V6 301 B 1 
HETATM 25 C CA6 8V6 . . . D 2 23.679 -7.956 -1.251 1 83.65 ? CA6 8V6 301 B 1 
HETATM 26 C CA7 8V6 . . . D 2 22.701 -7.822 -0.258 1 85.18 ? CA7 8V6 301 B 1 
HETATM 27 C CA0 8V6 . . . D 2 21.968 -8.937 0.163 1 85.22 ? CA0 8V6 301 B 1 
HETATM 28 C CA8 8V6 . . . D 2 22.466 -6.565 0.301 1 83.37 ? CA8 8V6 301 B 1 
HETATM 29 C CA9 8V6 . . . D 2 23.207 -5.467 -0.118 1 82.01 ? CA9 8V6 301 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           29 
#