data_4PD4
#
_model_server_result.job_id            jWF-2GWuzzPljQ4jK-OWJA 
_model_server_result.datetime_utc      '2025-02-28 13:46:35' 
_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          4pd4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":4005}' 
#
_entry.id    4PD4 
#
_exptl.entry_id    4PD4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              592.891 
_entity.id                          17 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL 
_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          115.18 
_cell.angle_gamma         90 
_cell.entry_id            4PD4 
_cell.length_a            212.26 
_cell.length_b            150.88 
_cell.length_c            143.09 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PD4 
_symmetry.cell_setting             . 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    22-meric 
_pdbx_struct_assembly.oligomeric_count      22 
_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,K,L,M,N,O,P,Q,R,S,T,U,V 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_756 -x+2,y,-z+1 -1 0 0 0 1 0 0 0 -1 363.640439 0 129.492962 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      17 
_struct_asym.id                             R 
_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
disulf ? disulf1 E SG CYS 134 E CYS 164 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
disulf ? disulf2 F SG CYS 28 F CYS 101 1_555 F SG CYS 50 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf3 J SG CYS 22 J CYS 22 1_555 J SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf4 K SG CYS 23 K CYS 23 1_555 K SG CYS 88 K CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
metalc ? metalc1 C NE2 HIS 82 C HIS 82 1_555 N FE HEM . C HEM 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? 
metalc ? metalc2 C NE2 HIS 96 C HIS 96 1_555 O FE HEM . C HEM 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? 
metalc ? metalc3 C NE2 HIS 183 C HIS 183 1_555 N FE HEM . C HEM 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc4 C NE2 HIS 197 C HIS 197 1_555 O FE HEM . C HEM 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? 
metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 T FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc6 D SD MET 164 D MET 225 1_555 T FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? 
metalc ? metalc7 E SG CYS 129 E CYS 159 1_555 U FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
metalc ? metalc8 E ND1 HIS 131 E HIS 161 1_555 U FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc9 E SG CYS 148 E CYS 178 1_555 U FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc10 E ND1 HIS 151 E HIS 181 1_555 U FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? 
#
_chem_comp.formula           'C39 H60 O4' 
_chem_comp.formula_weight    592.891 
_chem_comp.id                UQ6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL 
_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 C1M UQ6 sing 825 n n 
C1 C2 UQ6 doub 826 n y 
C1 C6 UQ6 sing 827 n y 
C1M H1M1 UQ6 sing 828 n n 
C1M H1M2 UQ6 sing 829 n n 
C1M H1M3 UQ6 sing 830 n n 
C2 O2 UQ6 sing 831 n n 
C2 C3 UQ6 sing 832 n y 
O2 HO2 UQ6 sing 833 n n 
C3 C4 UQ6 doub 834 n y 
C3 O3 UQ6 sing 835 n n 
C4 C5 UQ6 sing 836 n y 
C4 O4 UQ6 sing 837 n n 
C5 O5 UQ6 sing 838 n n 
C5 C6 UQ6 doub 839 n y 
O5 HO5 UQ6 sing 840 n n 
C6 C7 UQ6 sing 841 n n 
O3 C3M UQ6 sing 842 n n 
C3M H3M1 UQ6 sing 843 n n 
C3M H3M2 UQ6 sing 844 n n 
C3M H3M3 UQ6 sing 845 n n 
O4 C4M UQ6 sing 846 n n 
C4M H4M1 UQ6 sing 847 n n 
C4M H4M2 UQ6 sing 848 n n 
C4M H4M3 UQ6 sing 849 n n 
C7 C8 UQ6 sing 850 n n 
C7 H71 UQ6 sing 851 n n 
C7 H72 UQ6 sing 852 n n 
C8 C9 UQ6 doub 853 e n 
C8 H8 UQ6 sing 854 n n 
C9 C10 UQ6 sing 855 n n 
C9 C11 UQ6 sing 856 n n 
C10 H101 UQ6 sing 857 n n 
C10 H102 UQ6 sing 858 n n 
C10 H103 UQ6 sing 859 n n 
C11 C12 UQ6 sing 860 n n 
C11 H111 UQ6 sing 861 n n 
C11 H112 UQ6 sing 862 n n 
C12 C13 UQ6 sing 863 n n 
C12 H121 UQ6 sing 864 n n 
C12 H122 UQ6 sing 865 n n 
C13 C14 UQ6 doub 866 e n 
C13 H13 UQ6 sing 867 n n 
C14 C15 UQ6 sing 868 n n 
C14 C16 UQ6 sing 869 n n 
C15 H151 UQ6 sing 870 n n 
C15 H152 UQ6 sing 871 n n 
C15 H153 UQ6 sing 872 n n 
C16 C17 UQ6 sing 873 n n 
C16 H161 UQ6 sing 874 n n 
C16 H162 UQ6 sing 875 n n 
C17 C18 UQ6 sing 876 n n 
C17 H171 UQ6 sing 877 n n 
C17 H172 UQ6 sing 878 n n 
C18 C19 UQ6 doub 879 z n 
C18 H18 UQ6 sing 880 n n 
C19 C20 UQ6 sing 881 n n 
C19 C21 UQ6 sing 882 n n 
C20 H201 UQ6 sing 883 n n 
C20 H202 UQ6 sing 884 n n 
C20 H203 UQ6 sing 885 n n 
C21 C22 UQ6 sing 886 n n 
C21 H211 UQ6 sing 887 n n 
C21 H212 UQ6 sing 888 n n 
C22 C23 UQ6 sing 889 n n 
C22 H221 UQ6 sing 890 n n 
C22 H222 UQ6 sing 891 n n 
C23 C24 UQ6 doub 892 e n 
C23 H23 UQ6 sing 893 n n 
C24 C25 UQ6 sing 894 n n 
C24 C26 UQ6 sing 895 n n 
C25 H251 UQ6 sing 896 n n 
C25 H252 UQ6 sing 897 n n 
C25 H253 UQ6 sing 898 n n 
C26 C27 UQ6 sing 899 n n 
C26 H261 UQ6 sing 900 n n 
C26 H262 UQ6 sing 901 n n 
C27 C28 UQ6 sing 902 n n 
C27 H271 UQ6 sing 903 n n 
C27 H272 UQ6 sing 904 n n 
C28 C29 UQ6 doub 905 e n 
C28 H28 UQ6 sing 906 n n 
C29 C30 UQ6 sing 907 n n 
C29 C31 UQ6 sing 908 n n 
C30 H301 UQ6 sing 909 n n 
C30 H302 UQ6 sing 910 n n 
C30 H303 UQ6 sing 911 n n 
C31 C32 UQ6 sing 912 n n 
C31 H311 UQ6 sing 913 n n 
C31 H312 UQ6 sing 914 n n 
C32 C33 UQ6 sing 915 n n 
C32 H321 UQ6 sing 916 n n 
C32 H322 UQ6 sing 917 n n 
C33 C34 UQ6 doub 918 n n 
C33 H33 UQ6 sing 919 n n 
C34 C35 UQ6 sing 920 n n 
C34 C36 UQ6 sing 921 n n 
C35 H351 UQ6 sing 922 n n 
C35 H352 UQ6 sing 923 n n 
C35 H353 UQ6 sing 924 n n 
C36 H361 UQ6 sing 925 n n 
C36 H362 UQ6 sing 926 n n 
C36 H363 UQ6 sing 927 n n 
#
_atom_sites.entry_id                     4PD4 
_atom_sites.fract_transf_matrix[1][1]    0.004711 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002215 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006628 
_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]    0.007722 
_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
L 12 UMQ A 1 501 721 UMQ UMQ . 
M 13 3PH A 1 502 713 3PH 3PH . 
N 14 HEM C 1 4001 4001 HEM HEM . 
O 14 HEM C 1 4002 4002 HEM HEM . 
P 15 AOQ C 1 4003 1 AOQ AOQ . 
Q 16 3PE C 1 4004 711 3PE 3PE . 
R 17 UQ6 C 1 4005 506 UQ6 UQ6 . 
S 13 3PH C 1 4006 710 3PH 3PH . 
T 14 HEM D 1 401 4003 HEM HEM . 
U 18 FES E 1 301 4004 FES FES . 
V 13 3PH E 1 302 714 3PH 3PH . 
#
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 UQ6 . . . R 17 196.498 -0.529 61.764 1 21.67 ? C1 UQ6 4005 C 1 
HETATM 2 C C1M UQ6 . . . R 17 195.03 -0.839 61.543 1 15.83 ? C1M UQ6 4005 C 1 
HETATM 3 C C2 UQ6 . . . R 17 196.745 0.487 62.657 1 21.9 ? C2 UQ6 4005 C 1 
HETATM 4 O O2 UQ6 . . . R 17 195.69 1.007 63.13 1 23.82 ? O2 UQ6 4005 C 1 
HETATM 5 C C3 UQ6 . . . R 17 198.077 0.874 62.948 1 20.85 ? C3 UQ6 4005 C 1 
HETATM 6 C C4 UQ6 . . . R 17 199.151 0.212 62.303 1 20.29 ? C4 UQ6 4005 C 1 
HETATM 7 C C5 UQ6 . . . R 17 198.897 -0.821 61.43 1 20.11 ? C5 UQ6 4005 C 1 
HETATM 8 O O5 UQ6 . . . R 17 199.933 -1.338 60.931 1 18.6 ? O5 UQ6 4005 C 1 
HETATM 9 C C6 UQ6 . . . R 17 197.559 -1.201 61.136 1 24.48 ? C6 UQ6 4005 C 1 
HETATM 10 O O3 UQ6 . . . R 17 198.396 1.908 63.835 1 22.02 ? O3 UQ6 4005 C 1 
HETATM 11 C C3M UQ6 . . . R 17 197.483 2.631 64.677 1 17.8 ? C3M UQ6 4005 C 1 
HETATM 12 O O4 UQ6 . . . R 17 200.504 0.491 62.505 1 21.58 ? O4 UQ6 4005 C 1 
HETATM 13 C C4M UQ6 . . . R 17 201.137 1.702 62.075 1 17.89 ? C4M UQ6 4005 C 1 
HETATM 14 C C7 UQ6 . . . R 17 197.196 -2.334 60.165 1 19.9 ? C7 UQ6 4005 C 1 
HETATM 15 C C8 UQ6 . . . R 17 196.696 -3.48 61.02 1 15.38 ? C8 UQ6 4005 C 1 
HETATM 16 C C9 UQ6 . . . R 17 195.579 -4.144 60.747 1 12.46 ? C9 UQ6 4005 C 1 
HETATM 17 C C10 UQ6 . . . R 17 194.807 -3.791 59.522 1 12.64 ? C10 UQ6 4005 C 1 
HETATM 18 C C11 UQ6 . . . R 17 195.179 -5.258 61.686 1 10.77 ? C11 UQ6 4005 C 1 
HETATM 19 C C12 UQ6 . . . R 17 193.716 -5.581 61.547 1 10.49 ? C12 UQ6 4005 C 1 
HETATM 20 C C13 UQ6 . . . R 17 193.407 -6.928 62.138 1 9.6 ? C13 UQ6 4005 C 1 
HETATM 21 C C14 UQ6 . . . R 17 192.24 -7.525 61.797 1 12.02 ? C14 UQ6 4005 C 1 
HETATM 22 C C15 UQ6 . . . R 17 191.265 -6.882 60.851 1 12.66 ? C15 UQ6 4005 C 1 
HETATM 23 C C16 UQ6 . . . R 17 191.892 -8.874 62.365 1 10.59 ? C16 UQ6 4005 C 1 
HETATM 24 C C17 UQ6 . . . R 17 190.41 -9.177 62.227 1 9.46 ? C17 UQ6 4005 C 1 
HETATM 25 C C18 UQ6 . . . R 17 190.257 -10.561 61.641 1 8.23 ? C18 UQ6 4005 C 1 
HETATM 26 C C19 UQ6 . . . R 17 189.075 -11.162 61.791 1 12.07 ? C19 UQ6 4005 C 1 
HETATM 27 C C20 UQ6 . . . R 17 188.021 -10.431 62.554 1 15.35 ? C20 UQ6 4005 C 1 
HETATM 28 C C21 UQ6 . . . R 17 188.817 -12.553 61.229 1 15.49 ? C21 UQ6 4005 C 1 
HETATM 29 C C22 UQ6 . . . R 17 187.401 -12.801 60.699 1 6.54 ? C22 UQ6 4005 C 1 
HETATM 30 C C23 UQ6 . . . R 17 187.602 -13.73 59.532 1 7.21 ? C23 UQ6 4005 C 1 
HETATM 31 C C24 UQ6 . . . R 17 186.645 -14.307 58.775 1 11.35 ? C24 UQ6 4005 C 1 
HETATM 32 C C25 UQ6 . . . R 17 185.153 -14.1 58.991 1 12.88 ? C25 UQ6 4005 C 1 
HETATM 33 C C26 UQ6 . . . R 17 187.125 -15.194 57.652 1 7.85 ? C26 UQ6 4005 C 1 
HETATM 34 C C27 UQ6 . . . R 17 186.379 -16.509 57.728 1 7.81 ? C27 UQ6 4005 C 1 
HETATM 35 C C28 UQ6 . . . R 17 185.728 -16.805 56.401 1 11.95 ? C28 UQ6 4005 C 1 
HETATM 36 C C29 UQ6 . . . R 17 185.868 -18.026 55.872 1 12.53 ? C29 UQ6 4005 C 1 
HETATM 37 C C30 UQ6 . . . R 17 186.676 -19.064 56.607 1 8.61 ? C30 UQ6 4005 C 1 
HETATM 38 C C31 UQ6 . . . R 17 185.238 -18.368 54.544 1 18.73 ? C31 UQ6 4005 C 1 
HETATM 39 C C32 UQ6 . . . R 17 185.812 -19.682 53.996 1 15.25 ? C32 UQ6 4005 C 1 
HETATM 40 C C33 UQ6 . . . R 17 184.748 -20.756 54.027 1 11.44 ? C33 UQ6 4005 C 1 
HETATM 41 C C34 UQ6 . . . R 17 184.349 -21.366 52.905 1 11.98 ? C34 UQ6 4005 C 1 
HETATM 42 C C35 UQ6 . . . R 17 184.932 -21.005 51.569 1 16.3 ? C35 UQ6 4005 C 1 
HETATM 43 C C36 UQ6 . . . R 17 183.295 -22.423 52.971 1 11.46 ? C36 UQ6 4005 C 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           43 
#