data_8Z9X
#
_model_server_result.job_id            ss3DRwhYD1gM39C-ZEiMwg 
_model_server_result.datetime_utc      '2024-10-10 08:20:37' 
_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          8z9x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":701}' 
#
_entry.id    8Z9X 
#
_exptl.entry_id    8Z9X 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              1062.049 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            phytanoyl-CoA 
_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            8Z9X 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8Z9X 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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    ? 
_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           'C41 H74 N7 O17 P3 S' 
_chem_comp.formula_weight    1062.049 
_chem_comp.id                A1L1A 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              phytanoyl-CoA 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'S-[2-[3-[[4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-2-hydroxy-3,3-dimethylbutanoyl]amino]propanoylamino]ethyl] (3S,7R,11R)-3,7,11,15-tetramethylhexadecanethioate;Phytanoyl-coenzyme A' 
#
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
N1A C2A A1L1A doub 1 n y 
N1A C6A A1L1A sing 2 n y 
C2A N3A A1L1A sing 3 n y 
N6A C6A A1L1A sing 4 n n 
C6A C5A A1L1A doub 5 n y 
N3A C4A A1L1A doub 6 n y 
C5A C4A A1L1A sing 7 n y 
C5A N7A A1L1A sing 8 n y 
C4A N9A A1L1A sing 9 n y 
N7A C8A A1L1A doub 10 n y 
N9A C1B A1L1A sing 11 n n 
N9A C8A A1L1A sing 12 n y 
O2B C2B A1L1A sing 13 n n 
C1B C2B A1L1A sing 14 n n 
C1B O4B A1L1A sing 15 n n 
C2B C3B A1L1A sing 16 n n 
O9A P3B A1L1A doub 17 n n 
C03 C02 A1L1A sing 18 n n 
O4B C4B A1L1A sing 19 n n 
C3B C4B A1L1A sing 20 n n 
C3B O3B A1L1A sing 21 n n 
C4B C5B A1L1A sing 22 n n 
P3B O3B A1L1A sing 23 n n 
P3B O8A A1L1A sing 24 n n 
P3B O7A A1L1A sing 25 n n 
C02 C01 A1L1A sing 26 n n 
C02 C04 A1L1A sing 27 n n 
C04 C05 A1L1A sing 28 n n 
C5B O5B A1L1A sing 29 n n 
O5B P1A A1L1A sing 30 n n 
O2A P1A A1L1A doub 31 n n 
C05 C06 A1L1A sing 32 n n 
P1A O1A A1L1A sing 33 n n 
P1A O3A A1L1A sing 34 n n 
C06 C07 A1L1A sing 35 n n 
O3A P2A A1L1A sing 36 n n 
O4A P2A A1L1A doub 37 n n 
C07 C09 A1L1A sing 38 n n 
C07 C08 A1L1A sing 39 n n 
P2A O6A A1L1A sing 40 n n 
P2A O5A A1L1A sing 41 n n 
C09 C10 A1L1A sing 42 n n 
O6A CCP A1L1A sing 43 n n 
CCP CBP A1L1A sing 44 n n 
C10 C11 A1L1A sing 45 n n 
OAP CAP A1L1A sing 46 n n 
C11 C12 A1L1A sing 47 n n 
CAP CBP A1L1A sing 48 n n 
CAP C9P A1L1A sing 49 n n 
CBP CDP A1L1A sing 50 n n 
CBP CEP A1L1A sing 51 n n 
O9P C9P A1L1A doub 52 n n 
C9P N8P A1L1A sing 53 n n 
C12 C13 A1L1A sing 54 n n 
C12 C14 A1L1A sing 55 n n 
N8P C7P A1L1A sing 56 n n 
C7P C6P A1L1A sing 57 n n 
C14 C15 A1L1A sing 58 n n 
O5P C5P A1L1A doub 59 n n 
C5P C6P A1L1A sing 60 n n 
C5P N4P A1L1A sing 61 n n 
C15 C16 A1L1A sing 62 n n 
C16 C17 A1L1A sing 63 n n 
N4P C3P A1L1A sing 64 n n 
C17 C18 A1L1A sing 65 n n 
C17 C19 A1L1A sing 66 n n 
S1P C20 A1L1A sing 67 n n 
S1P C2P A1L1A sing 68 n n 
C3P C2P A1L1A sing 69 n n 
C19 C20 A1L1A sing 70 n n 
C20 O21 A1L1A doub 71 n n 
C10 H1 A1L1A sing 72 n n 
C10 H2 A1L1A sing 73 n n 
C13 H3 A1L1A sing 74 n n 
C13 H4 A1L1A sing 75 n n 
C13 H5 A1L1A sing 76 n n 
C15 H6 A1L1A sing 77 n n 
C17 H7 A1L1A sing 78 n n 
C3P H8 A1L1A sing 79 n n 
C6P H9 A1L1A sing 80 n n 
C6P H10 A1L1A sing 81 n n 
C01 H11 A1L1A sing 82 n n 
C01 H12 A1L1A sing 83 n n 
C01 H13 A1L1A sing 84 n n 
C02 H14 A1L1A sing 85 n n 
C03 H15 A1L1A sing 86 n n 
C03 H16 A1L1A sing 87 n n 
C03 H17 A1L1A sing 88 n n 
C04 H18 A1L1A sing 89 n n 
C05 H19 A1L1A sing 90 n n 
C06 H20 A1L1A sing 91 n n 
C06 H21 A1L1A sing 92 n n 
C07 H22 A1L1A sing 93 n n 
C08 H23 A1L1A sing 94 n n 
C08 H24 A1L1A sing 95 n n 
C08 H25 A1L1A sing 96 n n 
C09 H26 A1L1A sing 97 n n 
C09 H27 A1L1A sing 98 n n 
C11 H28 A1L1A sing 99 n n 
C11 H29 A1L1A sing 100 n n 
C12 H30 A1L1A sing 101 n n 
C14 H31 A1L1A sing 102 n n 
C16 H32 A1L1A sing 103 n n 
C16 H33 A1L1A sing 104 n n 
C18 H34 A1L1A sing 105 n n 
C18 H35 A1L1A sing 106 n n 
C18 H36 A1L1A sing 107 n n 
C19 H37 A1L1A sing 108 n n 
C19 H38 A1L1A sing 109 n n 
C2P H39 A1L1A sing 110 n n 
C2P H40 A1L1A sing 111 n n 
C7P H41 A1L1A sing 112 n n 
C7P H42 A1L1A sing 113 n n 
CAP H43 A1L1A sing 114 n n 
CEP H44 A1L1A sing 115 n n 
CEP H45 A1L1A sing 116 n n 
CEP H46 A1L1A sing 117 n n 
CDP H47 A1L1A sing 118 n n 
CDP H48 A1L1A sing 119 n n 
CDP H49 A1L1A sing 120 n n 
CCP H50 A1L1A sing 121 n n 
CCP H51 A1L1A sing 122 n n 
C5B H52 A1L1A sing 123 n n 
C5B H53 A1L1A sing 124 n n 
C4B H54 A1L1A sing 125 n n 
C3B H55 A1L1A sing 126 n n 
C2B H56 A1L1A sing 127 n n 
C1B H57 A1L1A sing 128 n n 
C8A H58 A1L1A sing 129 n n 
C2A H59 A1L1A sing 130 n n 
N8P H60 A1L1A sing 131 n n 
N6A H61 A1L1A sing 132 n n 
N6A H62 A1L1A sing 133 n n 
O5A H63 A1L1A sing 134 n n 
O1A H64 A1L1A sing 135 n n 
O2B H65 A1L1A sing 136 n n 
O7A H66 A1L1A sing 137 n n 
O8A H67 A1L1A sing 138 n n 
OAP H68 A1L1A sing 139 n n 
C15 H69 A1L1A sing 140 n n 
C04 H70 A1L1A sing 141 n n 
C05 H71 A1L1A sing 142 n n 
C14 H72 A1L1A sing 143 n n 
C3P H73 A1L1A sing 144 n n 
N4P H74 A1L1A sing 145 n n 
#
_atom_sites.entry_id                     8Z9X 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 A1L1A B 1 701 3 A1L1A LIG . 
D 2 A1L1A A 1 701 2 A1L1A LIG . 
#
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 C10 A1L1A . . . D 2 158.676 133.483 122.889 1 20 ? C10 A1L1A 701 A 1 
HETATM 2 C C13 A1L1A . . . D 2 158.093 133.73 125.582 1 20 ? C13 A1L1A 701 A 1 
HETATM 3 C C15 A1L1A . . . D 2 157.859 136.973 126.683 1 20 ? C15 A1L1A 701 A 1 
HETATM 4 C C17 A1L1A . . . D 2 157.605 139.212 127.892 1 20 ? C17 A1L1A 701 A 1 
HETATM 5 C C20 A1L1A . . . D 2 157.675 141.637 129.117 1 20 ? C20 A1L1A 701 A 1 
HETATM 6 C C3P A1L1A . . . D 2 153.828 143.281 128.544 1 20 ? C3P A1L1A 701 A 1 
HETATM 7 C C5P A1L1A . . . D 2 152.61 141.983 126.655 1 20 ? C5P A1L1A 701 A 1 
HETATM 8 C C6P A1L1A . . . D 2 151.248 142.514 126.921 1 20 ? C6P A1L1A 701 A 1 
HETATM 9 C C01 A1L1A . . . D 2 159.368 128.451 116.915 1 20 ? C01 A1L1A 701 A 1 
HETATM 10 C C02 A1L1A . . . D 2 160.587 129.318 116.629 1 20 ? C02 A1L1A 701 A 1 
HETATM 11 C C03 A1L1A . . . D 2 160.725 129.511 115.114 1 20 ? C03 A1L1A 701 A 1 
HETATM 12 C C04 A1L1A . . . D 2 160.752 130.579 117.495 1 20 ? C04 A1L1A 701 A 1 
HETATM 13 C C05 A1L1A . . . D 2 160.432 130.468 118.993 1 20 ? C05 A1L1A 701 A 1 
HETATM 14 C C06 A1L1A . . . D 2 160.512 131.796 119.785 1 20 ? C06 A1L1A 701 A 1 
HETATM 15 C C07 A1L1A . . . D 2 159.422 132.108 120.848 1 20 ? C07 A1L1A 701 A 1 
HETATM 16 C C08 A1L1A . . . D 2 159.443 131.127 121.99 1 20 ? C08 A1L1A 701 A 1 
HETATM 17 C C09 A1L1A . . . D 2 159.516 133.445 121.584 1 20 ? C09 A1L1A 701 A 1 
HETATM 18 C C11 A1L1A . . . D 2 158.442 134.92 123.41 1 20 ? C11 A1L1A 701 A 1 
HETATM 19 C C12 A1L1A . . . D 2 157.968 135.068 124.865 1 20 ? C12 A1L1A 701 A 1 
HETATM 20 C C14 A1L1A . . . D 2 158.687 136.214 125.621 1 20 ? C14 A1L1A 701 A 1 
HETATM 21 C C16 A1L1A . . . D 2 158.574 138.157 127.346 1 20 ? C16 A1L1A 701 A 1 
HETATM 22 C C18 A1L1A . . . D 2 156.346 138.488 128.339 1 20 ? C18 A1L1A 701 A 1 
HETATM 23 C C19 A1L1A . . . D 2 158.183 140.165 128.979 1 20 ? C19 A1L1A 701 A 1 
HETATM 24 C C2P A1L1A . . . D 2 155.075 143.182 129.408 1 20 ? C2P A1L1A 701 A 1 
HETATM 25 C C7P A1L1A . . . D 2 150.507 142.636 125.619 1 20 ? C7P A1L1A 701 A 1 
HETATM 26 C C9P A1L1A . . . D 2 149.038 140.932 124.444 1 20 ? C9P A1L1A 701 A 1 
HETATM 27 C CAP A1L1A . . . D 2 148.004 141.749 123.727 1 20 ? CAP A1L1A 701 A 1 
HETATM 28 C CBP A1L1A . . . D 2 146.533 141.636 123.991 1 20 ? CBP A1L1A 701 A 1 
HETATM 29 C CEP A1L1A . . . D 2 146.152 142.871 124.84 1 20 ? CEP A1L1A 701 A 1 
HETATM 30 C CDP A1L1A . . . D 2 145.997 140.316 124.545 1 20 ? CDP A1L1A 701 A 1 
HETATM 31 C CCP A1L1A . . . D 2 146.041 141.68 122.571 1 20 ? CCP A1L1A 701 A 1 
HETATM 32 C C5B A1L1A . . . D 2 146.734 141.461 117.501 1 20 ? C5B A1L1A 701 A 1 
HETATM 33 C C4B A1L1A . . . D 2 146.293 141.916 116.18 1 20 ? C4B A1L1A 701 A 1 
HETATM 34 C C3B A1L1A . . . D 2 144.899 142.52 116.024 1 20 ? C3B A1L1A 701 A 1 
HETATM 35 C C2B A1L1A . . . D 2 144.897 142.669 114.726 1 20 ? C2B A1L1A 701 A 1 
HETATM 36 C C1B A1L1A . . . D 2 145.763 141.441 114.182 1 20 ? C1B A1L1A 701 A 1 
HETATM 37 C C8A A1L1A . . . D 2 143.679 140.342 114.466 1 20 ? C8A A1L1A 701 A 1 
HETATM 38 C C5A A1L1A . . . D 2 143.072 140.345 112.483 1 20 ? C5A A1L1A 701 A 1 
HETATM 39 C C6A A1L1A . . . D 2 142.469 140.157 111.247 1 20 ? C6A A1L1A 701 A 1 
HETATM 40 C C2A A1L1A . . . D 2 144.277 141.118 110.251 1 20 ? C2A A1L1A 701 A 1 
HETATM 41 C C4A A1L1A . . . D 2 144.296 140.934 112.538 1 20 ? C4A A1L1A 701 A 1 
HETATM 42 N N4P A1L1A . . . D 2 153.766 142.349 127.419 1 20 ? N4P A1L1A 701 A 1 
HETATM 43 N N8P A1L1A . . . D 2 150.147 141.302 125.268 1 20 ? N8P A1L1A 701 A 1 
HETATM 44 N N9A A1L1A . . . D 2 144.663 140.77 113.744 1 20 ? N9A A1L1A 701 A 1 
HETATM 45 N N7A A1L1A . . . D 2 142.701 140.002 113.705 1 20 ? N7A A1L1A 701 A 1 
HETATM 46 N N1A A1L1A . . . D 2 143.093 140.559 110.172 1 20 ? N1A A1L1A 701 A 1 
HETATM 47 N N3A A1L1A . . . D 2 144.844 141.287 111.399 1 20 ? N3A A1L1A 701 A 1 
HETATM 48 N N6A A1L1A . . . D 2 141.183 139.538 111.182 1 20 ? N6A A1L1A 701 A 1 
HETATM 49 O O21 A1L1A . . . D 2 158.259 142.457 129.715 1 20 ? O21 A1L1A 701 A 1 
HETATM 50 O O5P A1L1A . . . D 2 152.72 141.219 125.803 1 20 ? O5P A1L1A 701 A 1 
HETATM 51 O O9P A1L1A . . . D 2 148.928 139.826 124.308 1 20 ? O9P A1L1A 701 A 1 
HETATM 52 O O6A A1L1A . . . D 2 145.838 142.994 122.228 1 20 ? O6A A1L1A 701 A 1 
HETATM 53 O O5A A1L1A . . . D 2 143.361 143.228 122.618 1 20 ? O5A A1L1A 701 A 1 
HETATM 54 O O4A A1L1A . . . D 2 144.425 144.499 120.817 1 20 ? O4A A1L1A 701 A 1 
HETATM 55 O O3A A1L1A . . . D 2 144.228 142.127 120.396 1 20 ? O3A A1L1A 701 A 1 
HETATM 56 O O1A A1L1A . . . D 2 146.52 142.711 119.805 1 20 ? O1A A1L1A 701 A 1 
HETATM 57 O O2A A1L1A . . . D 2 144.522 143.452 118.515 1 20 ? O2A A1L1A 701 A 1 
HETATM 58 O O5B A1L1A . . . D 2 145.616 141.185 118.208 1 20 ? O5B A1L1A 701 A 1 
HETATM 59 O O4B A1L1A . . . D 2 146.16 140.821 115.211 1 20 ? O4B A1L1A 701 A 1 
HETATM 60 O O2B A1L1A . . . D 2 143.8 143.193 113.936 1 20 ? O2B A1L1A 701 A 1 
HETATM 61 O O3B A1L1A . . . D 2 143.809 141.907 116.636 1 20 ? O3B A1L1A 701 A 1 
HETATM 62 O O7A A1L1A . . . D 2 142.177 143.502 117.542 1 20 ? O7A A1L1A 701 A 1 
HETATM 63 O O8A A1L1A . . . D 2 141.228 141.486 116.803 1 20 ? O8A A1L1A 701 A 1 
HETATM 64 O O9A A1L1A . . . D 2 142.129 142.958 115.082 1 20 ? O9A A1L1A 701 A 1 
HETATM 65 O OAP A1L1A . . . D 2 148.304 143.056 123.358 1 20 ? OAP A1L1A 701 A 1 
HETATM 66 P P2A A1L1A . . . D 2 144.409 143.237 121.542 1 20 ? P2A A1L1A 701 A 1 
HETATM 67 P P1A A1L1A . . . D 2 145.228 142.374 119.174 1 20 ? P1A A1L1A 701 A 1 
HETATM 68 P P3B A1L1A . . . D 2 142.304 142.465 116.491 1 20 ? P3B A1L1A 701 A 1 
HETATM 69 S S1P A1L1A . . . D 2 156.188 142.272 128.355 1 20 ? S1P A1L1A 701 A 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           69 
#