data_4PDK
#
_model_server_result.job_id            OnFp7rZIR7RL9_k3Yov5yg 
_model_server_result.datetime_utc      '2024-11-24 10:47:39' 
_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          4pdk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":302}' 
#
_entry.id    4PDK 
#
_exptl.entry_id    4PDK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              1031.98 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)' 
_entity.pdbx_number_of_molecules    4 
_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            4PDK 
_cell.length_a            116.92 
_cell.length_b            88.69 
_cell.length_c            62.86 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PDK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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 
? 2 E N N 
? 2 F N N 
#
_chem_comp.formula           'C39 H68 N7 O17 P3 S' 
_chem_comp.formula_weight    1031.98 
_chem_comp.id                3VV 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     oleoyl-CoA 
#
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
C03 C02 3VV sing 1 n n 
C03 C04 3VV sing 2 n n 
C01 C02 3VV sing 3 n n 
C04 C05 3VV sing 4 n n 
C05 C06 3VV sing 5 n n 
C07 C06 3VV sing 6 n n 
C07 C08 3VV sing 7 n n 
C08 C09 3VV sing 8 n n 
C09 C10 3VV doub 9 z n 
C11 C10 3VV sing 10 n n 
C11 C12 3VV sing 11 n n 
C12 C13 3VV sing 12 n n 
C13 C14 3VV sing 13 n n 
C14 C15 3VV sing 14 n n 
C15 C16 3VV sing 15 n n 
C16 C17 3VV sing 16 n n 
O19 C18 3VV doub 17 n n 
C17 C18 3VV sing 18 n n 
C18 S20 3VV sing 19 n n 
S20 C21 3VV sing 20 n n 
C21 C22 3VV sing 21 n n 
N23 C22 3VV sing 22 n n 
N23 C24 3VV sing 23 n n 
O25 C24 3VV doub 24 n n 
C65 N64 3VV doub 25 n y 
C65 N66 3VV sing 26 n y 
C24 C26 3VV sing 27 n n 
N64 C62 3VV sing 28 n y 
N66 C67 3VV doub 29 n y 
C62 N63 3VV sing 30 n n 
C62 C61 3VV doub 31 n y 
C34 C33 3VV sing 32 n n 
C67 C61 3VV sing 33 n y 
C67 N58 3VV sing 34 n y 
O48 C47 3VV sing 35 n n 
O48 C49 3VV sing 36 n n 
C26 C27 3VV sing 37 n n 
O56 P54 3VV doub 38 n n 
O30 C29 3VV doub 39 n n 
C61 N60 3VV sing 40 n y 
C47 C46 3VV sing 41 n n 
C47 C52 3VV sing 42 n n 
C49 N58 3VV sing 43 n n 
C49 C50 3VV sing 44 n n 
C27 N28 3VV sing 45 n n 
O32 C31 3VV sing 46 n n 
N58 C59 3VV sing 47 n y 
C29 N28 3VV sing 48 n n 
C29 C31 3VV sing 49 n n 
C46 O45 3VV sing 50 n n 
O53 P54 3VV sing 51 n n 
O53 C52 3VV sing 52 n n 
C33 C31 3VV sing 53 n n 
C33 C36 3VV sing 54 n n 
C33 C35 3VV sing 55 n n 
O55 P54 3VV sing 56 n n 
P54 O57 3VV sing 57 n n 
N60 C59 3VV doub 58 n y 
C52 C50 3VV sing 59 n n 
C36 O37 3VV sing 60 n n 
C50 O51 3VV sing 61 n n 
O45 P42 3VV sing 62 n n 
O41 P42 3VV sing 63 n n 
O41 P38 3VV sing 64 n n 
P42 O44 3VV doub 65 n n 
P42 O43 3VV sing 66 n n 
O37 P38 3VV sing 67 n n 
O40 P38 3VV doub 68 n n 
P38 O39 3VV sing 69 n n 
C10 H1 3VV sing 70 n n 
C13 H2 3VV sing 71 n n 
C13 H3 3VV sing 72 n n 
C15 H4 3VV sing 73 n n 
C15 H5 3VV sing 74 n n 
C17 H6 3VV sing 75 n n 
C17 H7 3VV sing 76 n n 
C21 H8 3VV sing 77 n n 
C21 H9 3VV sing 78 n n 
C22 H10 3VV sing 79 n n 
C22 H11 3VV sing 80 n n 
C26 H12 3VV sing 81 n n 
C26 H13 3VV sing 82 n n 
C01 H14 3VV sing 83 n n 
C01 H15 3VV sing 84 n n 
C01 H16 3VV sing 85 n n 
C02 H17 3VV sing 86 n n 
C02 H18 3VV sing 87 n n 
C03 H19 3VV sing 88 n n 
C03 H20 3VV sing 89 n n 
C04 H21 3VV sing 90 n n 
C04 H22 3VV sing 91 n n 
C05 H23 3VV sing 92 n n 
C05 H24 3VV sing 93 n n 
C06 H25 3VV sing 94 n n 
C06 H26 3VV sing 95 n n 
C07 H27 3VV sing 96 n n 
C07 H28 3VV sing 97 n n 
C08 H29 3VV sing 98 n n 
C08 H30 3VV sing 99 n n 
C09 H31 3VV sing 100 n n 
C11 H32 3VV sing 101 n n 
C11 H33 3VV sing 102 n n 
C12 H34 3VV sing 103 n n 
C12 H35 3VV sing 104 n n 
C14 H36 3VV sing 105 n n 
C14 H37 3VV sing 106 n n 
C16 H38 3VV sing 107 n n 
C16 H39 3VV sing 108 n n 
N23 H40 3VV sing 109 n n 
C27 H41 3VV sing 110 n n 
C27 H42 3VV sing 111 n n 
N28 H43 3VV sing 112 n n 
C31 H44 3VV sing 113 n n 
O32 H45 3VV sing 114 n n 
C34 H46 3VV sing 115 n n 
C34 H47 3VV sing 116 n n 
C34 H48 3VV sing 117 n n 
C35 H49 3VV sing 118 n n 
C35 H50 3VV sing 119 n n 
C35 H51 3VV sing 120 n n 
C36 H52 3VV sing 121 n n 
C36 H53 3VV sing 122 n n 
O39 H54 3VV sing 123 n n 
O43 H55 3VV sing 124 n n 
C46 H56 3VV sing 125 n n 
C46 H57 3VV sing 126 n n 
C47 H58 3VV sing 127 n n 
C49 H59 3VV sing 128 n n 
C50 H60 3VV sing 129 n n 
O51 H61 3VV sing 130 n n 
C52 H62 3VV sing 131 n n 
O55 H63 3VV sing 132 n n 
O57 H64 3VV sing 133 n n 
C59 H65 3VV sing 134 n n 
N63 H66 3VV sing 135 n n 
N63 H67 3VV sing 136 n n 
C65 H68 3VV sing 137 n n 
#
_atom_sites.entry_id                     4PDK 
_atom_sites.fract_transf_matrix[1][1]    0.008553 
_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]    0.011275 
_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]    0.015908 
_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 3VV A 1 301 1267 3VV LIG . 
D 2 3VV A 1 302 1268 3VV LIG . 
E 2 3VV B 1 301 1267 3VV LIG . 
F 2 3VV B 1 302 1268 3VV 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 3VV . . . D 2 15.419 -22.896 -15.733 1 60.44 ? C10 3VV 302 A 1 
HETATM 2 C C13 3VV . . . D 2 15.605 -22.305 -19.555 1 59.7 ? C13 3VV 302 A 1 
HETATM 3 C C15 3VV . . . D 2 14.565 -20.451 -20.948 1 56.64 ? C15 3VV 302 A 1 
HETATM 4 C C17 3VV . . . D 2 14.562 -19.129 -23.115 1 56.74 ? C17 3VV 302 A 1 
HETATM 5 C C21 3VV . . . D 2 16.587 -16.581 -23.256 1 67.61 ? C21 3VV 302 A 1 
HETATM 6 C C22 3VV . . . D 2 17.342 -15.447 -22.538 1 67.51 ? C22 3VV 302 A 1 
HETATM 7 C C24 3VV . . . D 2 19.443 -14.099 -22.91 1 67.5 ? C24 3VV 302 A 1 
HETATM 8 C C26 3VV . . . D 2 20.888 -13.991 -23.405 1 70.44 ? C26 3VV 302 A 1 
HETATM 9 P P38 3VV . . . D 2 25.383 -6.94 -23.305 1 124.57 ? P38 3VV 302 A 1 
HETATM 10 P P42 3VV . . . D 2 24.212 -4.642 -24.661 1 94.28 ? P42 3VV 302 A 1 
HETATM 11 P P54 3VV . . . D 2 19.412 -1.37 -27.069 1 78.34 ? P54 3VV 302 A 1 
HETATM 12 C C01 3VV . . . D 2 10.809 -17.568 -10.464 1 71.8 ? C01 3VV 302 A 1 
HETATM 13 C C02 3VV . . . D 2 11.965 -16.749 -11.036 1 71.1 ? C02 3VV 302 A 1 
HETATM 14 C C03 3VV . . . D 2 12.293 -17.135 -12.482 1 69.97 ? C03 3VV 302 A 1 
HETATM 15 C C04 3VV . . . D 2 13.77 -17.542 -12.645 1 69.17 ? C04 3VV 302 A 1 
HETATM 16 C C05 3VV . . . D 2 14 -18.467 -13.885 1 33.02 ? C05 3VV 302 A 1 
HETATM 17 C C06 3VV . . . D 2 14.868 -19.711 -13.516 1 70.02 ? C06 3VV 302 A 1 
HETATM 18 C C07 3VV . . . D 2 16.337 -19.632 -14.086 1 68.42 ? C07 3VV 302 A 1 
HETATM 19 C C08 3VV . . . D 2 16.7 -20.859 -14.99 1 61.74 ? C08 3VV 302 A 1 
HETATM 20 C C09 3VV . . . D 2 15.7 -22.037 -14.733 1 59.12 ? C09 3VV 302 A 1 
HETATM 21 C C11 3VV . . . D 2 16.087 -22.699 -17.092 1 60.55 ? C11 3VV 302 A 1 
HETATM 22 C C12 3VV . . . D 2 15.033 -22.773 -18.211 1 60.31 ? C12 3VV 302 A 1 
HETATM 23 C C14 3VV . . . D 2 14.498 -21.935 -20.55 1 57.6 ? C14 3VV 302 A 1 
HETATM 24 C C16 3VV . . . D 2 13.805 -20.171 -22.257 1 56.04 ? C16 3VV 302 A 1 
HETATM 25 C C18 3VV . . . D 2 16.063 -19.494 -23.215 1 57.77 ? C18 3VV 302 A 1 
HETATM 26 O O19 3VV . . . D 2 16.395 -20.586 -23.534 1 58.73 ? O19 3VV 302 A 1 
HETATM 27 S S20 3VV . . . D 2 17.324 -18.211 -22.827 1 64.77 ? S20 3VV 302 A 1 
HETATM 28 N N23 3VV . . . D 2 18.724 -15.366 -23.027 1 66.77 ? N23 3VV 302 A 1 
HETATM 29 O O25 3VV . . . D 2 18.907 -13.157 -22.431 1 65.76 ? O25 3VV 302 A 1 
HETATM 30 C C27 3VV . . . D 2 21.668 -12.968 -22.558 1 71.46 ? C27 3VV 302 A 1 
HETATM 31 N N28 3VV . . . D 2 20.993 -11.667 -22.656 1 74.36 ? N28 3VV 302 A 1 
HETATM 32 C C29 3VV . . . D 2 21.778 -10.494 -23.037 1 78.7 ? C29 3VV 302 A 1 
HETATM 33 O O30 3VV . . . D 2 22.933 -10.649 -23.239 1 79.5 ? O30 3VV 302 A 1 
HETATM 34 C C31 3VV . . . D 2 21.069 -9.12 -23.145 1 78.47 ? C31 3VV 302 A 1 
HETATM 35 O O32 3VV . . . D 2 20.036 -9.187 -24.068 1 79.56 ? O32 3VV 302 A 1 
HETATM 36 C C33 3VV . . . D 2 21.997 -7.964 -23.558 1 82.73 ? C33 3VV 302 A 1 
HETATM 37 C C34 3VV . . . D 2 21.122 -6.708 -23.673 1 80.45 ? C34 3VV 302 A 1 
HETATM 38 C C35 3VV . . . D 2 22.63 -8.218 -24.943 1 80.51 ? C35 3VV 302 A 1 
HETATM 39 C C36 3VV . . . D 2 23.036 -7.724 -22.446 1 82.09 ? C36 3VV 302 A 1 
HETATM 40 O O37 3VV . . . D 2 24.314 -8.125 -22.856 1 85 ? O37 3VV 302 A 1 
HETATM 41 O O39 3VV . . . D 2 25.863 -7.232 -24.709 1 124.26 1 O39 3VV 302 A 1 
HETATM 42 O O40 3VV . . . D 2 26.56 -6.903 -22.357 1 123.8 ? O40 3VV 302 A 1 
HETATM 43 O O41 3VV . . . D 2 24.595 -5.486 -23.287 1 71.55 ? O41 3VV 302 A 1 
HETATM 44 O O43 3VV . . . D 2 25.187 -3.494 -24.813 1 94.55 1 O43 3VV 302 A 1 
HETATM 45 O O44 3VV . . . D 2 24.269 -5.544 -25.872 1 93.05 ? O44 3VV 302 A 1 
HETATM 46 O O45 3VV . . . D 2 22.689 -3.988 -24.513 1 56.1 ? O45 3VV 302 A 1 
HETATM 47 C C46 3VV . . . D 2 22.634 -2.833 -23.708 1 55.86 ? C46 3VV 302 A 1 
HETATM 48 C C47 3VV . . . D 2 21.307 -2.112 -23.913 1 55.27 ? C47 3VV 302 A 1 
HETATM 49 O O48 3VV . . . D 2 21.146 -1.288 -22.941 1 54.46 ? O48 3VV 302 A 1 
HETATM 50 C C49 3VV . . . D 2 21.58 0.055 -23.491 1 45.74 ? C49 3VV 302 A 1 
HETATM 51 C C50 3VV . . . D 2 22.164 -0.278 -24.904 1 67.69 ? C50 3VV 302 A 1 
HETATM 52 O O51 3VV . . . D 2 22.07 0.934 -25.82 1 66.4 ? O51 3VV 302 A 1 
HETATM 53 C C52 3VV . . . D 2 21.439 -1.216 -25.281 1 69.23 ? C52 3VV 302 A 1 
HETATM 54 O O53 3VV . . . D 2 20.115 -0.717 -25.735 1 69.87 ? O53 3VV 302 A 1 
HETATM 55 O O55 3VV . . . D 2 19.173 -0.29 -28.1 1 77.69 1 O55 3VV 302 A 1 
HETATM 56 O O56 3VV . . . D 2 20.324 -2.425 -27.643 1 77.84 1 O56 3VV 302 A 1 
HETATM 57 O O57 3VV . . . D 2 18.095 -2.011 -26.71 1 78.64 ? O57 3VV 302 A 1 
HETATM 58 N N58 3VV . . . D 2 22.53 0.668 -22.76 1 36.7 ? N58 3VV 302 A 1 
HETATM 59 C C59 3VV . . . D 2 23.835 0.485 -22.884 1 35.04 ? C59 3VV 302 A 1 
HETATM 60 N N60 3VV . . . D 2 24.478 1.266 -22.027 1 29.93 ? N60 3VV 302 A 1 
HETATM 61 C C61 3VV . . . D 2 23.562 1.972 -21.343 1 26.23 ? C61 3VV 302 A 1 
HETATM 62 C C62 3VV . . . D 2 23.625 2.944 -20.325 1 21.6 ? C62 3VV 302 A 1 
HETATM 63 N N63 3VV . . . D 2 24.918 3.373 -19.799 1 19.91 ? N63 3VV 302 A 1 
HETATM 64 N N64 3VV . . . D 2 22.504 3.463 -19.85 1 20.33 ? N64 3VV 302 A 1 
HETATM 65 C C65 3VV . . . D 2 21.324 3.07 -20.326 1 20.14 ? C65 3VV 302 A 1 
HETATM 66 N N66 3VV . . . D 2 21.219 2.164 -21.287 1 21.47 ? N66 3VV 302 A 1 
HETATM 67 C C67 3VV . . . D 2 22.322 1.599 -21.809 1 27.31 ? C67 3VV 302 A 1 
#
_model_server_stats.io_time_ms              50 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           67 
#