data_4PDK # _model_server_result.job_id XC6yORw14zEuvJutW4GiWQ _model_server_result.datetime_utc '2024-11-28 04:09:28' _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":"C","auth_seq_id":301}' # _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 . . . C 2 15.2 -9.856 -6.181 1 32.91 ? C10 3VV 301 A 1 HETATM 2 C C13 3VV . . . C 2 16.564 -7.054 -4.532 1 31.4 ? C13 3VV 301 A 1 HETATM 3 C C15 3VV . . . C 2 18.246 -5.192 -4.841 1 31.65 ? C15 3VV 301 A 1 HETATM 4 C C17 3VV . . . C 2 18.802 -2.788 -4.234 1 18.03 ? C17 3VV 301 A 1 HETATM 5 C C21 3VV . . . C 2 20.687 -4.304 -0.531 1 32.87 ? C21 3VV 301 A 1 HETATM 6 C C22 3VV . . . C 2 20.264 -4.672 0.905 1 28.71 ? C22 3VV 301 A 1 HETATM 7 C C24 3VV . . . C 2 20.779 -6.799 2.213 1 24.34 ? C24 3VV 301 A 1 HETATM 8 C C26 3VV . . . C 2 21.829 -7.779 2.732 1 24.52 ? C26 3VV 301 A 1 HETATM 9 P P38 3VV . . . C 2 26.469 -14.062 6.687 1 106.61 ? P38 3VV 301 A 1 HETATM 10 P P42 3VV . . . C 2 26.584 -13.963 9.579 1 68.09 ? P42 3VV 301 A 1 HETATM 11 P P54 3VV . . . C 2 30.304 -17.96 12.555 1 80.49 ? P54 3VV 301 A 1 HETATM 12 C C01 3VV . . . C 2 20.216 -18.526 -5.931 1 36.6 ? C01 3VV 301 A 1 HETATM 13 C C02 3VV . . . C 2 19.099 -17.486 -5.863 1 36.59 ? C02 3VV 301 A 1 HETATM 14 C C03 3VV . . . C 2 19.602 -16.088 -6.234 1 35.13 ? C03 3VV 301 A 1 HETATM 15 C C04 3VV . . . C 2 18.561 -14.982 -5.979 1 32.81 ? C04 3VV 301 A 1 HETATM 16 C C05 3VV . . . C 2 19.186 -13.566 -6.193 1 17.25 ? C05 3VV 301 A 1 HETATM 17 C C06 3VV . . . C 2 18.119 -12.429 -6.113 1 11.36 ? C06 3VV 301 A 1 HETATM 18 C C07 3VV . . . C 2 18.75 -11.02 -6.428 1 45.9 ? C07 3VV 301 A 1 HETATM 19 C C08 3VV . . . C 2 17.736 -9.858 -6.166 1 14.44 ? C08 3VV 301 A 1 HETATM 20 C C09 3VV . . . C 2 16.347 -10.176 -6.819 1 34.41 ? C09 3VV 301 A 1 HETATM 21 C C11 3VV . . . C 2 15.242 -9.2 -4.8 1 31.28 ? C11 3VV 301 A 1 HETATM 22 C C12 3VV . . . C 2 15.209 -7.663 -4.917 1 30.57 ? C12 3VV 301 A 1 HETATM 23 C C14 3VV . . . C 2 16.756 -5.584 -4.929 1 33.8 ? C14 3VV 301 A 1 HETATM 24 C C16 3VV . . . C 2 18.527 -3.784 -5.39 1 29.88 ? C16 3VV 301 A 1 HETATM 25 C C18 3VV . . . C 2 19.795 -3.367 -3.2 1 18.35 ? C18 3VV 301 A 1 HETATM 26 O O19 3VV . . . C 2 20.939 -3.498 -3.48 1 17.06 ? O19 3VV 301 A 1 HETATM 27 S S20 3VV . . . C 2 19.205 -3.86 -1.525 1 30.68 ? S20 3VV 301 A 1 HETATM 28 N N23 3VV . . . C 2 21.225 -5.644 1.437 1 26.27 ? N23 3VV 301 A 1 HETATM 29 O O25 3VV . . . C 2 19.634 -6.981 2.448 1 23.19 ? O25 3VV 301 A 1 HETATM 30 C C27 3VV . . . C 2 21.466 -9.227 2.365 1 25.21 ? C27 3VV 301 A 1 HETATM 31 N N28 3VV . . . C 2 22.002 -10.111 3.4 1 23.8 ? N28 3VV 301 A 1 HETATM 32 C C29 3VV . . . C 2 23.419 -10.464 3.318 1 26.15 ? C29 3VV 301 A 1 HETATM 33 O O30 3VV . . . C 2 24.073 -10.04 2.431 1 16.62 ? O30 3VV 301 A 1 HETATM 34 C C31 3VV . . . C 2 24.022 -11.39 4.385 1 26.64 ? C31 3VV 301 A 1 HETATM 35 O O32 3VV . . . C 2 23.024 -11.722 5.288 1 30.97 ? O32 3VV 301 A 1 HETATM 36 C C33 3VV . . . C 2 25.156 -10.703 5.162 1 47.02 ? C33 3VV 301 A 1 HETATM 37 C C34 3VV . . . C 2 24.674 -9.367 5.746 1 38.55 ? C34 3VV 301 A 1 HETATM 38 C C35 3VV . . . C 2 26.41 -10.481 4.293 1 35.19 ? C35 3VV 301 A 1 HETATM 39 C C36 3VV . . . C 2 25.536 -11.655 6.298 1 50.69 ? C36 3VV 301 A 1 HETATM 40 O O37 3VV . . . C 2 25.989 -12.833 5.691 1 64.83 ? O37 3VV 301 A 1 HETATM 41 O O39 3VV . . . C 2 25.269 -14.925 7.006 1 107.12 1 O39 3VV 301 A 1 HETATM 42 O O40 3VV . . . C 2 27.53 -14.89 5.999 1 105.75 ? O40 3VV 301 A 1 HETATM 43 O O41 3VV . . . C 2 27.059 -13.414 8.089 1 63.28 ? O41 3VV 301 A 1 HETATM 44 O O43 3VV . . . C 2 25.508 -15.014 9.408 1 68.2 1 O43 3VV 301 A 1 HETATM 45 O O44 3VV . . . C 2 26.044 -12.814 10.4 1 68.61 ? O44 3VV 301 A 1 HETATM 46 O O45 3VV . . . C 2 27.894 -14.641 10.353 1 35.85 ? O45 3VV 301 A 1 HETATM 47 C C46 3VV . . . C 2 29.142 -14.637 9.687 1 36.24 ? C46 3VV 301 A 1 HETATM 48 C C47 3VV . . . C 2 30.257 -15.059 10.656 1 38.99 ? C47 3VV 301 A 1 HETATM 49 O O48 3VV . . . C 2 31.121 -14.115 10.777 1 40.77 ? O48 3VV 301 A 1 HETATM 50 C C49 3VV . . . C 2 30.955 -13.539 12.169 1 36.63 ? C49 3VV 301 A 1 HETATM 51 C C50 3VV . . . C 2 29.707 -14.272 12.767 1 55.02 ? C50 3VV 301 A 1 HETATM 52 O O51 3VV . . . C 2 29.873 -14.504 14.262 1 53.15 ? O51 3VV 301 A 1 HETATM 53 C C52 3VV . . . C 2 29.662 -15.362 12.159 1 54.69 ? C52 3VV 301 A 1 HETATM 54 O O53 3VV . . . C 2 30.509 -16.361 12.861 1 54.94 ? O53 3VV 301 A 1 HETATM 55 O O55 3VV . . . C 2 31.191 -18.767 13.477 1 80.4 ? O55 3VV 301 A 1 HETATM 56 O O56 3VV . . . C 2 30.678 -18.25 11.122 1 80.76 1 O56 3VV 301 A 1 HETATM 57 O O57 3VV . . . C 2 28.863 -18.341 12.785 1 80.54 ? O57 3VV 301 A 1 HETATM 58 N N58 3VV . . . C 2 30.753 -12.208 12.095 1 30.74 ? N58 3VV 301 A 1 HETATM 59 C C59 3VV . . . C 2 29.631 -11.617 11.716 1 29.48 ? C59 3VV 301 A 1 HETATM 60 N N60 3VV . . . C 2 29.785 -10.3 11.756 1 29.34 ? N60 3VV 301 A 1 HETATM 61 C C61 3VV . . . C 2 31.038 -10.039 12.168 1 28.02 ? C61 3VV 301 A 1 HETATM 62 C C62 3VV . . . C 2 31.778 -8.862 12.403 1 24.36 ? C62 3VV 301 A 1 HETATM 63 N N63 3VV . . . C 2 31.162 -7.557 12.188 1 22.82 ? N63 3VV 301 A 1 HETATM 64 N N64 3VV . . . C 2 33.033 -8.948 12.819 1 26.27 ? N64 3VV 301 A 1 HETATM 65 C C65 3VV . . . C 2 33.595 -10.139 13.018 1 27.7 ? C65 3VV 301 A 1 HETATM 66 N N66 3VV . . . C 2 32.936 -11.27 12.806 1 28.34 ? N66 3VV 301 A 1 HETATM 67 C C67 3VV . . . C 2 31.658 -11.249 12.384 1 29.15 ? C67 3VV 301 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 67 #