data_4PDK # _model_server_result.job_id TyEbod9oZj7qkyc2vmHLTA _model_server_result.datetime_utc '2025-02-17 18:26:44' _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":"E","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 . . . E 2 17.886 -29.953 -12.344 1 58.15 ? C10 3VV 301 B 1 HETATM 2 C C13 3VV . . . E 2 20.041 -32.635 -12.224 1 58.73 ? C13 3VV 301 B 1 HETATM 3 C C15 3VV . . . E 2 20.939 -34.355 -10.594 1 59.67 ? C15 3VV 301 B 1 HETATM 4 C C17 3VV . . . E 2 21.955 -36.572 -11.341 1 40.48 ? C17 3VV 301 B 1 HETATM 5 C C21 3VV . . . E 2 25.948 -34.83 -12.163 1 44.87 ? C21 3VV 301 B 1 HETATM 6 C C22 3VV . . . E 2 27.043 -35.202 -13.183 1 41.84 ? C22 3VV 301 B 1 HETATM 7 C C24 3VV . . . E 2 27.944 -32.932 -13.82 1 37.18 ? C24 3VV 301 B 1 HETATM 8 C C26 3VV . . . E 2 29.031 -31.863 -13.733 1 36.15 ? C26 3VV 301 B 1 HETATM 9 P P38 3VV . . . E 2 33.796 -25.347 -14.155 1 64.42 ? P38 3VV 301 B 1 HETATM 10 P P42 3VV . . . E 2 36.683 -25.253 -14.547 1 84.83 ? P42 3VV 301 B 1 HETATM 11 P P54 3VV . . . E 2 40.792 -20.44 -12.181 1 104.81 ? P54 3VV 301 B 1 HETATM 12 C C01 3VV . . . E 2 21.066 -21.159 -9.039 1 44.57 ? C01 3VV 301 B 1 HETATM 13 C C02 3VV . . . E 2 20.399 -22.353 -9.72 1 41.03 ? C02 3VV 301 B 1 HETATM 14 C C03 3VV . . . E 2 20.897 -23.687 -9.154 1 40.09 ? C03 3VV 301 B 1 HETATM 15 C C04 3VV . . . E 2 20.568 -24.867 -10.087 1 41.88 ? C04 3VV 301 B 1 HETATM 16 C C05 3VV . . . E 2 20.882 -26.251 -9.431 1 46.7 ? C05 3VV 301 B 1 HETATM 17 C C06 3VV . . . E 2 19.593 -27.122 -9.285 1 18.69 ? C06 3VV 301 B 1 HETATM 18 C C07 3VV . . . E 2 19.904 -28.664 -9.381 1 25.39 ? C07 3VV 301 B 1 HETATM 19 C C08 3VV . . . E 2 19.773 -29.195 -10.849 1 51.06 ? C08 3VV 301 B 1 HETATM 20 C C09 3VV . . . E 2 18.257 -29.293 -11.229 1 57.14 ? C09 3VV 301 B 1 HETATM 21 C C11 3VV . . . E 2 18.95 -30.594 -13.234 1 59.05 ? C11 3VV 301 B 1 HETATM 22 C C12 3VV . . . E 2 18.88 -32.124 -13.085 1 58.83 ? C12 3VV 301 B 1 HETATM 23 C C14 3VV . . . E 2 19.707 -33.877 -11.387 1 59.21 ? C14 3VV 301 B 1 HETATM 24 C C16 3VV . . . E 2 20.952 -35.879 -10.381 1 60.36 ? C16 3VV 301 B 1 HETATM 25 C C18 3VV . . . E 2 23.385 -35.995 -11.205 1 39.33 ? C18 3VV 301 B 1 HETATM 26 O O19 3VV . . . E 2 23.889 -35.88 -10.139 1 38.35 ? O19 3VV 301 B 1 HETATM 27 S S20 3VV . . . E 2 24.317 -35.48 -12.71 1 19.92 ? S20 3VV 301 B 1 HETATM 28 N N23 3VV . . . E 2 28.103 -34.191 -13.095 1 39.84 ? N23 3VV 301 B 1 HETATM 29 O O25 3VV . . . E 2 26.979 -32.734 -14.473 1 36.34 ? O25 3VV 301 B 1 HETATM 30 C C27 3VV . . . E 2 28.423 -30.472 -13.469 1 36.24 ? C27 3VV 301 B 1 HETATM 31 N N28 3VV . . . E 2 29.476 -29.473 -13.669 1 36.44 ? N28 3VV 301 B 1 HETATM 32 C C29 3VV . . . E 2 30.374 -29.189 -12.551 1 35.11 ? C29 3VV 301 B 1 HETATM 33 O O30 3VV . . . E 2 30.212 -29.76 -11.528 1 34.62 ? O30 3VV 301 B 1 HETATM 34 C C31 3VV . . . E 2 31.494 -28.146 -12.726 1 37.98 ? C31 3VV 301 B 1 HETATM 35 O O32 3VV . . . E 2 31.274 -27.455 -13.904 1 34.56 ? O32 3VV 301 B 1 HETATM 36 C C33 3VV . . . E 2 32.869 -28.822 -12.828 1 39.69 ? C33 3VV 301 B 1 HETATM 37 C C34 3VV . . . E 2 32.828 -29.942 -13.878 1 41.1 ? C34 3VV 301 B 1 HETATM 38 C C35 3VV . . . E 2 33.256 -29.404 -11.456 1 40.61 ? C35 3VV 301 B 1 HETATM 39 C C36 3VV . . . E 2 33.935 -27.781 -13.218 1 45.08 ? C36 3VV 301 B 1 HETATM 40 O O37 3VV . . . E 2 33.501 -26.977 -14.284 1 51.3 ? O37 3VV 301 B 1 HETATM 41 O O39 3VV . . . E 2 33.621 -24.648 -15.486 1 64.06 1 O39 3VV 301 B 1 HETATM 42 O O40 3VV . . . E 2 32.837 -24.749 -13.151 1 63.07 ? O40 3VV 301 B 1 HETATM 43 O O41 3VV . . . E 2 35.336 -25.13 -13.592 1 56.14 ? O41 3VV 301 B 1 HETATM 44 O O43 3VV . . . E 2 36.292 -24.921 -15.972 1 87.63 1 O43 3VV 301 B 1 HETATM 45 O O44 3VV . . . E 2 37.234 -26.66 -14.483 1 82 ? O44 3VV 301 B 1 HETATM 46 O O45 3VV . . . E 2 37.82 -24.161 -13.994 0.5 64.11 ? O45 3VV 301 B 1 HETATM 47 C C46 3VV . . . E 2 37.771 -22.843 -14.503 0.5 62.77 ? C46 3VV 301 B 1 HETATM 48 C C47 3VV . . . E 2 37.21 -21.869 -13.452 0.5 61.97 ? C47 3VV 301 B 1 HETATM 49 O O48 3VV . . . E 2 36.258 -22.351 -12.747 0.5 60.82 ? O48 3VV 301 B 1 HETATM 50 C C49 3VV . . . E 2 36.139 -21.225 -11.737 0.5 59.11 ? C49 3VV 301 B 1 HETATM 51 C C50 3VV . . . E 2 37.63 -20.846 -11.427 0.5 83.3 ? C50 3VV 301 B 1 HETATM 52 O O51 3VV . . . E 2 37.796 -19.341 -11.588 0.5 83.96 ? O51 3VV 301 B 1 HETATM 53 C C52 3VV . . . E 2 38.303 -21.436 -12.305 0.5 81.5 ? C52 3VV 301 B 1 HETATM 54 O O53 3VV . . . E 2 39.316 -20.522 -12.889 0.5 79.79 ? O53 3VV 301 B 1 HETATM 55 O O55 3VV . . . E 2 41.862 -20.693 -13.218 0.5 104.87 ? O55 3VV 301 B 1 HETATM 56 O O56 3VV . . . E 2 40.99 -19.069 -11.581 0.5 103.73 1 O56 3VV 301 B 1 HETATM 57 O O57 3VV . . . E 2 40.883 -21.482 -11.096 0.5 105.24 ? O57 3VV 301 B 1 HETATM 58 N N58 3VV . . . E 2 35.386 -21.571 -10.667 0.5 57.14 ? N58 3VV 301 B 1 HETATM 59 C C59 3VV . . . E 2 35.224 -22.799 -10.212 0.5 55.85 ? C59 3VV 301 B 1 HETATM 60 N N60 3VV . . . E 2 34.41 -22.787 -9.165 0.5 55.96 ? N60 3VV 301 B 1 HETATM 61 C C61 3VV . . . E 2 34.026 -21.523 -8.941 0.5 56.2 ? C61 3VV 301 B 1 HETATM 62 C C62 3VV . . . E 2 33.188 -20.899 -7.993 0.5 56.05 ? C62 3VV 301 B 1 HETATM 63 N N63 3VV . . . E 2 32.519 -21.69 -6.964 0.5 55.43 ? N63 3VV 301 B 1 HETATM 64 N N64 3VV . . . E 2 33.011 -19.59 -8.041 0.5 56.34 ? N64 3VV 301 B 1 HETATM 65 C C65 3VV . . . E 2 33.62 -18.872 -8.981 0.5 56.55 ? C65 3VV 301 B 1 HETATM 66 N N66 3VV . . . E 2 34.418 -19.417 -9.891 0.5 56.25 ? N66 3VV 301 B 1 HETATM 67 C C67 3VV . . . E 2 34.641 -20.744 -9.897 0.5 56.35 ? C67 3VV 301 B 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 67 #