data_6VZ1 # _model_server_result.job_id bxDq3iNsBdzlZqdlMQbhIg _model_server_result.datetime_utc '2024-11-05 03:42:31' _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 6vz1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":503}' # _entry.id 6VZ1 # _exptl.entry_id 6VZ1 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 1031.98 _entity.id 3 _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 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 6VZ1 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VZ1 _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,E,F,G,H _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 ? 3 E N N ? 3 H 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 6VZ1 _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 6OU A 1 501 1 6OU PPE . D 2 6OU A 1 502 3 6OU PPE . E 3 3VV A 1 503 1 3VV 3VV . F 2 6OU B 1 501 2 6OU PPE . G 2 6OU B 1 502 4 6OU PPE . H 3 3VV B 1 503 2 3VV 3VV . # 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 3 128.303 117.987 114.815 1 75.64 ? C10 3VV 503 A 1 HETATM 2 C C13 3VV . . . E 3 128.962 115.84 111.66 1 75.64 ? C13 3VV 503 A 1 HETATM 3 C C15 3VV . . . E 3 129.046 114.643 109.449 1 75.64 ? C15 3VV 503 A 1 HETATM 4 C C17 3VV . . . E 3 130.452 114.804 107.331 1 75.64 ? C17 3VV 503 A 1 HETATM 5 C C21 3VV . . . E 3 130.364 113.267 103.47 1 75.64 ? C21 3VV 503 A 1 HETATM 6 C C22 3VV . . . E 3 130.185 113.707 102.03 1 75.64 ? C22 3VV 503 A 1 HETATM 7 C C24 3VV . . . E 3 129.841 112.692 99.831 1 75.64 ? C24 3VV 503 A 1 HETATM 8 C C26 3VV . . . E 3 129.772 111.406 99.049 1 75.64 ? C26 3VV 503 A 1 HETATM 9 P P38 3VV . . . E 3 130.053 107.387 91.579 1 75.64 ? P38 3VV 503 A 1 HETATM 10 P P42 3VV . . . E 3 131.843 105.826 89.912 1 75.64 ? P42 3VV 503 A 1 HETATM 11 P P54 3VV . . . E 3 131.612 109.824 84.967 1 75.64 ? P54 3VV 503 A 1 HETATM 12 C C01 3VV . . . E 3 126.916 120.419 124.274 1 75.64 ? C01 3VV 503 A 1 HETATM 13 C C02 3VV . . . E 3 126.765 119.136 123.496 1 75.64 ? C02 3VV 503 A 1 HETATM 14 C C03 3VV . . . E 3 127.334 119.209 122.098 1 75.64 ? C03 3VV 503 A 1 HETATM 15 C C04 3VV . . . E 3 126.762 120.343 121.275 1 75.64 ? C04 3VV 503 A 1 HETATM 16 C C05 3VV . . . E 3 126.652 120.034 119.793 1 75.64 ? C05 3VV 503 A 1 HETATM 17 C C06 3VV . . . E 3 127.975 119.836 119.082 1 75.64 ? C06 3VV 503 A 1 HETATM 18 C C07 3VV . . . E 3 127.815 119.294 117.675 1 75.64 ? C07 3VV 503 A 1 HETATM 19 C C08 3VV . . . E 3 129.122 119.081 116.928 1 75.64 ? C08 3VV 503 A 1 HETATM 20 C C09 3VV . . . E 3 129.01 117.976 115.927 1 75.64 ? C09 3VV 503 A 1 HETATM 21 C C11 3VV . . . E 3 128.204 116.862 113.835 1 75.64 ? C11 3VV 503 A 1 HETATM 22 C C12 3VV . . . E 3 128.77 117.128 112.439 1 75.64 ? C12 3VV 503 A 1 HETATM 23 C C14 3VV . . . E 3 129.174 115.98 110.166 1 75.64 ? C14 3VV 503 A 1 HETATM 24 C C16 3VV . . . E 3 129.056 114.716 107.933 1 75.64 ? C16 3VV 503 A 1 HETATM 25 C C18 3VV . . . E 3 130.624 113.884 106.154 1 75.64 ? C18 3VV 503 A 1 HETATM 26 O O19 3VV . . . E 3 130.842 112.707 106.26 1 75.64 ? O19 3VV 503 A 1 HETATM 27 S S20 3VV . . . E 3 130.441 114.685 104.6 1 75.64 ? S20 3VV 503 A 1 HETATM 28 N N23 3VV . . . E 3 130.143 112.572 101.12 1 75.64 ? N23 3VV 503 A 1 HETATM 29 O O25 3VV . . . E 3 129.613 113.773 99.302 1 75.64 ? O25 3VV 503 A 1 HETATM 30 C C27 3VV . . . E 3 131.093 111.044 98.419 1 75.64 ? C27 3VV 503 A 1 HETATM 31 N N28 3VV . . . E 3 131.124 111.338 96.993 1 75.64 ? N28 3VV 503 A 1 HETATM 32 C C29 3VV . . . E 3 130.396 110.665 96.103 1 75.64 ? C29 3VV 503 A 1 HETATM 33 O O30 3VV . . . E 3 129.552 109.837 96.423 1 75.64 ? O30 3VV 503 A 1 HETATM 34 C C31 3VV . . . E 3 130.667 110.965 94.636 1 75.64 ? C31 3VV 503 A 1 HETATM 35 O O32 3VV . . . E 3 129.451 111.239 93.943 1 75.64 ? O32 3VV 503 A 1 HETATM 36 C C33 3VV . . . E 3 131.579 109.958 93.889 1 75.64 ? C33 3VV 503 A 1 HETATM 37 C C34 3VV . . . E 3 132.974 110.562 93.718 1 75.64 ? C34 3VV 503 A 1 HETATM 38 C C35 3VV . . . E 3 131.687 108.651 94.68 1 75.64 ? C35 3VV 503 A 1 HETATM 39 C C36 3VV . . . E 3 131.018 109.645 92.508 1 75.64 ? C36 3VV 503 A 1 HETATM 40 O O37 3VV . . . E 3 131.235 108.265 92.188 1 75.64 ? O37 3VV 503 A 1 HETATM 41 O O39 3VV . . . E 3 129.551 108.116 90.345 1 75.64 ? O39 3VV 503 A 1 HETATM 42 O O40 3VV . . . E 3 129.019 107.072 92.584 1 75.64 ? O40 3VV 503 A 1 HETATM 43 O O41 3VV . . . E 3 130.78 106.07 91.069 1 75.64 ? O41 3VV 503 A 1 HETATM 44 O O43 3VV . . . E 3 133.109 106.539 90.324 1 75.64 ? O43 3VV 503 A 1 HETATM 45 O O44 3VV . . . E 3 132.028 104.384 89.645 1 75.64 ? O44 3VV 503 A 1 HETATM 46 O O45 3VV . . . E 3 131.27 106.643 88.654 1 75.64 ? O45 3VV 503 A 1 HETATM 47 C C46 3VV . . . E 3 132.113 107.15 87.601 1 75.64 ? C46 3VV 503 A 1 HETATM 48 C C47 3VV . . . E 3 131.628 106.578 86.294 1 75.64 ? C47 3VV 503 A 1 HETATM 49 O O48 3VV . . . E 3 131.05 105.282 86.541 1 75.64 ? O48 3VV 503 A 1 HETATM 50 C C49 3VV . . . E 3 130.044 105.01 85.583 1 75.64 ? C49 3VV 503 A 1 HETATM 51 C C50 3VV . . . E 3 129.803 106.297 84.771 1 75.64 ? C50 3VV 503 A 1 HETATM 52 O O51 3VV . . . E 3 130.403 106.219 83.483 1 75.64 ? O51 3VV 503 A 1 HETATM 53 C C52 3VV . . . E 3 130.505 107.353 85.623 1 75.64 ? C52 3VV 503 A 1 HETATM 54 O O53 3VV . . . E 3 131.074 108.315 84.708 1 75.64 ? O53 3VV 503 A 1 HETATM 55 O O55 3VV . . . E 3 132.836 109.982 84.056 1 75.64 ? O55 3VV 503 A 1 HETATM 56 O O56 3VV . . . E 3 131.936 110.059 86.394 1 75.64 ? O56 3VV 503 A 1 HETATM 57 O O57 3VV . . . E 3 130.524 110.769 84.444 1 75.64 ? O57 3VV 503 A 1 HETATM 58 N N58 3VV . . . E 3 128.863 104.511 86.283 1 75.64 ? N58 3VV 503 A 1 HETATM 59 C C59 3VV . . . E 3 128.557 104.678 87.608 1 75.64 ? C59 3VV 503 A 1 HETATM 60 N N60 3VV . . . E 3 127.401 104.169 87.959 1 75.64 ? N60 3VV 503 A 1 HETATM 61 C C61 3VV . . . E 3 126.911 103.624 86.782 1 75.64 ? C61 3VV 503 A 1 HETATM 62 C C62 3VV . . . E 3 125.714 102.95 86.473 1 75.64 ? C62 3VV 503 A 1 HETATM 63 N N63 3VV . . . E 3 124.748 102.7 87.363 1 75.64 ? N63 3VV 503 A 1 HETATM 64 N N64 3VV . . . E 3 125.535 102.541 85.199 1 75.64 ? N64 3VV 503 A 1 HETATM 65 C C65 3VV . . . E 3 126.493 102.79 84.302 1 75.64 ? C65 3VV 503 A 1 HETATM 66 N N66 3VV . . . E 3 127.657 103.419 84.475 1 75.64 ? N66 3VV 503 A 1 HETATM 67 C C67 3VV . . . E 3 127.806 103.819 85.743 1 75.64 ? C67 3VV 503 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 67 #