data_9UDE # _model_server_result.job_id uEfI9GzDWM-PMKsw-72YYg _model_server_result.datetime_utc '2025-07-10 20:27:05' _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 9ude # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 9UDE # _exptl.entry_id 9UDE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 296.402 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'diepoxidized farnesyl acetate' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.37 _cell.angle_gamma 90 _cell.entry_id 9UDE _cell.length_a 67.622 _cell.length_b 52.765 _cell.length_c 145.829 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9UDE _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,G,H,I _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C17 H28 O4' _chem_comp.formula_weight 296.402 _chem_comp.id YK6 _chem_comp.mon_nstd_flag . _chem_comp.name 'diepoxidized farnesyl acetate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '[(~{E})-5-[(2~{S},3~{S})-3-[2-[(2~{R})-3,3-dimethyloxiran-2-yl]ethyl]-3-methyl-oxiran-2-yl]-3-methyl-pent-2-enyl] ethanoate' # 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 C19 C14 YK6 sing 480 n n C07 C06 YK6 sing 481 n n C07 C08 YK6 sing 482 n n C17 C06 YK6 sing 483 n n O20 C14 YK6 sing 484 n n O20 C13 YK6 sing 485 n n C06 C05 YK6 doub 486 e n C12 C11 YK6 sing 487 n n C12 C13 YK6 sing 488 n n C09 O21 YK6 sing 489 n n C09 C08 YK6 sing 490 n n C09 C10 YK6 sing 491 n n C14 C13 YK6 sing 492 n n C14 C15 YK6 sing 493 n n O21 C10 YK6 sing 494 n n C11 C10 YK6 sing 495 n n C05 C04 YK6 sing 496 n n C10 C18 YK6 sing 497 n n C04 O03 YK6 sing 498 n n O16 C02 YK6 doub 499 n n O03 C02 YK6 sing 500 n n C02 C01 YK6 sing 501 n n C01 H1 YK6 sing 502 n n C01 H2 YK6 sing 503 n n C01 H3 YK6 sing 504 n n C04 H4 YK6 sing 505 n n C04 H5 YK6 sing 506 n n C05 H6 YK6 sing 507 n n C07 H7 YK6 sing 508 n n C07 H8 YK6 sing 509 n n C08 H9 YK6 sing 510 n n C08 H10 YK6 sing 511 n n C09 H11 YK6 sing 512 n n C11 H12 YK6 sing 513 n n C11 H13 YK6 sing 514 n n C12 H14 YK6 sing 515 n n C12 H15 YK6 sing 516 n n C13 H16 YK6 sing 517 n n C15 H17 YK6 sing 518 n n C15 H18 YK6 sing 519 n n C15 H19 YK6 sing 520 n n C17 H20 YK6 sing 521 n n C17 H21 YK6 sing 522 n n C17 H22 YK6 sing 523 n n C18 H23 YK6 sing 524 n n C18 H24 YK6 sing 525 n n C18 H25 YK6 sing 526 n n C19 H26 YK6 sing 527 n n C19 H27 YK6 sing 528 n n C19 H28 YK6 sing 529 n n # _atom_sites.entry_id 9UDE _atom_sites.fract_transf_matrix[1][1] 0.014788 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000612 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018952 _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] 0.006863 _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 FAD A 1 501 700 FAD FAD . D 3 YK6 A 1 502 801 YK6 EDO . E 4 GOL A 1 503 901 GOL GOL . F 5 CL A 1 504 1 CL CL . G 2 FAD B 1 700 700 FAD FAD . H 6 HOH A 1 601 23 HOH HOH . H 6 HOH A 2 602 3 HOH HOH . H 6 HOH A 3 603 1 HOH HOH . H 6 HOH A 4 604 30 HOH HOH . H 6 HOH A 5 605 36 HOH HOH . H 6 HOH A 6 606 47 HOH HOH . H 6 HOH A 7 607 48 HOH HOH . H 6 HOH A 8 608 49 HOH HOH . H 6 HOH A 9 609 31 HOH HOH . H 6 HOH A 10 610 9 HOH HOH . H 6 HOH A 11 611 26 HOH HOH . H 6 HOH A 12 612 69 HOH HOH . H 6 HOH A 13 613 5 HOH HOH . H 6 HOH A 14 614 15 HOH HOH . H 6 HOH A 15 615 19 HOH HOH . H 6 HOH A 16 616 8 HOH HOH . H 6 HOH A 17 617 60 HOH HOH . H 6 HOH A 18 618 10 HOH HOH . H 6 HOH A 19 619 42 HOH HOH . H 6 HOH A 20 620 4 HOH HOH . H 6 HOH A 21 621 29 HOH HOH . H 6 HOH A 22 622 6 HOH HOH . H 6 HOH A 23 623 43 HOH HOH . H 6 HOH A 24 624 27 HOH HOH . H 6 HOH A 25 625 24 HOH HOH . H 6 HOH A 26 626 52 HOH HOH . H 6 HOH A 27 627 7 HOH HOH . H 6 HOH A 28 628 68 HOH HOH . H 6 HOH A 29 629 2 HOH HOH . H 6 HOH A 30 630 18 HOH HOH . H 6 HOH A 31 631 22 HOH HOH . H 6 HOH A 32 632 54 HOH HOH . H 6 HOH A 33 633 20 HOH HOH . H 6 HOH A 34 634 57 HOH HOH . H 6 HOH A 35 635 17 HOH HOH . H 6 HOH A 36 636 28 HOH HOH . H 6 HOH A 37 637 63 HOH HOH . H 6 HOH A 38 638 58 HOH HOH . H 6 HOH A 39 639 37 HOH HOH . H 6 HOH A 40 640 32 HOH HOH . H 6 HOH A 41 641 70 HOH HOH . H 6 HOH A 42 642 50 HOH HOH . H 6 HOH A 43 643 41 HOH HOH . H 6 HOH A 44 644 64 HOH HOH . H 6 HOH A 45 645 38 HOH HOH . I 6 HOH B 1 801 12 HOH HOH . I 6 HOH B 2 802 55 HOH HOH . I 6 HOH B 3 803 59 HOH HOH . I 6 HOH B 4 804 11 HOH HOH . I 6 HOH B 5 805 34 HOH HOH . I 6 HOH B 6 806 71 HOH HOH . I 6 HOH B 7 807 33 HOH HOH . I 6 HOH B 8 808 62 HOH HOH . # 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 C01 YK6 . . . D 3 39.623 -2.719 51.129 1 95.29 ? C01 YK6 502 A 1 HETATM 2 C C02 YK6 . . . D 3 40.049 -3.826 50.184 1 88.5 ? C02 YK6 502 A 1 HETATM 3 C C04 YK6 . . . D 3 38.666 -5.034 48.683 1 86.03 ? C04 YK6 502 A 1 HETATM 4 C C05 YK6 . . . D 3 37.974 -3.857 48.047 1 77.21 ? C05 YK6 502 A 1 HETATM 5 C C06 YK6 . . . D 3 36.853 -3.887 47.308 1 74.46 ? C06 YK6 502 A 1 HETATM 6 C C07 YK6 . . . D 3 36.291 -2.597 46.75 1 70.95 ? C07 YK6 502 A 1 HETATM 7 C C08 YK6 . . . D 3 36.316 -1.485 47.81 1 75.31 ? C08 YK6 502 A 1 HETATM 8 C C09 YK6 . . . D 3 37.075 -0.248 47.344 1 86.92 ? C09 YK6 502 A 1 HETATM 9 C C10 YK6 . . . D 3 37.683 0.663 48.277 1 84.16 ? C10 YK6 502 A 1 HETATM 10 C C11 YK6 . . . D 3 37.93 2.099 47.819 1 85.93 ? C11 YK6 502 A 1 HETATM 11 C C12 YK6 . . . D 3 36.667 2.828 47.325 1 83.96 ? C12 YK6 502 A 1 HETATM 12 C C13 YK6 . . . D 3 36.517 4.228 47.915 1 93.17 ? C13 YK6 502 A 1 HETATM 13 C C14 YK6 . . . D 3 35.624 5.223 47.375 1 87.09 ? C14 YK6 502 A 1 HETATM 14 C C15 YK6 . . . D 3 35.225 6.399 48.252 1 58.92 ? C15 YK6 502 A 1 HETATM 15 C C17 YK6 . . . D 3 36.079 -5.145 46.987 1 63.28 ? C17 YK6 502 A 1 HETATM 16 C C18 YK6 . . . D 3 37.803 0.379 49.765 1 63.05 ? C18 YK6 502 A 1 HETATM 17 C C19 YK6 . . . D 3 34.845 5.064 46.08 1 84.43 ? C19 YK6 502 A 1 HETATM 18 O O03 YK6 . . . D 3 39.02 -4.704 50.009 1 92.69 ? O03 YK6 502 A 1 HETATM 19 O O16 YK6 . . . D 3 41.139 -3.904 49.662 1 65.01 ? O16 YK6 502 A 1 HETATM 20 O O20 YK6 . . . D 3 37.209 5.172 47.133 1 99.36 ? O20 YK6 502 A 1 HETATM 21 O O21 YK6 . . . D 3 38.472 -0.419 47.396 1 83.05 ? O21 YK6 502 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #