data_7OMF # _model_server_result.job_id vm4UPMnSq66PAaVOZHWSpg _model_server_result.datetime_utc '2025-01-18 06:40:30' _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 7omf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":104}' # _entry.id 7OMF # _exptl.entry_id 7OMF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 476.649 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(~{Z},2~{S})-5-[[4-[(2~{E},4~{E})-3-methyl-5-[(2~{S},4~{R})-4,6,6-trimethyl-4-oxidanyl-oxan-2-yl]penta-2,4-dienyl]cyclohexyl]amino]-5-oxidanylidene-pent-3-en-2-yl] ~{N}-methylcarbamate' _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 90 _cell.angle_gamma 90 _cell.entry_id 7OMF _cell.length_a 106.355 _cell.length_b 109.846 _cell.length_c 253.3 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7OMF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 6 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 D SG CYS 36 D CYS 26 1_555 H C2 T2W . D T2W 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? metalc ? metalc1 D SG CYS 21 D CYS 11 1_555 F ZN ZN . D ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc2 D SG CYS 33 D CYS 23 1_555 E ZN ZN . D ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc3 D SG CYS 40 D CYS 30 1_555 G ZN ZN . D ZN 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc4 D SG CYS 43 D CYS 33 1_555 G ZN ZN . D ZN 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc5 D SG CYS 56 D CYS 46 1_555 F ZN ZN . D ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc6 D SG CYS 59 D CYS 49 1_555 F ZN ZN . D ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc7 D SG CYS 68 D CYS 58 1_555 E ZN ZN . D ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc8 D SG CYS 71 D CYS 61 1_555 E ZN ZN . D ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc9 D SG CYS 82 D CYS 72 1_555 G ZN ZN . D ZN 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc10 D SG CYS 85 D CYS 75 1_555 G ZN ZN . D ZN 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc11 D SG CYS 95 D CYS 85 1_555 F ZN ZN . D ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc12 E ZN ZN . D ZN 101 1_555 I S SCN . D SCN 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? # _chem_comp.formula 'C27 H44 N2 O5' _chem_comp.formula_weight 476.649 _chem_comp.id T2W _chem_comp.mon_nstd_flag . _chem_comp.name '[(~{Z},2~{S})-5-[[4-[(2~{E},4~{E})-3-methyl-5-[(2~{S},4~{R})-4,6,6-trimethyl-4-oxidanyl-oxan-2-yl]penta-2,4-dienyl]cyclohexyl]amino]-5-oxidanylidene-pent-3-en-2-yl] ~{N}-methylcarbamate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C23 C22 T2W sing 290 n n C21 C20 T2W doub 291 z n C21 C22 T2W sing 292 n n C20 C19 T2W sing 293 n n C22 O3 T2W sing 294 n n O3 C24 T2W sing 295 n n C19 N T2W sing 296 n n C19 O2 T2W doub 297 n n N C16 T2W sing 298 n n C16 C17 T2W sing 299 n n C16 C15 T2W sing 300 n n C24 N1 T2W sing 301 n n C24 O4 T2W doub 302 n n C17 C18 T2W sing 303 n n N1 C25 T2W sing 304 n n C18 C13 T2W sing 305 n n C15 C14 T2W sing 306 n n C14 C13 T2W sing 307 n n C13 C12 T2W sing 308 n n C12 C11 T2W sing 309 n n C11 C10 T2W doub 310 e n C10 C26 T2W sing 311 n n C10 C9 T2W sing 312 n n C9 C8 T2W doub 313 e n C8 C7 T2W sing 314 n n C7 C T2W sing 315 n n C7 O1 T2W sing 316 n n C C1 T2W sing 317 n n O1 C4 T2W sing 318 n n O C1 T2W sing 319 n n C5 C4 T2W sing 320 n n C1 C2 T2W sing 321 n n C1 C3 T2W sing 322 n n C4 C3 T2W sing 323 n n C4 C6 T2W sing 324 n n N1 H1 T2W sing 325 n n C6 H2 T2W sing 326 n n C6 H3 T2W sing 327 n n C6 H4 T2W sing 328 n n C5 H5 T2W sing 329 n n C5 H6 T2W sing 330 n n C5 H7 T2W sing 331 n n C2 H8 T2W sing 332 n n C2 H9 T2W sing 333 n n C2 H10 T2W sing 334 n n C11 H11 T2W sing 335 n n C12 H12 T2W sing 336 n n C12 H13 T2W sing 337 n n C17 H14 T2W sing 338 n n C17 H15 T2W sing 339 n n C18 H16 T2W sing 340 n n C18 H17 T2W sing 341 n n C21 H18 T2W sing 342 n n C22 H19 T2W sing 343 n n C23 H20 T2W sing 344 n n C23 H21 T2W sing 345 n n C23 H22 T2W sing 346 n n C25 H23 T2W sing 347 n n C25 H24 T2W sing 348 n n C25 H25 T2W sing 349 n n C26 H26 T2W sing 350 n n C26 H27 T2W sing 351 n n C26 H28 T2W sing 352 n n N H29 T2W sing 353 n n C H30 T2W sing 354 n n C H31 T2W sing 355 n n O H32 T2W sing 356 n n C13 H33 T2W sing 357 n n C14 H34 T2W sing 358 n n C14 H35 T2W sing 359 n n C15 H36 T2W sing 360 n n C15 H37 T2W sing 361 n n C16 H38 T2W sing 362 n n C20 H39 T2W sing 363 n n C3 H40 T2W sing 364 n n C3 H41 T2W sing 365 n n C7 H42 T2W sing 366 n n C8 H43 T2W sing 367 n n C9 H44 T2W sing 368 n n # _atom_sites.entry_id 7OMF _atom_sites.fract_transf_matrix[1][1] 0.009402 _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] 0.009104 _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] 0.003948 _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 E 5 ZN D 1 101 1 ZN ZN . F 5 ZN D 1 102 2 ZN ZN . G 5 ZN D 1 103 3 ZN ZN . H 6 T2W D 1 104 101 T2W S6M . I 7 SCN D 1 105 101 SCN SCN . # 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 N N1 T2W . . . H 6 -12.948 36.644 -31.291 1 107.31 ? N1 T2W 104 D 1 HETATM 2 C C6 T2W . . . H 6 -17.625 43.052 -44.525 1 125.88 ? C6 T2W 104 D 1 HETATM 3 C C5 T2W . . . H 6 -19.124 42.817 -42.541 1 117.53 ? C5 T2W 104 D 1 HETATM 4 C C4 T2W . . . H 6 -17.887 42.286 -43.242 1 122.17 ? C4 T2W 104 D 1 HETATM 5 C C2 T2W . . . H 6 -17.508 38.427 -42.756 1 104.28 ? C2 T2W 104 D 1 HETATM 6 O O2 T2W . . . H 6 -16.71 41.221 -30.663 1 104.62 ? O2 T2W 104 D 1 HETATM 7 O O4 T2W . . . H 6 -13.8 38.552 -32.163 1 112.32 ? O4 T2W 104 D 1 HETATM 8 C C11 T2W . . . H 6 -15.975 43.99 -36.938 1 113.13 ? C11 T2W 104 D 1 HETATM 9 C C12 T2W . . . H 6 -15.442 44.75 -35.761 1 101.7 ? C12 T2W 104 D 1 HETATM 10 C C17 T2W . . . H 6 -17.071 45.164 -32.246 1 106.09 ? C17 T2W 104 D 1 HETATM 11 C C18 T2W . . . H 6 -16.091 45.378 -33.395 1 104.76 ? C18 T2W 104 D 1 HETATM 12 C C19 T2W . . . H 6 -15.751 41.997 -30.808 1 105.62 ? C19 T2W 104 D 1 HETATM 13 C C21 T2W . . . H 6 -13.906 40.529 -29.902 1 109.64 ? C21 T2W 104 D 1 HETATM 14 C C22 T2W . . . H 6 -14.711 39.28 -29.715 1 106.64 ? C22 T2W 104 D 1 HETATM 15 C C23 T2W . . . H 6 -15.285 39.158 -28.323 1 91.23 ? C23 T2W 104 D 1 HETATM 16 C C24 T2W . . . H 6 -13.536 37.831 -31.226 1 109.44 ? C24 T2W 104 D 1 HETATM 17 C C25 T2W . . . H 6 -12.544 36.063 -32.557 1 95.7 ? C25 T2W 104 D 1 HETATM 18 C C26 T2W . . . H 6 -13.949 43.964 -38.429 1 107.94 ? C26 T2W 104 D 1 HETATM 19 O O1 T2W . . . H 6 -16.784 42.581 -42.395 1 117.57 ? O1 T2W 104 D 1 HETATM 20 N N T2W . . . H 6 -15.903 43.228 -31.321 1 106.95 ? N T2W 104 D 1 HETATM 21 C C T2W . . . H 6 -16.554 40.363 -41.463 1 103.86 ? C T2W 104 D 1 HETATM 22 O O T2W . . . H 6 -18.912 39.861 -41.454 1 97.41 ? O T2W 104 D 1 HETATM 23 C C1 T2W . . . H 6 -17.738 39.857 -42.285 1 103.5 ? C1 T2W 104 D 1 HETATM 24 C C10 T2W . . . H 6 -15.374 43.644 -38.077 1 108.22 ? C10 T2W 104 D 1 HETATM 25 C C13 T2W . . . H 6 -16.453 44.555 -34.626 1 101.99 ? C13 T2W 104 D 1 HETATM 26 C C14 T2W . . . H 6 -16.575 43.087 -34.236 1 99.25 ? C14 T2W 104 D 1 HETATM 27 C C15 T2W . . . H 6 -17.557 42.873 -33.09 1 109.27 ? C15 T2W 104 D 1 HETATM 28 C C16 T2W . . . H 6 -17.172 43.697 -31.876 1 110.09 ? C16 T2W 104 D 1 HETATM 29 C C20 T2W . . . H 6 -14.367 41.666 -30.397 1 110 ? C20 T2W 104 D 1 HETATM 30 C C3 T2W . . . H 6 -17.965 40.78 -43.487 1 115.65 ? C3 T2W 104 D 1 HETATM 31 C C7 T2W . . . H 6 -16.797 41.838 -41.173 1 113.27 ? C7 T2W 104 D 1 HETATM 32 C C8 T2W . . . H 6 -15.819 42.465 -40.229 1 113.31 ? C8 T2W 104 D 1 HETATM 33 C C9 T2W . . . H 6 -16.172 42.909 -39.039 1 111.29 ? C9 T2W 104 D 1 HETATM 34 O O3 T2W . . . H 6 -13.821 38.126 -29.937 1 114.83 ? O3 T2W 104 D 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 51 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 34 #