data_8PFT # _model_server_result.job_id SRKdhcH8gn_Hjda1P21d1g _model_server_result.datetime_utc '2024-11-28 10:26:31' _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 8pft # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 8PFT # _exptl.entry_id 8PFT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 528.392 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6,8-bis(4-fluorophenyl)-1,5-bis(oxidanyl)-2,4-dioxa-6,8-diaza-1$l^{4},5$l^{4}-diruthenabicyclo[3.3.0]octan-3-one _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 8PFT _cell.length_a 77.75 _cell.length_b 77.75 _cell.length_c 37.34 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PFT _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? 4 D N N ? 4 E N 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 disulf ? disulf1 A SG CYS 6 A CYS 6 1_555 A SG CYS 127 A CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 115 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 80 A CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf4 A SG CYS 76 A CYS 76 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc1 A O SER 60 A SER 60 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc2 A O CYS 64 A CYS 64 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc3 A OG SER 72 A SER 72 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc4 A O ARG 73 A ARG 73 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc5 A OD1 ASP 101 A ASP 101 1_555 D RU2 YJT . A YJT 203 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.447 ? metalc ? metalc6 A OD2 ASP 101 A ASP 101 1_555 D RU2 YJT . A YJT 203 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.68 ? metalc ? metalc7 A OD2 ASP 101 A ASP 101 1_555 D RU1 YJT . A YJT 203 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.036 ? metalc ? metalc8 A OD1 ASP 119 A ASP 119 1_555 E RU1 YJT . A YJT 204 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.088 ? metalc ? metalc9 A OD2 ASP 119 A ASP 119 1_555 E RU2 YJT . A YJT 204 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.104 ? metalc ? metalc10 C NA NA . A NA 202 1_555 G O HOH . A HOH 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? metalc ? metalc11 C NA NA . A NA 202 1_555 G O HOH . A HOH 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? # _chem_comp.formula 'C14 H12 F2 N2 O5 Ru2' _chem_comp.formula_weight 528.392 _chem_comp.id YJT _chem_comp.mon_nstd_flag . _chem_comp.name 6,8-bis(4-fluorophenyl)-1,5-bis(oxidanyl)-2,4-dioxa-6,8-diaza-1$l^{4},5$l^{4}-diruthenabicyclo[3.3.0]octan-3-one _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 C6 C7 YJT doub 379 n y C6 C5 YJT sing 380 n y F1 C5 YJT sing 381 n n C7 C2 YJT sing 382 n y C5 C4 YJT doub 383 n y O3 RU1 YJT sing 384 n n RU1 O1 YJT sing 385 n n RU1 N1 YJT sing 386 n n RU1 RU2 YJT sing 387 n n O1 C14 YJT sing 388 n n C2 N1 YJT sing 389 n n C2 C3 YJT doub 390 n y O7 C14 YJT doub 391 n n C14 O2 YJT sing 392 n n C4 C3 YJT sing 393 n y N1 C1 YJT sing 394 n n O4 RU2 YJT sing 395 n n RU2 O2 YJT sing 396 n n RU2 N2 YJT sing 397 n n C1 N2 YJT sing 398 n n N2 C8 YJT sing 399 n n C8 C9 YJT doub 400 n y C8 C13 YJT sing 401 n y C9 C10 YJT sing 402 n y C13 C12 YJT doub 403 n y C10 C11 YJT doub 404 n y C12 C11 YJT sing 405 n y C11 F2 YJT sing 406 n n C4 H1 YJT sing 407 n n O4 H2 YJT sing 408 n n C6 H3 YJT sing 409 n n C3 H4 YJT sing 410 n n O3 H5 YJT sing 411 n n C1 H6 YJT sing 412 n n C1 H7 YJT sing 413 n n C7 H8 YJT sing 414 n n C10 H9 YJT sing 415 n n C9 H10 YJT sing 416 n n C12 H11 YJT sing 417 n n C13 H12 YJT sing 418 n n # _atom_sites.entry_id 8PFT _atom_sites.fract_transf_matrix[1][1] 0.012862 _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] 0.012862 _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] 0.026781 _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 B 2 CL A 1 201 130 CL CL . C 3 NA A 1 202 131 NA NA . D 4 YJT A 1 203 1 YJT TM9 . E 4 YJT A 1 204 2 YJT TM9 . F 5 NO3 A 1 205 133 NO3 NO3 . G 6 HOH A 1 301 25 HOH HOH . G 6 HOH A 2 302 138 HOH HOH . G 6 HOH A 3 303 21 HOH HOH . G 6 HOH A 4 304 60 HOH HOH . G 6 HOH A 5 305 72 HOH HOH . G 6 HOH A 6 306 91 HOH HOH . G 6 HOH A 7 307 56 HOH HOH . G 6 HOH A 8 308 20 HOH HOH . G 6 HOH A 9 309 111 HOH HOH . G 6 HOH A 10 310 98 HOH HOH . G 6 HOH A 11 311 62 HOH HOH . G 6 HOH A 12 312 92 HOH HOH . G 6 HOH A 13 313 36 HOH HOH . G 6 HOH A 14 314 45 HOH HOH . G 6 HOH A 15 315 63 HOH HOH . G 6 HOH A 16 316 46 HOH HOH . G 6 HOH A 17 317 99 HOH HOH . G 6 HOH A 18 318 37 HOH HOH . G 6 HOH A 19 319 10 HOH HOH . G 6 HOH A 20 320 33 HOH HOH . G 6 HOH A 21 321 129 HOH HOH . G 6 HOH A 22 322 2 HOH HOH . G 6 HOH A 23 323 112 HOH HOH . G 6 HOH A 24 324 27 HOH HOH . G 6 HOH A 25 325 61 HOH HOH . G 6 HOH A 26 326 3 HOH HOH . G 6 HOH A 27 327 122 HOH HOH . G 6 HOH A 28 328 120 HOH HOH . G 6 HOH A 29 329 11 HOH HOH . G 6 HOH A 30 330 31 HOH HOH . G 6 HOH A 31 331 18 HOH HOH . G 6 HOH A 32 332 70 HOH HOH . G 6 HOH A 33 333 110 HOH HOH . G 6 HOH A 34 334 15 HOH HOH . G 6 HOH A 35 335 44 HOH HOH . G 6 HOH A 36 336 12 HOH HOH . G 6 HOH A 37 337 13 HOH HOH . G 6 HOH A 38 338 130 HOH HOH . G 6 HOH A 39 339 105 HOH HOH . G 6 HOH A 40 340 64 HOH HOH . G 6 HOH A 41 341 29 HOH HOH . G 6 HOH A 42 342 121 HOH HOH . G 6 HOH A 43 343 67 HOH HOH . G 6 HOH A 44 344 53 HOH HOH . G 6 HOH A 45 345 24 HOH HOH . G 6 HOH A 46 346 22 HOH HOH . G 6 HOH A 47 347 1 HOH HOH . G 6 HOH A 48 348 41 HOH HOH . G 6 HOH A 49 349 90 HOH HOH . G 6 HOH A 50 350 81 HOH HOH . G 6 HOH A 51 351 59 HOH HOH . G 6 HOH A 52 352 100 HOH HOH . G 6 HOH A 53 353 66 HOH HOH . G 6 HOH A 54 354 17 HOH HOH . G 6 HOH A 55 355 6 HOH HOH . G 6 HOH A 56 356 49 HOH HOH . G 6 HOH A 57 357 58 HOH HOH . G 6 HOH A 58 358 28 HOH HOH . G 6 HOH A 59 359 136 HOH HOH . G 6 HOH A 60 360 127 HOH HOH . G 6 HOH A 61 361 5 HOH HOH . G 6 HOH A 62 362 7 HOH HOH . G 6 HOH A 63 363 106 HOH HOH . G 6 HOH A 64 364 14 HOH HOH . G 6 HOH A 65 365 104 HOH HOH . G 6 HOH A 66 366 69 HOH HOH . G 6 HOH A 67 367 133 HOH HOH . G 6 HOH A 68 368 54 HOH HOH . G 6 HOH A 69 369 132 HOH HOH . G 6 HOH A 70 370 102 HOH HOH . G 6 HOH A 71 371 128 HOH HOH . G 6 HOH A 72 372 79 HOH HOH . G 6 HOH A 73 373 101 HOH HOH . G 6 HOH A 74 374 9 HOH HOH . G 6 HOH A 75 375 65 HOH HOH . G 6 HOH A 76 376 16 HOH HOH . G 6 HOH A 77 377 39 HOH HOH . G 6 HOH A 78 378 19 HOH HOH . G 6 HOH A 79 379 131 HOH HOH . G 6 HOH A 80 380 108 HOH HOH . G 6 HOH A 81 381 40 HOH HOH . G 6 HOH A 82 382 73 HOH HOH . G 6 HOH A 83 383 86 HOH HOH . G 6 HOH A 84 384 23 HOH HOH . G 6 HOH A 85 385 118 HOH HOH . G 6 HOH A 86 386 38 HOH HOH . G 6 HOH A 87 387 115 HOH HOH . G 6 HOH A 88 388 125 HOH HOH . G 6 HOH A 89 389 103 HOH HOH . G 6 HOH A 90 390 55 HOH HOH . G 6 HOH A 91 391 107 HOH HOH . G 6 HOH A 92 392 74 HOH HOH . G 6 HOH A 93 393 119 HOH HOH . G 6 HOH A 94 394 109 HOH HOH . G 6 HOH A 95 395 52 HOH HOH . G 6 HOH A 96 396 57 HOH HOH . G 6 HOH A 97 397 71 HOH HOH . G 6 HOH A 98 398 68 HOH HOH . G 6 HOH A 99 399 43 HOH HOH . G 6 HOH A 100 400 97 HOH HOH . G 6 HOH A 101 401 42 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 C2 YJT . A . D 4 -26.726 3.031 6.513 0.35 46.78 0 C2 YJT 203 A 1 HETATM 2 C C4 YJT . A . D 4 -28.209 4.9 6.622 0.35 51.91 0 C4 YJT 203 A 1 HETATM 3 O O4 YJT . A . D 4 -23.016 -0.349 7.096 0.35 30.78 0 O4 YJT 203 A 1 HETATM 4 C C5 YJT . A . D 4 -28.546 4.667 5.302 0.35 51.81 0 C5 YJT 203 A 1 HETATM 5 C C6 YJT . A . D 4 -28.018 3.648 4.567 0.35 51.98 0 C6 YJT 203 A 1 HETATM 6 N N2 YJT . A . D 4 -25.283 0.649 8.707 0.35 36.28 0 N2 YJT 203 A 1 HETATM 7 C C3 YJT . A . D 4 -27.281 4.071 7.247 0.35 49.35 0 C3 YJT 203 A 1 HETATM 8 O O3 YJT . A . D 4 -23.435 0.939 5.586 0.35 35.26 0 O3 YJT 203 A 1 HETATM 9 C C1 YJT . A . D 4 -25.639 1.853 8.268 0.35 37.21 0 C1 YJT 203 A 1 HETATM 10 O O1 YJT . A . D 4 -27.378 -0.005 5.711 0.35 36.23 0 O1 YJT 203 A 1 HETATM 11 RU RU1 YJT . A . D 4 -25.437 0.601 5.631 0.35 37.73 0 RU1 YJT 203 A 1 HETATM 12 RU RU2 YJT . A . D 4 -24.961 -0.808 7.375 0.35 33.24 0 RU2 YJT 203 A 1 HETATM 13 F F1 YJT . A . D 4 -29.451 5.493 4.706 0.35 55.69 0 F1 YJT 203 A 1 HETATM 14 F F2 YJT . A . D 4 -23.577 -0.395 13.836 0.35 38.99 0 F2 YJT 203 A 1 HETATM 15 O O2 YJT . A . D 4 -26.917 -1.405 7.475 0.35 34.88 0 O2 YJT 203 A 1 HETATM 16 N N1 YJT . A . D 4 -25.766 2.082 6.974 0.35 39.46 0 N1 YJT 203 A 1 HETATM 17 C C7 YJT . A . D 4 -27.105 2.84 5.188 0.35 50.71 0 C7 YJT 203 A 1 HETATM 18 C C14 YJT . A . D 4 -27.745 -0.896 6.615 0.35 36.74 0 C14 YJT 203 A 1 HETATM 19 C C11 YJT . A . D 4 -23.979 -0.125 12.583 0.35 43.69 0 C11 YJT 203 A 1 HETATM 20 C C8 YJT . A . D 4 -24.837 0.414 10.046 0.35 42.02 0 C8 YJT 203 A 1 HETATM 21 C C10 YJT . A . D 4 -23.363 0.849 11.877 0.35 43.99 0 C10 YJT 203 A 1 HETATM 22 C C9 YJT . A . D 4 -23.77 1.125 10.593 0.35 45.46 0 C9 YJT 203 A 1 HETATM 23 C C12 YJT . A . D 4 -25.006 -0.846 12.06 0.35 45.21 0 C12 YJT 203 A 1 HETATM 24 C C13 YJT . A . D 4 -25.434 -0.585 10.785 0.35 42.34 0 C13 YJT 203 A 1 HETATM 25 O O7 YJT . A . D 4 -28.949 -1.197 6.591 0.35 35.52 0 O7 YJT 203 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 459 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #