data_8PFX # _model_server_result.job_id GEQRmd4TT-2rtLfmVLk5eQ _model_server_result.datetime_utc '2024-11-28 05:10:39' _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 8pfx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":205}' # _entry.id 8PFX # _exptl.entry_id 8PFX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 528.392 _entity.id 5 _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 3 _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 8PFX _cell.length_a 76.72 _cell.length_b 76.72 _cell.length_c 38.39 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PFX _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,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 G N N ? 5 H 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 115 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 80 A CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf4 A SG CYS 76 A CYS 76 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc1 A O SER 60 A SER 60 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc2 A O CYS 64 A CYS 64 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc3 A OG SER 72 A SER 72 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc4 A O ARG 73 A ARG 73 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc5 A OD1 ASP 101 A ASP 101 1_555 F RU2 YJT . A YJT 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc6 A OD2 ASP 101 A ASP 101 1_555 F RU1 YJT . A YJT 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc7 A NH1 ARG 125 A ARG 125 1_555 G RU1 YJT . A YJT 206 4_444 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc8 B NA NA . A NA 201 1_555 I O HOH . A HOH 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc9 B NA NA . A NA 201 1_555 I O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc10 F RU2 YJT . A YJT 205 1_555 I O HOH . A HOH 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc11 F RU1 YJT . A YJT 205 1_555 I O HOH . A HOH 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? # _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 413 n y C6 C5 YJT sing 414 n y F1 C5 YJT sing 415 n n C7 C2 YJT sing 416 n y C5 C4 YJT doub 417 n y O3 RU1 YJT sing 418 n n RU1 O1 YJT sing 419 n n RU1 N1 YJT sing 420 n n RU1 RU2 YJT sing 421 n n O1 C14 YJT sing 422 n n C2 N1 YJT sing 423 n n C2 C3 YJT doub 424 n y O7 C14 YJT doub 425 n n C14 O2 YJT sing 426 n n C4 C3 YJT sing 427 n y N1 C1 YJT sing 428 n n O4 RU2 YJT sing 429 n n RU2 O2 YJT sing 430 n n RU2 N2 YJT sing 431 n n C1 N2 YJT sing 432 n n N2 C8 YJT sing 433 n n C8 C9 YJT doub 434 n y C8 C13 YJT sing 435 n y C9 C10 YJT sing 436 n y C13 C12 YJT doub 437 n y C10 C11 YJT doub 438 n y C12 C11 YJT sing 439 n y C11 F2 YJT sing 440 n n C4 H1 YJT sing 441 n n O4 H2 YJT sing 442 n n C6 H3 YJT sing 443 n n C3 H4 YJT sing 444 n n O3 H5 YJT sing 445 n n C1 H6 YJT sing 446 n n C1 H7 YJT sing 447 n n C7 H8 YJT sing 448 n n C10 H9 YJT sing 449 n n C9 H10 YJT sing 450 n n C12 H11 YJT sing 451 n n C13 H12 YJT sing 452 n n # _atom_sites.entry_id 8PFX _atom_sites.fract_transf_matrix[1][1] 0.013034 _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] 0.013034 _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] 0.026048 _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 NA A 1 201 131 NA NA . C 3 EPE A 1 202 132 EPE EPE . D 4 FMT A 1 203 133 FMT FMT . E 4 FMT A 1 204 135 FMT FMT . F 5 YJT A 1 205 1 YJT TM9 . G 5 YJT A 1 206 1 YJT TM9 . H 5 YJT A 1 207 1 YJT TM9 . I 6 HOH A 1 301 94 HOH HOH . I 6 HOH A 2 302 160 HOH HOH . I 6 HOH A 3 303 28 HOH HOH . I 6 HOH A 4 304 45 HOH HOH . I 6 HOH A 5 305 71 HOH HOH . I 6 HOH A 6 306 128 HOH HOH . I 6 HOH A 7 307 133 HOH HOH . I 6 HOH A 8 308 116 HOH HOH . I 6 HOH A 9 309 77 HOH HOH . I 6 HOH A 10 310 109 HOH HOH . I 6 HOH A 11 311 122 HOH HOH . I 6 HOH A 12 312 15 HOH HOH . I 6 HOH A 13 313 104 HOH HOH . I 6 HOH A 14 314 124 HOH HOH . I 6 HOH A 15 315 93 HOH HOH . I 6 HOH A 16 316 42 HOH HOH . I 6 HOH A 17 317 61 HOH HOH . I 6 HOH A 18 318 22 HOH HOH . I 6 HOH A 19 319 16 HOH HOH . I 6 HOH A 20 320 34 HOH HOH . I 6 HOH A 21 321 17 HOH HOH . I 6 HOH A 22 322 3 HOH HOH . I 6 HOH A 23 323 37 HOH HOH . I 6 HOH A 24 324 149 HOH HOH . I 6 HOH A 25 325 19 HOH HOH . I 6 HOH A 26 326 48 HOH HOH . I 6 HOH A 27 327 101 HOH HOH . I 6 HOH A 28 328 50 HOH HOH . I 6 HOH A 29 329 65 HOH HOH . I 6 HOH A 30 330 1 HOH HOH . I 6 HOH A 31 331 84 HOH HOH . I 6 HOH A 32 332 120 HOH HOH . I 6 HOH A 33 333 43 HOH HOH . I 6 HOH A 34 334 103 HOH HOH . I 6 HOH A 35 335 32 HOH HOH . I 6 HOH A 36 336 73 HOH HOH . I 6 HOH A 37 337 46 HOH HOH . I 6 HOH A 38 338 5 HOH HOH . I 6 HOH A 39 339 54 HOH HOH . I 6 HOH A 40 340 14 HOH HOH . I 6 HOH A 41 341 31 HOH HOH . I 6 HOH A 42 342 41 HOH HOH . I 6 HOH A 43 343 10 HOH HOH . I 6 HOH A 44 344 107 HOH HOH . I 6 HOH A 45 345 24 HOH HOH . I 6 HOH A 46 346 29 HOH HOH . I 6 HOH A 47 347 98 HOH HOH . I 6 HOH A 48 348 138 HOH HOH . I 6 HOH A 49 349 145 HOH HOH . I 6 HOH A 50 350 62 HOH HOH . I 6 HOH A 51 351 158 HOH HOH . I 6 HOH A 52 352 115 HOH HOH . I 6 HOH A 53 353 140 HOH HOH . I 6 HOH A 54 354 75 HOH HOH . I 6 HOH A 55 355 36 HOH HOH . I 6 HOH A 56 356 74 HOH HOH . I 6 HOH A 57 357 40 HOH HOH . I 6 HOH A 58 358 25 HOH HOH . I 6 HOH A 59 359 82 HOH HOH . I 6 HOH A 60 360 99 HOH HOH . I 6 HOH A 61 361 26 HOH HOH . I 6 HOH A 62 362 39 HOH HOH . I 6 HOH A 63 363 7 HOH HOH . I 6 HOH A 64 364 67 HOH HOH . I 6 HOH A 65 365 2 HOH HOH . I 6 HOH A 66 366 119 HOH HOH . I 6 HOH A 67 367 21 HOH HOH . I 6 HOH A 68 368 8 HOH HOH . I 6 HOH A 69 369 33 HOH HOH . I 6 HOH A 70 370 78 HOH HOH . I 6 HOH A 71 371 30 HOH HOH . I 6 HOH A 72 372 86 HOH HOH . I 6 HOH A 73 373 12 HOH HOH . I 6 HOH A 74 374 129 HOH HOH . I 6 HOH A 75 375 80 HOH HOH . I 6 HOH A 76 376 23 HOH HOH . I 6 HOH A 77 377 152 HOH HOH . I 6 HOH A 78 378 83 HOH HOH . I 6 HOH A 79 379 70 HOH HOH . I 6 HOH A 80 380 118 HOH HOH . I 6 HOH A 81 381 6 HOH HOH . I 6 HOH A 82 382 49 HOH HOH . I 6 HOH A 83 383 141 HOH HOH . I 6 HOH A 84 384 153 HOH HOH . I 6 HOH A 85 385 72 HOH HOH . I 6 HOH A 86 386 137 HOH HOH . I 6 HOH A 87 387 58 HOH HOH . I 6 HOH A 88 388 53 HOH HOH . I 6 HOH A 89 389 20 HOH HOH . I 6 HOH A 90 390 59 HOH HOH . I 6 HOH A 91 391 18 HOH HOH . I 6 HOH A 92 392 56 HOH HOH . I 6 HOH A 93 393 4 HOH HOH . I 6 HOH A 94 394 47 HOH HOH . I 6 HOH A 95 395 131 HOH HOH . I 6 HOH A 96 396 161 HOH HOH . I 6 HOH A 97 397 64 HOH HOH . I 6 HOH A 98 398 162 HOH HOH . I 6 HOH A 99 399 60 HOH HOH . I 6 HOH A 100 400 143 HOH HOH . I 6 HOH A 101 401 117 HOH HOH . I 6 HOH A 102 402 87 HOH HOH . I 6 HOH A 103 403 110 HOH HOH . I 6 HOH A 104 404 106 HOH HOH . I 6 HOH A 105 405 112 HOH HOH . I 6 HOH A 106 406 13 HOH HOH . I 6 HOH A 107 407 108 HOH HOH . I 6 HOH A 108 408 123 HOH HOH . I 6 HOH A 109 409 85 HOH HOH . I 6 HOH A 110 410 121 HOH HOH . I 6 HOH A 111 411 68 HOH HOH . I 6 HOH A 112 412 105 HOH HOH . I 6 HOH A 113 413 136 HOH HOH . I 6 HOH A 114 414 146 HOH HOH . I 6 HOH A 115 415 111 HOH HOH . I 6 HOH A 116 416 139 HOH HOH . I 6 HOH A 117 417 156 HOH HOH . I 6 HOH A 118 418 114 HOH HOH . I 6 HOH A 119 419 154 HOH HOH . I 6 HOH A 120 420 148 HOH HOH . I 6 HOH A 121 421 35 HOH HOH . I 6 HOH A 122 422 79 HOH HOH . I 6 HOH A 123 423 151 HOH HOH . I 6 HOH A 124 424 57 HOH HOH . I 6 HOH A 125 425 135 HOH HOH . I 6 HOH A 126 426 125 HOH HOH . I 6 HOH A 127 427 159 HOH HOH . I 6 HOH A 128 428 134 HOH HOH . I 6 HOH A 129 429 142 HOH HOH . I 6 HOH A 130 430 97 HOH HOH . I 6 HOH A 131 431 127 HOH HOH . I 6 HOH A 132 432 66 HOH HOH . I 6 HOH A 133 433 157 HOH HOH . I 6 HOH A 134 434 130 HOH HOH . I 6 HOH A 135 435 113 HOH HOH . I 6 HOH A 136 436 126 HOH HOH . I 6 HOH A 137 437 144 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 . . . F 5 -25.486 3.459 5.958 0.35 18.69 0 C2 YJT 205 A 1 HETATM 2 C C4 YJT . . . F 5 -25.584 5.409 4.568 0.35 20.06 0 C4 YJT 205 A 1 HETATM 3 O O4 YJT . . . F 5 -21.709 0.511 5.382 0.35 16.75 0 O4 YJT 205 A 1 HETATM 4 C C5 YJT . . . F 5 -26.797 5.744 5.077 0.35 20.58 0 C5 YJT 205 A 1 HETATM 5 C C6 YJT . . . F 5 -27.377 4.957 6.007 0.35 20.52 0 C6 YJT 205 A 1 HETATM 6 N N2 YJT . . . F 5 -23.31 1.123 7.678 0.35 17.56 0 N2 YJT 205 A 1 HETATM 7 C C3 YJT . . . F 5 -24.939 4.276 4.991 0.35 19.23 0 C3 YJT 205 A 1 HETATM 8 O O3 YJT . . . F 5 -23.237 1.667 4.054 0.35 13.45 0 O3 YJT 205 A 1 HETATM 9 C C1 YJT . . . F 5 -24.07 2.171 7.441 0.35 17 0 C1 YJT 205 A 1 HETATM 10 O O1 YJT . . . F 5 -26.171 -0.278 6.074 0.35 15.45 0 O1 YJT 205 A 1 HETATM 11 RU RU1 YJT . . . F 5 -24.763 0.751 5.006 0.35 14.38 0 RU1 YJT 205 A 1 HETATM 12 RU RU2 YJT . . . F 5 -23.261 -0.383 6.326 0.35 15.41 0 RU2 YJT 205 A 1 HETATM 13 F F1 YJT . . . F 5 -27.404 6.865 4.641 0.35 19.6 0 F1 YJT 205 A 1 HETATM 14 F F2 YJT . . . F 5 -19.798 1.532 11.937 0.35 25.3 0 F2 YJT 205 A 1 HETATM 15 O O2 YJT . . . F 5 -24.663 -1.419 7.371 0.35 16.84 0 O2 YJT 205 A 1 HETATM 16 N N1 YJT . . . F 5 -24.812 2.251 6.338 0.35 16.9 0 N1 YJT 205 A 1 HETATM 17 C C7 YJT . . . F 5 -26.74 3.818 6.447 0.35 18.62 0 C7 YJT 205 A 1 HETATM 18 C C14 YJT . . . F 5 -25.892 -1.141 6.996 0.35 15.34 0 C14 YJT 205 A 1 HETATM 19 C C11 YJT . . . F 5 -20.685 1.435 10.905 0.35 22.47 0 C11 YJT 205 A 1 HETATM 20 C C8 YJT . . . F 5 -22.438 1.239 8.805 0.35 19.41 0 C8 YJT 205 A 1 HETATM 21 C C10 YJT . . . F 5 -20.187 1.17 9.664 0.35 20.71 0 C10 YJT 205 A 1 HETATM 22 C C9 YJT . . . F 5 -21.071 1.068 8.624 0.35 20.8 0 C9 YJT 205 A 1 HETATM 23 C C12 YJT . . . F 5 -22.035 1.602 11.157 0.35 21.63 0 C12 YJT 205 A 1 HETATM 24 C C13 YJT . . . F 5 -22.917 1.499 10.083 0.35 20.78 0 C13 YJT 205 A 1 HETATM 25 O O7 YJT . . . F 5 -26.806 -1.705 7.615 0.35 17.77 0 O7 YJT 205 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #