data_8PH5 # _model_server_result.job_id '_Nrtg2tLLgClGEL2GJLF3Q' _model_server_result.datetime_utc '2025-01-09 05:30:43' _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 8ph5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 8PH5 # _exptl.entry_id 8PH5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 657.668 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-oxidanyl-6,8,9,11-tetraphenyl-2,4-dioxa-6,8,9,11-tetraza-1$l^{5},5$l^{4}-diruthenatricyclo[3.3.3.0^{1,5}]undecane _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 8PH5 _cell.length_a 77 _cell.length_b 77 _cell.length_c 39.2 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PH5 _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 ? 3 C N N ? 3 D 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 AAA CYS 6 1_555 A SG CYS 127 AAA CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 A SG CYS 30 AAA CYS 30 1_555 A SG CYS 115 AAA CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? disulf ? disulf3 A SG CYS 64 AAA CYS 64 1_555 A SG CYS 80 AAA CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf4 A SG CYS 76 AAA CYS 76 1_555 A SG CYS 94 AAA CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc1 A OD1 ASP 101 AAA ASP 101 1_555 C RU1 ZJK . AAA ZJK 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc2 A OD2 ASP 101 AAA ASP 101 1_555 C RU2 ZJK . AAA ZJK 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc3 A OD1 ASP 119 AAA ASP 119 1_555 D RU2 ZJK . AAA ZJK 203 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc4 A OD2 ASP 119 AAA ASP 119 1_555 D RU1 ZJK . AAA ZJK 203 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc5 C RU1 ZJK . AAA ZJK 202 1_555 E O HOH . AAA HOH 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? # _chem_comp.formula 'C27 H27 N4 O3 Ru2' _chem_comp.formula_weight 657.668 _chem_comp.id ZJK _chem_comp.mon_nstd_flag . _chem_comp.name 1-oxidanyl-6,8,9,11-tetraphenyl-2,4-dioxa-6,8,9,11-tetraza-1$l^{5},5$l^{4}-diruthenatricyclo[3.3.3.0^{1,5}]undecane _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 O5 RU2 ZJK sing 409 n n C29 C25 ZJK doub 410 n y C29 C26 ZJK sing 411 n y C25 C15 ZJK sing 412 n y O1 C8 ZJK sing 413 n n O1 RU2 ZJK sing 414 n n C26 C20 ZJK doub 415 n y C8 O2 ZJK sing 416 n n C15 C5 ZJK doub 417 n y C20 C5 ZJK sing 418 n y RU2 N1 ZJK sing 419 n n RU2 RU1 ZJK sing 420 n n RU2 N4 ZJK sing 421 n n C5 N1 ZJK sing 422 n n C12 C4 ZJK doub 423 n y C12 C6 ZJK sing 424 n y C4 C1 ZJK sing 425 n y O2 RU1 ZJK sing 426 n n N1 C13 ZJK sing 427 n n C6 C17 ZJK doub 428 n y C1 N4 ZJK sing 429 n n C1 C11 ZJK doub 430 n y RU1 N2 ZJK sing 431 n n RU1 N3 ZJK sing 432 n n C13 N2 ZJK sing 433 n n N4 C16 ZJK sing 434 n n C17 C11 ZJK sing 435 n y N2 C9 ZJK sing 436 n n C23 C9 ZJK doub 437 n y C23 C27 ZJK sing 438 n y C16 N3 ZJK sing 439 n n C9 C21 ZJK sing 440 n y N3 C3 ZJK sing 441 n n C27 C30 ZJK doub 442 n y C7 C3 ZJK doub 443 n y C7 C10 ZJK sing 444 n y C3 C2 ZJK sing 445 n y C21 C28 ZJK doub 446 n y C30 C28 ZJK sing 447 n y C10 C14 ZJK doub 448 n y C2 C18 ZJK doub 449 n y C14 C18 ZJK sing 450 n y C2 H1 ZJK sing 451 n n C4 H2 ZJK sing 452 n n C6 H3 ZJK sing 453 n n C7 H4 ZJK sing 454 n n C8 H5 ZJK sing 455 n n C8 H6 ZJK sing 456 n n C10 H7 ZJK sing 457 n n C11 H8 ZJK sing 458 n n C12 H9 ZJK sing 459 n n C13 H10 ZJK sing 460 n n C13 H11 ZJK sing 461 n n C14 H12 ZJK sing 462 n n C15 H13 ZJK sing 463 n n C16 H14 ZJK sing 464 n n C16 H15 ZJK sing 465 n n C17 H16 ZJK sing 466 n n C18 H17 ZJK sing 467 n n C20 H18 ZJK sing 468 n n C21 H19 ZJK sing 469 n n C23 H20 ZJK sing 470 n n C25 H21 ZJK sing 471 n n C26 H22 ZJK sing 472 n n C27 H23 ZJK sing 473 n n C28 H24 ZJK sing 474 n n C29 H25 ZJK sing 475 n n C30 H26 ZJK sing 476 n n O5 H27 ZJK sing 477 n n # _atom_sites.entry_id 8PH5 _atom_sites.fract_transf_matrix[1][1] 0.012987 _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] 0.012987 _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] 0.02551 _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 EPE AAA 1 201 202 EPE EPE . C 3 ZJK AAA 1 202 1 ZJK TMB . D 3 ZJK AAA 1 203 2 ZJK TMB . E 4 HOH AAA 1 301 5 HOH HOH . E 4 HOH AAA 2 302 8 HOH HOH . E 4 HOH AAA 3 303 46 HOH HOH . E 4 HOH AAA 4 304 137 HOH HOH . E 4 HOH AAA 5 305 119 HOH HOH . E 4 HOH AAA 6 306 72 HOH HOH . E 4 HOH AAA 7 307 39 HOH HOH . E 4 HOH AAA 8 308 126 HOH HOH . E 4 HOH AAA 9 309 136 HOH HOH . E 4 HOH AAA 10 310 25 HOH HOH . E 4 HOH AAA 11 311 45 HOH HOH . E 4 HOH AAA 12 312 71 HOH HOH . E 4 HOH AAA 13 313 55 HOH HOH . E 4 HOH AAA 14 314 123 HOH HOH . E 4 HOH AAA 15 315 57 HOH HOH . E 4 HOH AAA 16 316 31 HOH HOH . E 4 HOH AAA 17 317 58 HOH HOH . E 4 HOH AAA 18 318 34 HOH HOH . E 4 HOH AAA 19 319 65 HOH HOH . E 4 HOH AAA 20 320 139 HOH HOH . E 4 HOH AAA 21 321 33 HOH HOH . E 4 HOH AAA 22 322 3 HOH HOH . E 4 HOH AAA 23 323 86 HOH HOH . E 4 HOH AAA 24 324 20 HOH HOH . E 4 HOH AAA 25 325 107 HOH HOH . E 4 HOH AAA 26 326 64 HOH HOH . E 4 HOH AAA 27 327 26 HOH HOH . E 4 HOH AAA 28 328 70 HOH HOH . E 4 HOH AAA 29 329 19 HOH HOH . E 4 HOH AAA 30 330 93 HOH HOH . E 4 HOH AAA 31 331 2 HOH HOH . E 4 HOH AAA 32 332 116 HOH HOH . E 4 HOH AAA 33 333 32 HOH HOH . E 4 HOH AAA 34 334 13 HOH HOH . E 4 HOH AAA 35 335 24 HOH HOH . E 4 HOH AAA 36 336 114 HOH HOH . E 4 HOH AAA 37 337 91 HOH HOH . E 4 HOH AAA 38 338 12 HOH HOH . E 4 HOH AAA 39 339 105 HOH HOH . E 4 HOH AAA 40 340 14 HOH HOH . E 4 HOH AAA 41 341 117 HOH HOH . E 4 HOH AAA 42 342 9 HOH HOH . E 4 HOH AAA 43 343 4 HOH HOH . E 4 HOH AAA 44 344 36 HOH HOH . E 4 HOH AAA 45 345 40 HOH HOH . E 4 HOH AAA 46 346 104 HOH HOH . E 4 HOH AAA 47 347 47 HOH HOH . E 4 HOH AAA 48 348 63 HOH HOH . E 4 HOH AAA 49 349 52 HOH HOH . E 4 HOH AAA 50 350 18 HOH HOH . E 4 HOH AAA 51 351 7 HOH HOH . E 4 HOH AAA 52 352 30 HOH HOH . E 4 HOH AAA 53 353 77 HOH HOH . E 4 HOH AAA 54 354 109 HOH HOH . E 4 HOH AAA 55 355 54 HOH HOH . E 4 HOH AAA 56 356 16 HOH HOH . E 4 HOH AAA 57 357 53 HOH HOH . E 4 HOH AAA 58 358 27 HOH HOH . E 4 HOH AAA 59 359 110 HOH HOH . E 4 HOH AAA 60 360 83 HOH HOH . E 4 HOH AAA 61 361 10 HOH HOH . E 4 HOH AAA 62 362 22 HOH HOH . E 4 HOH AAA 63 363 43 HOH HOH . E 4 HOH AAA 64 364 67 HOH HOH . E 4 HOH AAA 65 365 48 HOH HOH . E 4 HOH AAA 66 366 74 HOH HOH . E 4 HOH AAA 67 367 98 HOH HOH . E 4 HOH AAA 68 368 28 HOH HOH . E 4 HOH AAA 69 369 6 HOH HOH . E 4 HOH AAA 70 370 37 HOH HOH . E 4 HOH AAA 71 371 23 HOH HOH . E 4 HOH AAA 72 372 69 HOH HOH . E 4 HOH AAA 73 373 38 HOH HOH . E 4 HOH AAA 74 374 59 HOH HOH . E 4 HOH AAA 75 375 76 HOH HOH . E 4 HOH AAA 76 376 29 HOH HOH . E 4 HOH AAA 77 377 11 HOH HOH . E 4 HOH AAA 78 378 108 HOH HOH . E 4 HOH AAA 79 379 81 HOH HOH . E 4 HOH AAA 80 380 15 HOH HOH . E 4 HOH AAA 81 381 129 HOH HOH . E 4 HOH AAA 82 382 84 HOH HOH . E 4 HOH AAA 83 383 42 HOH HOH . E 4 HOH AAA 84 384 1 HOH HOH . E 4 HOH AAA 85 385 21 HOH HOH . E 4 HOH AAA 86 386 94 HOH HOH . E 4 HOH AAA 87 387 125 HOH HOH . E 4 HOH AAA 88 388 99 HOH HOH . E 4 HOH AAA 89 389 135 HOH HOH . E 4 HOH AAA 90 390 120 HOH HOH . E 4 HOH AAA 91 391 62 HOH HOH . E 4 HOH AAA 92 392 115 HOH HOH . E 4 HOH AAA 93 393 49 HOH HOH . E 4 HOH AAA 94 394 118 HOH HOH . E 4 HOH AAA 95 395 60 HOH HOH . E 4 HOH AAA 96 396 106 HOH HOH . E 4 HOH AAA 97 397 113 HOH HOH . E 4 HOH AAA 98 398 41 HOH HOH . E 4 HOH AAA 99 399 121 HOH HOH . E 4 HOH AAA 100 400 66 HOH HOH . E 4 HOH AAA 101 401 97 HOH HOH . E 4 HOH AAA 102 402 78 HOH HOH . E 4 HOH AAA 103 403 111 HOH HOH . E 4 HOH AAA 104 404 92 HOH HOH . E 4 HOH AAA 105 405 35 HOH HOH . E 4 HOH AAA 106 406 56 HOH HOH . E 4 HOH AAA 107 407 79 HOH HOH . E 4 HOH AAA 108 408 61 HOH HOH . E 4 HOH AAA 109 409 100 HOH HOH . E 4 HOH AAA 110 410 140 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 RU RU1 ZJK . . . D 3 7.954 -39.486 -10.36 0.3 9.19 0 RU1 ZJK 203 AAA 1 HETATM 2 RU RU2 ZJK . . . D 3 9.217 -39.006 -8.509 0.3 9.43 0 RU2 ZJK 203 AAA 1 HETATM 3 O O1 ZJK . . . D 3 10.813 -38.951 -9.828 0.3 9.58 0 O1 ZJK 203 AAA 1 HETATM 4 O O2 ZJK . . . D 3 9.617 -39.251 -11.616 0.3 8.23 0 O2 ZJK 203 AAA 1 HETATM 5 N N1 ZJK . . . D 3 7.605 -38.852 -7.26 0.3 8.23 0 N1 ZJK 203 AAA 1 HETATM 6 N N4 ZJK . . . D 3 9.729 -40.958 -8.304 0.3 10.16 0 N4 ZJK 203 AAA 1 HETATM 7 N N3 ZJK . . . D 3 8.441 -41.454 -10.13 0.3 10.38 0 N3 ZJK 203 AAA 1 HETATM 8 N N2 ZJK . . . D 3 6.353 -39.509 -9.064 0.3 9.96 0 N2 ZJK 203 AAA 1 HETATM 9 C C1 ZJK . . . D 3 10.43 -41.402 -7.14 0.3 11.67 0 C1 ZJK 203 AAA 1 HETATM 10 C C2 ZJK . . . D 3 7.111 -42.706 -11.734 0.3 11.93 0 C2 ZJK 203 AAA 1 HETATM 11 C C3 ZJK . . . D 3 8.343 -42.428 -11.171 0.3 11.29 0 C3 ZJK 203 AAA 1 HETATM 12 C C4 ZJK . . . D 3 11.805 -41.228 -7.145 0.3 13.31 0 C4 ZJK 203 AAA 1 HETATM 13 C C5 ZJK . . . D 3 7.598 -38.765 -5.842 0.3 8.08 0 C5 ZJK 203 AAA 1 HETATM 14 C C6 ZJK . . . D 3 11.987 -42.206 -5.016 0.3 12.53 0 C6 ZJK 203 AAA 1 HETATM 15 C C7 ZJK . . . D 3 9.497 -43.038 -11.616 0.3 11.89 0 C7 ZJK 203 AAA 1 HETATM 16 C C8 ZJK . . . D 3 10.72 -39.018 -11.097 0.3 7.82 0 C8 ZJK 203 AAA 1 HETATM 17 C C9 ZJK . . . D 3 5.051 -39.858 -9.559 0.3 10.92 0 C9 ZJK 203 AAA 1 HETATM 18 C C10 ZJK . . . D 3 9.389 -43.95 -12.649 0.3 12.24 0 C10 ZJK 203 AAA 1 HETATM 19 C C11 ZJK . . . D 3 9.832 -41.953 -6.031 0.3 11.87 0 C11 ZJK 203 AAA 1 HETATM 20 C C12 ZJK . . . D 3 12.601 -41.623 -6.086 0.3 13.11 0 C12 ZJK 203 AAA 1 HETATM 21 C C13 ZJK . . . D 3 6.469 -39.274 -7.759 0.3 8.93 0 C13 ZJK 203 AAA 1 HETATM 22 C C14 ZJK . . . D 3 8.179 -44.219 -13.217 0.3 13.23 0 C14 ZJK 203 AAA 1 HETATM 23 C C15 ZJK . . . D 3 8.09 -37.602 -5.302 0.3 8.57 0 C15 ZJK 203 AAA 1 HETATM 24 C C16 ZJK . . . D 3 9.053 -41.822 -9.022 0.3 10.09 0 C16 ZJK 203 AAA 1 HETATM 25 C C17 ZJK . . . D 3 10.632 -42.345 -4.983 0.3 11.73 0 C17 ZJK 203 AAA 1 HETATM 26 C C18 ZJK . . . D 3 7.025 -43.61 -12.786 0.3 12.46 0 C18 ZJK 203 AAA 1 HETATM 27 C C20 ZJK . . . D 3 7.103 -39.834 -5.131 0.3 9.28 0 C20 ZJK 203 AAA 1 HETATM 28 C C21 ZJK . . . D 3 4.383 -41.004 -9.189 0.3 11.8 0 C21 ZJK 203 AAA 1 HETATM 29 C C23 ZJK . . . D 3 4.478 -39.11 -10.57 0.3 12.74 0 C23 ZJK 203 AAA 1 HETATM 30 C C25 ZJK . . . D 3 8.094 -37.48 -3.906 0.3 8.29 0 C25 ZJK 203 AAA 1 HETATM 31 C C26 ZJK . . . D 3 7.118 -39.686 -3.748 0.3 9.28 0 C26 ZJK 203 AAA 1 HETATM 32 C C27 ZJK . . . D 3 3.242 -39.467 -11.107 0.3 12.95 0 C27 ZJK 203 AAA 1 HETATM 33 C C28 ZJK . . . D 3 3.152 -41.35 -9.692 0.3 11.95 0 C28 ZJK 203 AAA 1 HETATM 34 C C29 ZJK . . . D 3 7.61 -38.539 -3.202 0.3 9.65 0 C29 ZJK 203 AAA 1 HETATM 35 C C30 ZJK . . . D 3 2.583 -40.59 -10.667 0.3 13 0 C30 ZJK 203 AAA 1 HETATM 36 O O5 ZJK . . . D 3 10.724 -37.934 -7.009 0.3 9.17 0 O5 ZJK 203 AAA 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 36 #