data_8BPU # _model_server_result.job_id L8MeHYymkAD4q3tsxpbcOg _model_server_result.datetime_utc '2024-11-18 00:15:50' _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 8bpu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 8BPU # _exptl.entry_id 8BPU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 526.419 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 9,11-bis(4-fluorophenyl)-2,4,6,8-tetraoxa-9,11-diaza-1$l^{4},5$l^{4}-diruthenatricyclo[3.3.3.0^{1,5}]undecane _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 8BPU _cell.length_a 78.36 _cell.length_b 78.36 _cell.length_c 37.51 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8BPU _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 6 AAA CYS 6 1_555 A SG CYS 127 AAA CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf2 A SG CYS 30 AAA CYS 30 1_555 A SG CYS 115 AAA CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 64 AAA CYS 64 1_555 A SG CYS 80 AAA CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf4 A SG CYS 76 AAA CYS 76 1_555 A SG CYS 94 AAA CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc1 A OD1 ASP 18 AAA ASP 18 1_555 F RU2 R2U . AAA R2U 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? metalc ? metalc2 A OD2 ASP 18 AAA ASP 18 1_555 F RU1 R2U . AAA R2U 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? metalc ? metalc3 A OD2 ASP 18 AAA ASP 18 1_555 F RU2 R2U . AAA R2U 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc4 A O SER 60 AAA SER 60 1_555 B NA NA . AAA NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc5 A O CYS 64 AAA CYS 64 1_555 B NA NA . AAA NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc6 A OG SER 72 AAA SER 72 1_555 B NA NA . AAA NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc7 A O ARG 73 AAA ARG 73 1_555 B NA NA . AAA NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc8 A OD1 ASP 101 AAA ASP 101 1_555 D RU2 R2I . AAA R2I 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc9 A OD2 ASP 101 AAA ASP 101 1_555 D RU1 R2I . AAA R2I 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc10 A OD1 ASP 119 AAA ASP 119 1_555 E RU1 R2U . AAA R2U 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc11 A OD1 ASP 119 AAA ASP 119 1_555 E RU2 R2U . AAA R2U 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc12 A OD2 ASP 119 AAA ASP 119 1_555 E RU1 R2U . AAA R2U 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc13 B NA NA . AAA NA 201 1_555 G O HOH . AAA HOH 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc14 B NA NA . AAA NA 201 1_555 G O HOH . AAA HOH 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc15 D RU2 R2I . AAA R2I 203 1_555 G O HOH . AAA HOH 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc16 D RU1 R2I . AAA R2I 203 1_555 G O HOH . AAA HOH 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? # _chem_comp.formula 'C15 H14 F2 N2 O4 Ru2' _chem_comp.formula_weight 526.419 _chem_comp.id R2I _chem_comp.mon_nstd_flag . _chem_comp.name 9,11-bis(4-fluorophenyl)-2,4,6,8-tetraoxa-9,11-diaza-1$l^{4},5$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 O3 RU1 R2I sing 310 n n O3 C16 R2I sing 311 n n RU1 O1 R2I sing 312 n n RU1 N1 R2I sing 313 n n RU1 RU2 R2I sing 314 n n C16 O4 R2I sing 315 n n F1 C5 R2I sing 316 n n C4 C5 R2I doub 317 n y C4 C3 R2I sing 318 n y O1 C14 R2I sing 319 n n C5 C6 R2I sing 320 n y C3 C2 R2I doub 321 n y C6 C7 R2I doub 322 n y O4 RU2 R2I sing 323 n n C7 C2 R2I sing 324 n y C2 N1 R2I sing 325 n n C14 O2 R2I sing 326 n n N1 C1 R2I sing 327 n n RU2 O2 R2I sing 328 n n RU2 N2 R2I sing 329 n n C1 N2 R2I sing 330 n n N2 C8 R2I sing 331 n n C8 C9 R2I doub 332 n y C8 C13 R2I sing 333 n y C9 C10 R2I sing 334 n y C13 C12 R2I doub 335 n y C10 C11 R2I doub 336 n y C12 C11 R2I sing 337 n y C11 F2 R2I sing 338 n n C12 H1 R2I sing 339 n n C13 H2 R2I sing 340 n n C14 H3 R2I sing 341 n n C14 H4 R2I sing 342 n n C3 H5 R2I sing 343 n n C4 H6 R2I sing 344 n n C7 H7 R2I sing 345 n n C1 H8 R2I sing 346 n n C1 H9 R2I sing 347 n n C6 H10 R2I sing 348 n n C16 H11 R2I sing 349 n n C16 H12 R2I sing 350 n n C10 H13 R2I sing 351 n n C9 H14 R2I sing 352 n n # _atom_sites.entry_id 8BPU _atom_sites.fract_transf_matrix[1][1] 0.012762 _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] 0.012762 _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] 0.02666 _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 AAA 1 201 131 NA NA . C 3 EPE AAA 1 202 133 EPE EPE . D 4 R2I AAA 1 203 1 R2I TM5 . E 5 R2U AAA 1 204 1 R2U DWR . F 5 R2U AAA 1 205 1 R2U DWR . G 6 HOH AAA 1 301 60 HOH HOH . G 6 HOH AAA 2 302 27 HOH HOH . G 6 HOH AAA 3 303 68 HOH HOH . G 6 HOH AAA 4 304 33 HOH HOH . G 6 HOH AAA 5 305 26 HOH HOH . G 6 HOH AAA 6 306 40 HOH HOH . G 6 HOH AAA 7 307 69 HOH HOH . G 6 HOH AAA 8 308 45 HOH HOH . G 6 HOH AAA 9 309 8 HOH HOH . G 6 HOH AAA 10 310 31 HOH HOH . G 6 HOH AAA 11 311 59 HOH HOH . G 6 HOH AAA 12 312 20 HOH HOH . G 6 HOH AAA 13 313 56 HOH HOH . G 6 HOH AAA 14 314 34 HOH HOH . G 6 HOH AAA 15 315 30 HOH HOH . G 6 HOH AAA 16 316 46 HOH HOH . G 6 HOH AAA 17 317 7 HOH HOH . G 6 HOH AAA 18 318 16 HOH HOH . G 6 HOH AAA 19 319 1 HOH HOH . G 6 HOH AAA 20 320 13 HOH HOH . G 6 HOH AAA 21 321 23 HOH HOH . G 6 HOH AAA 22 322 95 HOH HOH . G 6 HOH AAA 23 323 2 HOH HOH . G 6 HOH AAA 24 324 96 HOH HOH . G 6 HOH AAA 25 325 19 HOH HOH . G 6 HOH AAA 26 326 49 HOH HOH . G 6 HOH AAA 27 327 18 HOH HOH . G 6 HOH AAA 28 328 47 HOH HOH . G 6 HOH AAA 29 329 25 HOH HOH . G 6 HOH AAA 30 330 79 HOH HOH . G 6 HOH AAA 31 331 55 HOH HOH . G 6 HOH AAA 32 332 37 HOH HOH . G 6 HOH AAA 33 333 57 HOH HOH . G 6 HOH AAA 34 334 22 HOH HOH . G 6 HOH AAA 35 335 6 HOH HOH . G 6 HOH AAA 36 336 92 HOH HOH . G 6 HOH AAA 37 337 17 HOH HOH . G 6 HOH AAA 38 338 36 HOH HOH . G 6 HOH AAA 39 339 14 HOH HOH . G 6 HOH AAA 40 340 63 HOH HOH . G 6 HOH AAA 41 341 82 HOH HOH . G 6 HOH AAA 42 342 12 HOH HOH . G 6 HOH AAA 43 343 93 HOH HOH . G 6 HOH AAA 44 344 51 HOH HOH . G 6 HOH AAA 45 345 72 HOH HOH . G 6 HOH AAA 46 346 5 HOH HOH . G 6 HOH AAA 47 347 44 HOH HOH . G 6 HOH AAA 48 348 94 HOH HOH . G 6 HOH AAA 49 349 35 HOH HOH . G 6 HOH AAA 50 350 29 HOH HOH . G 6 HOH AAA 51 351 28 HOH HOH . G 6 HOH AAA 52 352 98 HOH HOH . G 6 HOH AAA 53 353 64 HOH HOH . G 6 HOH AAA 54 354 86 HOH HOH . G 6 HOH AAA 55 355 76 HOH HOH . G 6 HOH AAA 56 356 77 HOH HOH . G 6 HOH AAA 57 357 52 HOH HOH . G 6 HOH AAA 58 358 39 HOH HOH . G 6 HOH AAA 59 359 11 HOH HOH . G 6 HOH AAA 60 360 48 HOH HOH . G 6 HOH AAA 61 361 58 HOH HOH . G 6 HOH AAA 62 362 83 HOH HOH . G 6 HOH AAA 63 363 89 HOH HOH . G 6 HOH AAA 64 364 74 HOH HOH . G 6 HOH AAA 65 365 97 HOH HOH . G 6 HOH AAA 66 366 88 HOH HOH . G 6 HOH AAA 67 367 50 HOH HOH . G 6 HOH AAA 68 368 38 HOH HOH . G 6 HOH AAA 69 369 90 HOH HOH . G 6 HOH AAA 70 370 70 HOH HOH . G 6 HOH AAA 71 371 100 HOH HOH . G 6 HOH AAA 72 372 32 HOH HOH . G 6 HOH AAA 73 373 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 C11 R2I . . . D 4 -23.477 -0.619 12.082 0.7 51.15 0 C11 R2I 203 AAA 1 HETATM 2 C C12 R2I . . . D 4 -24.411 0.366 11.985 0.7 48.66 0 C12 R2I 203 AAA 1 HETATM 3 C C13 R2I . . . D 4 -24.814 0.807 10.752 0.7 45.55 0 C13 R2I 203 AAA 1 HETATM 4 C C14 R2I . . . D 4 -27.22 -1.071 6.836 0.7 42.31 0 C14 R2I 203 AAA 1 HETATM 5 RU RU1 R2I . . . D 4 -25.437 0.668 5.408 0.7 41.98 0 RU1 R2I 203 AAA 1 HETATM 6 RU RU2 R2I . . . D 4 -24.389 -0.745 6.853 0.7 42.54 0 RU2 R2I 203 AAA 1 HETATM 7 F F1 R2I . . . D 4 -28.731 6.542 5.696 0.7 49.3 0 F1 R2I 203 AAA 1 HETATM 8 F F2 R2I . . . D 4 -23.097 -1.058 13.298 0.7 47.59 0 F2 R2I 203 AAA 1 HETATM 9 O O3 R2I . . . D 4 -23.6 1.416 4.968 0.7 41.23 0 O3 R2I 203 AAA 1 HETATM 10 O O1 R2I . . . D 4 -27.213 -0.144 5.979 0.7 39.57 0 O1 R2I 203 AAA 1 HETATM 11 O O2 R2I . . . D 4 -26.184 -1.553 7.399 0.7 42.01 0 O2 R2I 203 AAA 1 HETATM 12 O O4 R2I . . . D 4 -22.587 0 6.342 0.7 40.28 0 O4 R2I 203 AAA 1 HETATM 13 N N1 R2I . . . D 4 -25.687 2.064 6.849 0.7 42.19 0 N1 R2I 203 AAA 1 HETATM 14 N N2 R2I . . . D 4 -24.605 0.639 8.287 0.7 44.28 0 N2 R2I 203 AAA 1 HETATM 15 C C2 R2I . . . D 4 -26.488 3.215 6.576 0.7 41.12 0 C2 R2I 203 AAA 1 HETATM 16 C C3 R2I . . . D 4 -25.881 4.421 6.249 0.7 43.16 0 C3 R2I 203 AAA 1 HETATM 17 C C4 R2I . . . D 4 -26.637 5.555 5.966 0.7 46.05 0 C4 R2I 203 AAA 1 HETATM 18 C C7 R2I . . . D 4 -27.877 3.141 6.566 0.7 44.04 0 C7 R2I 203 AAA 1 HETATM 19 C C1 R2I . . . D 4 -25.361 1.717 8.078 0.7 41.81 0 C1 R2I 203 AAA 1 HETATM 20 C C6 R2I . . . D 4 -28.639 4.245 6.276 0.7 43.65 0 C6 R2I 203 AAA 1 HETATM 21 C C5 R2I . . . D 4 -28.012 5.422 5.985 0.7 44.85 0 C5 R2I 203 AAA 1 HETATM 22 C C8 R2I . . . D 4 -24.258 0.257 9.618 0.7 47.26 0 C8 R2I 203 AAA 1 HETATM 23 C C16 R2I . . . D 4 -22.56 0.937 5.505 0.7 36.74 0 C16 R2I 203 AAA 1 HETATM 24 C C10 R2I . . . D 4 -22.927 -1.191 10.988 0.7 48.01 0 C10 R2I 203 AAA 1 HETATM 25 C C9 R2I . . . D 4 -23.307 -0.752 9.741 0.7 53.66 0 C9 R2I 203 AAA 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 25 #