data_1BEX # _model_server_result.job_id t_gavvqtObLrm4tF_O8BYg _model_server_result.datetime_utc '2024-12-03 03:58:04' _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 1bex # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":130}' # _entry.id 1BEX # _exptl.entry_id 1BEX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 481.515 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "RUTHEMIUM BIS(2,2'-BIPYRIDINE)-2-IMIDAZOLE" _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 106.5 _cell.angle_gamma 90 _cell.entry_id 1BEX _cell.length_a 100.6 _cell.length_b 35.4 _cell.length_c 74.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BEX _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,C,D,E,I 2 1 B,F,G,H,J 2 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 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 3 A CYS 3 1_555 A SG CYS 26 A CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 B SG CYS 3 B CYS 3 1_555 B SG CYS 26 B CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc1 A N ALA 1 A ALA 1 1_555 D CU CU . A CU 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.785 ? metalc ? metalc2 A O ALA 1 A ALA 1 1_555 D CU CU . A CU 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc3 A OD2 ASP 23 A ASP 23 1_555 D CU CU . A CU 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc4 A OD2 ASP 23 A ASP 23 2_555 G CU CU . B CU 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc5 A OD1 ASP 23 A ASP 23 2_555 G CU CU . B CU 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc6 A ND1 HIS 46 A HIS 46 1_555 C CU CU . A CU 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc7 A NE2 HIS 83 A HIS 83 1_555 E RU RBU . A RBU 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc8 A SG CYS 112 A CYS 112 1_555 C CU CU . A CU 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc9 A ND1 HIS 117 A HIS 117 1_555 C CU CU . A CU 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc10 D CU CU . A CU 131 1_555 B OD2 ASP 23 B ASP 23 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc11 D CU CU . A CU 131 1_555 B OD1 ASP 23 B ASP 23 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc12 B N ALA 1 B ALA 1 1_555 G CU CU . B CU 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc13 B O ALA 1 B ALA 1 1_555 G CU CU . B CU 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc14 B OD2 ASP 23 B ASP 23 1_555 G CU CU . B CU 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc15 B ND1 HIS 46 B HIS 46 1_555 F CU CU . B CU 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc16 B NE2 HIS 83 B HIS 83 1_555 H RU RBU . B RBU 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc17 B SG CYS 112 B CYS 112 1_555 F CU CU . B CU 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc18 B ND1 HIS 117 B HIS 117 1_555 F CU CU . B CU 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? # _chem_comp.formula 'C23 H20 N6 Ru' _chem_comp.formula_weight 481.515 _chem_comp.id RBU _chem_comp.mon_nstd_flag . _chem_comp.name "RUTHEMIUM BIS(2,2'-BIPYRIDINE)-2-IMIDAZOLE" _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 C1 C2 RBU doub 277 n y C1 N1 RBU sing 278 n y C1 H1 RBU sing 279 n n C2 C3 RBU sing 280 n y C2 H2 RBU sing 281 n n C3 C4 RBU doub 282 n y C3 H3 RBU sing 283 n n C4 C5 RBU sing 284 n y C4 H4 RBU sing 285 n n C5 N1 RBU doub 286 n y C5 C6 RBU sing 287 n n RU N1 RBU sing 288 n n RU N3 RBU sing 289 n n RU N5 RBU sing 290 n n N2 C6 RBU doub 291 n y N2 C10 RBU sing 292 n y N3 C11 RBU sing 293 n y N3 C15 RBU doub 294 n y N4 C16 RBU doub 295 n y N4 C20 RBU sing 296 n y N5 C21 RBU doub 297 n y N5 C23 RBU sing 298 n y N6 C21 RBU sing 299 n y N6 C22 RBU sing 300 n y N6 HN6 RBU sing 301 n n C6 C7 RBU sing 302 n y C7 C8 RBU doub 303 n y C7 H7 RBU sing 304 n n C8 C9 RBU sing 305 n y C8 H8 RBU sing 306 n n C9 C10 RBU doub 307 n y C9 H9 RBU sing 308 n n C10 H10 RBU sing 309 n n C11 C12 RBU doub 310 n y C11 H11 RBU sing 311 n n C12 C13 RBU sing 312 n y C12 H12 RBU sing 313 n n C13 C14 RBU doub 314 n y C13 H13 RBU sing 315 n n C14 C15 RBU sing 316 n y C14 H14 RBU sing 317 n n C15 C16 RBU sing 318 n n C16 C17 RBU sing 319 n y C17 C18 RBU doub 320 n y C17 H17 RBU sing 321 n n C18 C19 RBU sing 322 n y C18 H18 RBU sing 323 n n C19 C20 RBU doub 324 n y C19 H19 RBU sing 325 n n C20 H20 RBU sing 326 n n C21 H21 RBU sing 327 n n C22 C23 RBU doub 328 n y C22 H22 RBU sing 329 n n C23 H23 RBU sing 330 n n # _atom_sites.entry_id 1BEX _atom_sites.fract_transf_matrix[1][1] 0.00994 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002944 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028249 _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] 0.013962 _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 C 2 CU A 1 129 129 CU CU . D 2 CU A 1 131 131 CU CU . E 3 RBU A 1 130 130 RBU RBU . F 2 CU B 1 129 129 CU CU . G 2 CU B 1 131 131 CU CU . H 3 RBU B 1 130 130 RBU RBU . I 4 HOH A 1 501 501 HOH HOH . I 4 HOH A 2 502 502 HOH HOH . I 4 HOH A 3 503 503 HOH HOH . I 4 HOH A 4 504 504 HOH HOH . I 4 HOH A 5 505 505 HOH HOH . I 4 HOH A 6 506 506 HOH HOH . I 4 HOH A 7 507 507 HOH HOH . I 4 HOH A 8 508 508 HOH HOH . I 4 HOH A 9 509 509 HOH HOH . I 4 HOH A 10 510 510 HOH HOH . I 4 HOH A 11 511 511 HOH HOH . I 4 HOH A 12 512 512 HOH HOH . I 4 HOH A 13 513 513 HOH HOH . I 4 HOH A 14 514 514 HOH HOH . I 4 HOH A 15 515 515 HOH HOH . I 4 HOH A 16 516 516 HOH HOH . I 4 HOH A 17 517 517 HOH HOH . I 4 HOH A 18 518 518 HOH HOH . I 4 HOH A 19 519 519 HOH HOH . I 4 HOH A 20 520 520 HOH HOH . I 4 HOH A 21 531 531 HOH HOH . I 4 HOH A 22 533 533 HOH HOH . I 4 HOH A 23 534 534 HOH HOH . I 4 HOH A 24 538 538 HOH HOH . I 4 HOH A 25 539 539 HOH HOH . I 4 HOH A 26 540 540 HOH HOH . I 4 HOH A 27 542 542 HOH HOH . I 4 HOH A 28 543 543 HOH HOH . I 4 HOH A 29 544 544 HOH HOH . I 4 HOH A 30 545 545 HOH HOH . I 4 HOH A 31 546 546 HOH HOH . I 4 HOH A 32 547 547 HOH HOH . I 4 HOH A 33 548 548 HOH HOH . I 4 HOH A 34 549 549 HOH HOH . I 4 HOH A 35 550 550 HOH HOH . I 4 HOH A 36 551 551 HOH HOH . I 4 HOH A 37 552 552 HOH HOH . I 4 HOH A 38 553 553 HOH HOH . I 4 HOH A 39 554 554 HOH HOH . I 4 HOH A 40 555 555 HOH HOH . I 4 HOH A 41 556 556 HOH HOH . I 4 HOH A 42 557 557 HOH HOH . I 4 HOH A 43 558 558 HOH HOH . I 4 HOH A 44 561 561 HOH HOH . I 4 HOH A 45 562 562 HOH HOH . I 4 HOH A 46 563 563 HOH HOH . I 4 HOH A 47 564 564 HOH HOH . I 4 HOH A 48 574 574 HOH HOH . I 4 HOH A 49 575 575 HOH HOH . I 4 HOH A 50 576 576 HOH HOH . I 4 HOH A 51 578 578 HOH HOH . J 4 HOH B 1 521 521 HOH HOH . J 4 HOH B 2 522 522 HOH HOH . J 4 HOH B 3 523 523 HOH HOH . J 4 HOH B 4 524 524 HOH HOH . J 4 HOH B 5 525 525 HOH HOH . J 4 HOH B 6 526 526 HOH HOH . J 4 HOH B 7 527 527 HOH HOH . J 4 HOH B 8 528 528 HOH HOH . J 4 HOH B 9 529 529 HOH HOH . J 4 HOH B 10 530 530 HOH HOH . J 4 HOH B 11 532 532 HOH HOH . J 4 HOH B 12 535 535 HOH HOH . J 4 HOH B 13 536 536 HOH HOH . J 4 HOH B 14 537 537 HOH HOH . J 4 HOH B 15 541 541 HOH HOH . J 4 HOH B 16 559 559 HOH HOH . J 4 HOH B 17 560 560 HOH HOH . J 4 HOH B 18 565 565 HOH HOH . J 4 HOH B 19 566 566 HOH HOH . J 4 HOH B 20 567 567 HOH HOH . J 4 HOH B 21 568 568 HOH HOH . J 4 HOH B 22 569 569 HOH HOH . J 4 HOH B 23 570 570 HOH HOH . J 4 HOH B 24 571 571 HOH HOH . J 4 HOH B 25 572 572 HOH HOH . J 4 HOH B 26 573 573 HOH HOH . J 4 HOH B 27 577 577 HOH HOH . J 4 HOH B 28 579 579 HOH HOH . J 4 HOH B 29 580 580 HOH HOH . J 4 HOH B 30 581 581 HOH HOH . J 4 HOH B 31 582 582 HOH HOH . J 4 HOH B 32 583 583 HOH HOH . J 4 HOH B 33 584 584 HOH HOH . J 4 HOH B 34 585 585 HOH HOH . J 4 HOH B 35 586 586 HOH HOH . J 4 HOH B 36 587 587 HOH HOH . J 4 HOH B 37 588 588 HOH HOH . J 4 HOH B 38 589 589 HOH HOH . J 4 HOH B 39 590 590 HOH HOH . J 4 HOH B 40 591 591 HOH HOH . J 4 HOH B 41 592 592 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 C1 RBU . . . H 3 9.702 13.522 26.709 1 25.95 ? C1 RBU 130 B 1 HETATM 2 C C2 RBU . . . H 3 8.559 14.088 27.246 1 24.41 ? C2 RBU 130 B 1 HETATM 3 C C3 RBU . . . H 3 7.458 14.307 26.428 1 27.5 ? C3 RBU 130 B 1 HETATM 4 C C4 RBU . . . H 3 7.49 13.96 25.087 1 25.63 ? C4 RBU 130 B 1 HETATM 5 C C5 RBU . . . H 3 8.644 13.4 24.572 1 27.77 ? C5 RBU 130 B 1 HETATM 6 RU RU RBU . . . H 3 11.345 12.339 24.416 1 22.16 ? RU RBU 130 B 1 HETATM 7 N N1 RBU . . . H 3 9.74 13.178 25.391 1 23.75 ? N1 RBU 130 B 1 HETATM 8 N N2 RBU . . . H 3 9.973 12.479 22.836 1 22.08 ? N2 RBU 130 B 1 HETATM 9 N N3 RBU . . . H 3 12.153 14.171 23.963 0.5 13.64 ? N3 RBU 130 B 1 HETATM 10 N N4 RBU . . . H 3 12.622 12.608 26.039 0.5 15.04 ? N4 RBU 130 B 1 HETATM 11 N N5 RBU . . . H 3 10.309 10.573 24.942 0.5 18.46 ? N5 RBU 130 B 1 HETATM 12 N N6 RBU . . . H 3 9.254 9.007 26.101 0.5 20.82 ? N6 RBU 130 B 1 HETATM 13 C C6 RBU . . . H 3 8.763 13.021 23.218 1 27.39 ? C6 RBU 130 B 1 HETATM 14 C C7 RBU . . . H 3 7.739 13.196 22.286 1 28.05 ? C7 RBU 130 B 1 HETATM 15 C C8 RBU . . . H 3 7.952 12.798 20.979 1 26.3 ? C8 RBU 130 B 1 HETATM 16 C C9 RBU . . . H 3 9.172 12.244 20.606 1 27.59 ? C9 RBU 130 B 1 HETATM 17 C C10 RBU . . . H 3 10.178 12.085 21.552 1 22.92 ? C10 RBU 130 B 1 HETATM 18 C C11 RBU . . . H 3 11.846 14.92 22.875 0.5 8.96 ? C11 RBU 130 B 1 HETATM 19 C C12 RBU . . . H 3 12.45 16.152 22.69 0.5 10.86 ? C12 RBU 130 B 1 HETATM 20 C C13 RBU . . . H 3 13.369 16.612 23.618 0.5 7.78 ? C13 RBU 130 B 1 HETATM 21 C C14 RBU . . . H 3 13.68 15.85 24.727 0.5 10.9 ? C14 RBU 130 B 1 HETATM 22 C C15 RBU . . . H 3 13.06 14.619 24.89 0.5 9.1 ? C15 RBU 130 B 1 HETATM 23 C C16 RBU . . . H 3 13.306 13.789 25.995 0.5 11.16 ? C16 RBU 130 B 1 HETATM 24 C C17 RBU . . . H 3 14.188 14.124 27.01 0.5 12.25 ? C17 RBU 130 B 1 HETATM 25 C C18 RBU . . . H 3 14.359 13.252 28.073 0.5 13.64 ? C18 RBU 130 B 1 HETATM 26 C C19 RBU . . . H 3 13.661 12.059 28.117 0.5 14.56 ? C19 RBU 130 B 1 HETATM 27 C C20 RBU . . . H 3 12.79 11.747 27.086 0.5 14.42 ? C20 RBU 130 B 1 HETATM 28 C C21 RBU . . . H 3 9.885 10.194 26.129 0.5 18.25 ? C21 RBU 130 B 1 HETATM 29 C C22 RBU . . . H 3 9.272 8.583 24.825 0.5 20.79 ? C22 RBU 130 B 1 HETATM 30 C C23 RBU . . . H 3 9.925 9.544 24.101 0.5 20.5 ? C23 RBU 130 B 1 # _model_server_stats.io_time_ms 113 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 30 #