data_6BO2 # _model_server_result.job_id S03C0Uwavl4Uadt9ub-dCA _model_server_result.datetime_utc '2024-10-20 03:27:45' _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 6bo2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 6BO2 # _exptl.entry_id 6BO2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 318.165 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description dichloro(1,3-dimethyl-1H-benzimidazol-3-ium-2-yl)ruthenium _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 6BO2 _cell.length_a 78.762 _cell.length_b 78.762 _cell.length_c 36.928 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BO2 _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,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 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 115 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 80 A CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 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 NH2 ARG 14 A ARG 14 1_555 D RU1 E3D . A E3D 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc2 A NE2 HIS 15 A HIS 15 1_555 D RU1 E3D . A E3D 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc3 A NZ LYS 33 A LYS 33 1_555 E RU1 E3D . A E3D 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc4 A O SER 60 A SER 60 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc5 A O CYS 64 A CYS 64 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc6 A OG SER 72 A SER 72 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? metalc ? metalc7 A O ARG 73 A ARG 73 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc8 A O ALA 107 A ALA 107 1_555 C RU RU . A RU 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? metalc ? metalc9 B NA NA . A NA 201 1_555 G O HOH . A HOH 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc10 B NA NA . A NA 201 1_555 G O HOH . A HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc11 C RU RU . A RU 202 1_555 G O HOH . A HOH 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.786 ? metalc ? metalc12 C RU RU . A RU 202 1_555 G O HOH . A HOH 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc13 C RU RU . A RU 202 1_555 G O HOH . A HOH 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc14 D RU1 E3D . A E3D 203 1_555 G O HOH . A HOH 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc15 E RU1 E3D . A E3D 204 1_555 G O HOH . A HOH 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc16 E RU1 E3D . A E3D 204 1_555 G O HOH . A HOH 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? # _chem_comp.formula 'C9 H10 Cl2 N2 Ru 1' _chem_comp.formula_weight 318.165 _chem_comp.id E3D _chem_comp.mon_nstd_flag . _chem_comp.name dichloro(1,3-dimethyl-1H-benzimidazol-3-ium-2-yl)ruthenium _chem_comp.type non-polymer _chem_comp.pdbx_synonyms dichlorido(1,3-dimethylbenzimidazol-2-ylidene)ruthenium(II) # 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 C8 C9 E3D doub 83 n y C8 C7 E3D sing 84 n y C9 C4 E3D sing 85 n y C7 C6 E3D doub 86 n y C4 C5 E3D doub 87 n y C4 N1 E3D sing 88 n y C6 C5 E3D sing 89 n y C3 N1 E3D sing 90 n n C5 N2 E3D sing 91 n y N1 C1 E3D sing 92 n y N2 C1 E3D doub 93 n y N2 C2 E3D sing 94 n n C1 RU1 E3D sing 95 n n CL1 RU1 E3D sing 96 n n CL2 RU1 E3D sing 97 n n C2 H1 E3D sing 98 n n C2 H2 E3D sing 99 n n C2 H3 E3D sing 100 n n C3 H4 E3D sing 101 n n C3 H5 E3D sing 102 n n C3 H6 E3D sing 103 n n C6 H7 E3D sing 104 n n C7 H8 E3D sing 105 n n C8 H9 E3D sing 106 n n C9 H10 E3D sing 107 n n # _atom_sites.entry_id 6BO2 _atom_sites.fract_transf_matrix[1][1] 0.012696 _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] 0.012696 _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] 0.02708 _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 1 NA NA . C 3 RU A 1 202 1 RU RU . D 4 E3D A 1 203 1 E3D NCR . E 4 E3D A 1 204 2 E3D NCR . F 5 CL A 1 205 1 CL CL . G 6 HOH A 1 301 67 HOH HOH . G 6 HOH A 2 302 51 HOH HOH . G 6 HOH A 3 303 5 HOH HOH . G 6 HOH A 4 304 47 HOH HOH . G 6 HOH A 5 305 44 HOH HOH . G 6 HOH A 6 306 65 HOH HOH . G 6 HOH A 7 307 52 HOH HOH . G 6 HOH A 8 308 23 HOH HOH . G 6 HOH A 9 309 35 HOH HOH . G 6 HOH A 10 310 14 HOH HOH . G 6 HOH A 11 311 41 HOH HOH . G 6 HOH A 12 312 75 HOH HOH . G 6 HOH A 13 313 17 HOH HOH . G 6 HOH A 14 314 76 HOH HOH . G 6 HOH A 15 315 74 HOH HOH . G 6 HOH A 16 316 28 HOH HOH . G 6 HOH A 17 317 56 HOH HOH . G 6 HOH A 18 318 36 HOH HOH . G 6 HOH A 19 319 6 HOH HOH . G 6 HOH A 20 320 8 HOH HOH . G 6 HOH A 21 321 11 HOH HOH . G 6 HOH A 22 322 62 HOH HOH . G 6 HOH A 23 323 64 HOH HOH . G 6 HOH A 24 324 4 HOH HOH . G 6 HOH A 25 325 18 HOH HOH . G 6 HOH A 26 326 32 HOH HOH . G 6 HOH A 27 327 19 HOH HOH . G 6 HOH A 28 328 34 HOH HOH . G 6 HOH A 29 329 31 HOH HOH . G 6 HOH A 30 330 73 HOH HOH . G 6 HOH A 31 331 7 HOH HOH . G 6 HOH A 32 332 39 HOH HOH . G 6 HOH A 33 333 63 HOH HOH . G 6 HOH A 34 334 71 HOH HOH . G 6 HOH A 35 335 33 HOH HOH . G 6 HOH A 36 336 1 HOH HOH . G 6 HOH A 37 337 25 HOH HOH . G 6 HOH A 38 338 16 HOH HOH . G 6 HOH A 39 339 72 HOH HOH . G 6 HOH A 40 340 10 HOH HOH . G 6 HOH A 41 341 70 HOH HOH . G 6 HOH A 42 342 22 HOH HOH . G 6 HOH A 43 343 29 HOH HOH . G 6 HOH A 44 344 77 HOH HOH . G 6 HOH A 45 345 24 HOH HOH . G 6 HOH A 46 346 42 HOH HOH . G 6 HOH A 47 347 37 HOH HOH . G 6 HOH A 48 348 20 HOH HOH . G 6 HOH A 49 349 45 HOH HOH . G 6 HOH A 50 350 15 HOH HOH . G 6 HOH A 51 351 3 HOH HOH . G 6 HOH A 52 352 53 HOH HOH . G 6 HOH A 53 353 2 HOH HOH . G 6 HOH A 54 354 46 HOH HOH . G 6 HOH A 55 355 49 HOH HOH . G 6 HOH A 56 356 55 HOH HOH . G 6 HOH A 57 357 78 HOH HOH . G 6 HOH A 58 358 9 HOH HOH . G 6 HOH A 59 359 38 HOH HOH . G 6 HOH A 60 360 12 HOH HOH . G 6 HOH A 61 361 21 HOH HOH . G 6 HOH A 62 362 27 HOH HOH . G 6 HOH A 63 363 68 HOH HOH . G 6 HOH A 64 364 30 HOH HOH . G 6 HOH A 65 365 13 HOH HOH . G 6 HOH A 66 366 43 HOH HOH . G 6 HOH A 67 367 59 HOH HOH . G 6 HOH A 68 368 69 HOH HOH . G 6 HOH A 69 369 54 HOH HOH . G 6 HOH A 70 370 60 HOH HOH . G 6 HOH A 71 371 48 HOH HOH . G 6 HOH A 72 372 57 HOH HOH . G 6 HOH A 73 373 79 HOH HOH . G 6 HOH A 74 374 26 HOH HOH . G 6 HOH A 75 375 40 HOH HOH . G 6 HOH A 76 376 61 HOH HOH . G 6 HOH A 77 377 80 HOH HOH . G 6 HOH A 78 378 50 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 E3D . . . D 4 9.384 -8.277 -6.312 0.9 33.37 ? C1 E3D 203 A 1 HETATM 2 C C2 E3D . . . D 4 11.367 -8.874 -7.858 0.9 35.2 ? C2 E3D 203 A 1 HETATM 3 C C3 E3D . . . D 4 7.303 -7.069 -5.568 0.9 32.01 ? C3 E3D 203 A 1 HETATM 4 C C4 E3D . . . D 4 8.523 -6.703 -7.737 0.9 32.54 ? C4 E3D 203 A 1 HETATM 5 C C5 E3D . . . D 4 9.634 -7.223 -8.339 0.9 33.18 ? C5 E3D 203 A 1 HETATM 6 C C6 E3D . . . D 4 10.041 -6.771 -9.599 0.9 33.21 ? C6 E3D 203 A 1 HETATM 7 C C7 E3D . . . D 4 9.287 -5.794 -10.191 0.9 31.69 ? C7 E3D 203 A 1 HETATM 8 C C8 E3D . . . D 4 8.175 -5.264 -9.632 0.9 29.36 ? C8 E3D 203 A 1 HETATM 9 C C9 E3D . . . D 4 7.757 -5.713 -8.353 0.9 31.37 ? C9 E3D 203 A 1 HETATM 10 N N1 E3D . . . D 4 8.388 -7.368 -6.476 0.9 30.97 ? N1 E3D 203 A 1 HETATM 11 N N2 E3D . . . D 4 10.155 -8.169 -7.46 0.9 33.5 ? N2 E3D 203 A 1 HETATM 12 CL CL1 E3D . . . D 4 10.489 -11.286 -6.22 0.9 46.04 ? CL1 E3D 203 A 1 HETATM 13 CL CL2 E3D . . . D 4 7.486 -10.514 -4.926 0.9 47.88 ? CL2 E3D 203 A 1 HETATM 14 RU RU1 E3D . . . D 4 9.699 -9.545 -4.697 0.9 32.56 ? RU1 E3D 203 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 366 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #