data_4I60 # _model_server_result.job_id 0OvsS0L1tu2XQQ4upWg-9w _model_server_result.datetime_utc '2024-10-10 06:25:10' _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 4i60 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":203}' # _entry.id 4I60 # _exptl.entry_id 4I60 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 449.488 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}cyclopentadienyl]ruthenium' _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 4I60 _cell.length_a 60.22 _cell.length_b 60.22 _cell.length_c 62.47 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4I60 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 60.22 60.22 0 3 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 8_665 -y+1,-x+1,-z 0 -1 0 -1 0 0 0 0 -1 60.22 60.22 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG C 1 NAG 2 n B NAG 2 B 2 NAG C 2 NAG # 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 4 A CYS 4 1_555 A SG CYS 83 A CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? covale ? covale1 A ND2 ASN 17 A ASN 17 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? # _chem_comp.formula 'C20 H16 N2 O2 Ru S' _chem_comp.formula_weight 449.488 _chem_comp.id B1R _chem_comp.mon_nstd_flag . _chem_comp.name '[(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}cyclopentadienyl]ruthenium' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms biotinylruthenocene # 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 N1 C3 B1R sing 70 n n N1 C5 B1R sing 71 n n S1 C2 B1R sing 72 n n S1 C6 B1R sing 73 n n C2 C4 B1R sing 74 n n C2 C7 B1R sing 75 n n N2 C3 B1R sing 76 n n N2 C4 B1R sing 77 n n C3 O3 B1R doub 78 n n C4 C5 B1R sing 79 n n C5 C6 B1R sing 80 n n C7 C8 B1R sing 81 n n C8 C9 B1R sing 82 n n C9 C10 B1R sing 83 n n C10 C11 B1R sing 84 n n C11 O12 B1R doub 85 n n C11 C17 B1R sing 86 n n C14 C15 B1R sing 87 n n C14 C18 B1R doub 88 n n C15 C16 B1R doub 89 n n C16 C17 B1R sing 90 n n C17 C18 B1R sing 91 n n C19 C20 B1R sing 92 n n C19 C23 B1R doub 93 n n C20 C21 B1R doub 94 n n C21 C22 B1R sing 95 n n C22 C23 B1R sing 96 n n RU1 C14 B1R sing 97 n n RU1 C15 B1R sing 98 n n RU1 C16 B1R sing 99 n n RU1 C17 B1R sing 100 n n RU1 C18 B1R sing 101 n n RU1 C19 B1R sing 102 n n RU1 C20 B1R sing 103 n n RU1 C21 B1R sing 104 n n RU1 C22 B1R sing 105 n n RU1 C23 B1R sing 106 n n N1 H1 B1R sing 107 n n C2 H2 B1R sing 108 n n N2 H3 B1R sing 109 n n C4 H4 B1R sing 110 n n C5 H5 B1R sing 111 n n C6 H6 B1R sing 112 n n C6 H7 B1R sing 113 n n C7 H8 B1R sing 114 n n C7 H9 B1R sing 115 n n C8 H10 B1R sing 116 n n C8 H11 B1R sing 117 n n C9 H12 B1R sing 118 n n C9 H13 B1R sing 119 n n C10 H14 B1R sing 120 n n C10 H15 B1R sing 121 n n C22 H16 B1R sing 122 n n # _atom_sites.entry_id 4I60 _atom_sites.fract_transf_matrix[1][1] 0.016606 _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] 0.016606 _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] 0.016008 _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 3 B1R A 1 203 1 B1R B1R . D 4 HOH A 1 301 1 HOH HOH . D 4 HOH A 2 302 2 HOH HOH . D 4 HOH A 3 303 3 HOH HOH . D 4 HOH A 4 304 4 HOH HOH . D 4 HOH A 5 305 5 HOH HOH . D 4 HOH A 6 306 6 HOH HOH . D 4 HOH A 7 307 7 HOH HOH . D 4 HOH A 8 308 8 HOH HOH . D 4 HOH A 9 309 9 HOH HOH . D 4 HOH A 10 310 10 HOH HOH . D 4 HOH A 11 311 11 HOH HOH . D 4 HOH A 12 312 12 HOH HOH . D 4 HOH A 13 313 13 HOH HOH . D 4 HOH A 14 314 14 HOH HOH . D 4 HOH A 15 315 15 HOH HOH . D 4 HOH A 16 316 16 HOH HOH . D 4 HOH A 17 317 17 HOH HOH . D 4 HOH A 18 318 18 HOH HOH . D 4 HOH A 19 319 19 HOH HOH . D 4 HOH A 20 320 20 HOH HOH . D 4 HOH A 21 321 21 HOH HOH . D 4 HOH A 22 322 22 HOH HOH . D 4 HOH A 23 323 23 HOH HOH . D 4 HOH A 24 324 24 HOH HOH . D 4 HOH A 25 325 25 HOH HOH . D 4 HOH A 26 326 26 HOH HOH . D 4 HOH A 27 327 27 HOH HOH . D 4 HOH A 28 328 28 HOH HOH . D 4 HOH A 29 329 29 HOH HOH . D 4 HOH A 30 330 30 HOH HOH . D 4 HOH A 31 331 31 HOH HOH . D 4 HOH A 32 332 32 HOH HOH . D 4 HOH A 33 333 33 HOH HOH . D 4 HOH A 34 334 34 HOH HOH . D 4 HOH A 35 335 35 HOH HOH . D 4 HOH A 36 336 36 HOH HOH . D 4 HOH A 37 337 37 HOH HOH . D 4 HOH A 38 338 38 HOH HOH . D 4 HOH A 39 339 39 HOH HOH . D 4 HOH A 40 340 40 HOH HOH . D 4 HOH A 41 341 41 HOH HOH . D 4 HOH A 42 342 42 HOH HOH . D 4 HOH A 43 343 43 HOH HOH . D 4 HOH A 44 344 44 HOH HOH . D 4 HOH A 45 345 45 HOH HOH . D 4 HOH A 46 346 46 HOH HOH . D 4 HOH A 47 347 47 HOH HOH . D 4 HOH A 48 348 48 HOH HOH . D 4 HOH A 49 349 49 HOH HOH . D 4 HOH A 50 350 50 HOH HOH . D 4 HOH A 51 351 51 HOH HOH . D 4 HOH A 52 352 52 HOH HOH . D 4 HOH A 53 353 53 HOH HOH . D 4 HOH A 54 354 54 HOH HOH . D 4 HOH A 55 355 55 HOH HOH . D 4 HOH A 56 356 56 HOH HOH . D 4 HOH A 57 357 57 HOH HOH . D 4 HOH A 58 358 58 HOH HOH . D 4 HOH A 59 359 59 HOH HOH . D 4 HOH A 60 360 60 HOH HOH . D 4 HOH A 61 361 61 HOH HOH . D 4 HOH A 62 362 62 HOH HOH . D 4 HOH A 63 363 63 HOH HOH . D 4 HOH A 64 364 64 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 N N1 B1R . . . C 3 40.55 30.553 9.411 1 26.9 ? N1 B1R 203 A 1 HETATM 2 S S1 B1R . . . C 3 41.957 30.529 6.287 1 24.18 ? S1 B1R 203 A 1 HETATM 3 RU RU1 B1R . . . C 3 45.253 24.01 2.165 1 51.71 ? RU1 B1R 203 A 1 HETATM 4 C C2 B1R . . . C 3 42.528 29.049 7.025 1 24.74 ? C2 B1R 203 A 1 HETATM 5 N N2 B1R . . . C 3 42.453 29.505 9.44 1 23.95 ? N2 B1R 203 A 1 HETATM 6 C C3 B1R . . . C 3 41.731 30.459 9.985 1 25.87 ? C3 B1R 203 A 1 HETATM 7 O O3 B1R . . . C 3 42.129 31.211 10.862 1 27.24 ? O3 B1R 203 A 1 HETATM 8 C C4 B1R . . . C 3 41.762 28.868 8.323 1 25.55 ? C4 B1R 203 A 1 HETATM 9 C C5 B1R . . . C 3 40.427 29.666 8.274 1 26.05 ? C5 B1R 203 A 1 HETATM 10 C C6 B1R . . . C 3 40.359 30.481 7.016 1 23.64 ? C6 B1R 203 A 1 HETATM 11 C C7 B1R . . . C 3 44.054 29.149 7.252 1 25.6 ? C7 B1R 203 A 1 HETATM 12 C C8 B1R . . . C 3 44.803 27.927 6.689 1 29.55 ? C8 B1R 203 A 1 HETATM 13 C C9 B1R . . . C 3 45.016 28.02 5.169 1 31.18 ? C9 B1R 203 A 1 HETATM 14 C C10 B1R . . . C 3 46.347 27.355 4.728 1 32.04 ? C10 B1R 203 A 1 HETATM 15 C C11 B1R . . . C 3 46.142 25.86 4.422 1 34.96 ? C11 B1R 203 A 1 HETATM 16 O O12 B1R . . . C 3 45.676 25.146 5.271 1 34.28 ? O12 B1R 203 A 1 HETATM 17 C C14 B1R . . . C 3 47.249 23.589 1.709 1 44.3 ? C14 B1R 203 A 1 HETATM 18 C C15 B1R . . . C 3 46.877 24.672 1.004 1 43.52 ? C15 B1R 203 A 1 HETATM 19 C C16 B1R . . . C 3 46.477 25.652 1.714 1 43.08 ? C16 B1R 203 A 1 HETATM 20 C C17 B1R . . . C 3 46.779 25.24 3.114 1 41.54 ? C17 B1R 203 A 1 HETATM 21 C C18 B1R . . . C 3 47.236 23.958 2.981 1 42.3 ? C18 B1R 203 A 1 HETATM 22 C C19 B1R . . . C 3 43.588 23.563 3.293 1 43.63 ? C19 B1R 203 A 1 HETATM 23 C C20 B1R . . . C 3 43.882 22.494 2.562 1 43.44 ? C20 B1R 203 A 1 HETATM 24 C C21 B1R . . . C 3 43.874 22.74 1.292 1 41.91 ? C21 B1R 203 A 1 HETATM 25 C C22 B1R . . . C 3 43.419 24.057 1.197 1 43.07 ? C22 B1R 203 A 1 HETATM 26 C C23 B1R . . . C 3 43.226 24.448 2.403 1 44.95 ? C23 B1R 203 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 26 #