data_2YAK # _model_server_result.job_id Bme0ZhBBrxam9OzmUDvzsg _model_server_result.datetime_utc '2024-11-25 21:26:29' _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 2yak # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1279}' # _entry.id 2YAK # _exptl.entry_id 2YAK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 707.888 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'RUTHENIUM OCTASPORINE 4' _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 2YAK _cell.length_a 50.3 _cell.length_b 77.8 _cell.length_c 111.3 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YAK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C27 H31 F N4 O3 Ru S4' _chem_comp.formula_weight 707.888 _chem_comp.id OSV _chem_comp.mon_nstd_flag . _chem_comp.name 'RUTHENIUM OCTASPORINE 4' _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 N C OSV sing 237 n n C S OSV trip 238 n n RU N OSV sing 239 n n N HN OSV sing 240 n n S17 RU OSV sing 241 n n NAM RU OSV sing 242 n n NAK RU OSV sing 243 n n RU S18 OSV sing 244 n n RU S16 OSV sing 245 n n C7 C6 OSV sing 246 n n C6 S16 OSV sing 247 n n C6 H6 OSV sing 248 n n C6 H6A OSV sing 249 n n S17 C7 OSV sing 250 n n C7 H7 OSV sing 251 n n C7 H7A OSV sing 252 n n S17 C8 OSV sing 253 n n C8 C9 OSV sing 254 n n C8 H8 OSV sing 255 n n C8 H8A OSV sing 256 n n C9 S18 OSV sing 257 n n C9 H9 OSV sing 258 n n C9 H9A OSV sing 259 n n S18 C10 OSV sing 260 n n C10 C11 OSV sing 261 n n C10 H10 OSV sing 262 n n C10 H10A OSV sing 263 n n S16 C11 OSV sing 264 n n C11 H11 OSV sing 265 n n C11 H11A OSV sing 266 n n CBA CAA OSV sing 267 n n CAA HAA OSV sing 268 n n CAA HAAA OSV sing 269 n n CAA HAAB OSV sing 270 n n CAB CBA OSV sing 271 n n CAB HAB OSV sing 272 n n CAB HABA OSV sing 273 n n CAB HABB OSV sing 274 n n OAC CAQ OSV doub 275 n n OAD CAR OSV doub 276 n n F1 CAO OSV sing 277 n n CAP CAF OSV doub 278 n y CAF CAG OSV sing 279 n y CAF HAF OSV sing 280 n n CAS CAG OSV doub 281 n y CAG HAG OSV sing 282 n n CAO CAH OSV doub 283 n n NAK CAH OSV sing 284 n n CAH HAH OSV sing 285 n n CAI CAU OSV doub 286 n n CAI CAO OSV sing 287 n n CAI HAI OSV sing 288 n n CAJ CAT OSV doub 289 n y CAJ CAP OSV sing 290 n y CAJ HAJ OSV sing 291 n n CAV NAK OSV sing 292 n n NAL CAQ OSV sing 293 n n NAL CAR OSV sing 294 n n NAL HNAL OSV sing 295 n n CAW NAM OSV sing 296 n n CAS NAM OSV sing 297 n n CBA OAN OSV sing 298 n n OAN CAP OSV sing 299 n n CAQ CAX OSV sing 300 n n CAR CAY OSV sing 301 n n CAT CAS OSV sing 302 n y CAZ CAT OSV sing 303 n n CAX CAU OSV sing 304 n n CAU CAV OSV sing 305 n n CAW CAV OSV doub 306 n n CAZ CAW OSV sing 307 n n CAX CAY OSV sing 308 n n CAY CAZ OSV doub 309 n n CBA HBA OSV sing 310 n n S HS OSV sing 311 n n S16 HS16 OSV sing 312 n n S17 HS17 OSV sing 313 n n S18 HS18 OSV sing 314 n n CAX HAX OSV sing 315 n n # _atom_sites.entry_id 2YAK _atom_sites.fract_transf_matrix[1][1] 0.019881 _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] 0.012853 _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] 0.008985 _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 OSV A 1 1279 1279 OSV OSV . C 3 HOH A 1 2001 2001 HOH HOH . C 3 HOH A 2 2002 2002 HOH HOH . C 3 HOH A 3 2003 2003 HOH HOH . C 3 HOH A 4 2004 2004 HOH HOH . C 3 HOH A 5 2005 2005 HOH HOH . C 3 HOH A 6 2006 2006 HOH HOH . C 3 HOH A 7 2007 2007 HOH HOH . C 3 HOH A 8 2008 2008 HOH HOH . C 3 HOH A 9 2009 2009 HOH HOH . C 3 HOH A 10 2010 2010 HOH HOH . C 3 HOH A 11 2011 2011 HOH HOH . C 3 HOH A 12 2012 2012 HOH HOH . C 3 HOH A 13 2013 2013 HOH HOH . C 3 HOH A 14 2014 2014 HOH HOH . C 3 HOH A 15 2015 2015 HOH HOH . C 3 HOH A 16 2016 2016 HOH HOH . C 3 HOH A 17 2017 2017 HOH HOH . C 3 HOH A 18 2018 2018 HOH HOH . C 3 HOH A 19 2019 2019 HOH HOH . C 3 HOH A 20 2020 2020 HOH HOH . C 3 HOH A 21 2021 2021 HOH HOH . C 3 HOH A 22 2022 2022 HOH HOH . C 3 HOH A 23 2023 2023 HOH HOH . C 3 HOH A 24 2024 2024 HOH HOH . C 3 HOH A 25 2025 2025 HOH HOH . C 3 HOH A 26 2026 2026 HOH HOH . C 3 HOH A 27 2027 2027 HOH HOH . C 3 HOH A 28 2028 2028 HOH HOH . C 3 HOH A 29 2029 2029 HOH HOH . C 3 HOH A 30 2030 2030 HOH HOH . C 3 HOH A 31 2031 2031 HOH HOH . C 3 HOH A 32 2032 2032 HOH HOH . C 3 HOH A 33 2033 2033 HOH HOH . C 3 HOH A 34 2034 2034 HOH HOH . C 3 HOH A 35 2035 2035 HOH HOH . C 3 HOH A 36 2036 2036 HOH HOH . C 3 HOH A 37 2037 2037 HOH HOH . C 3 HOH A 38 2038 2038 HOH HOH . C 3 HOH A 39 2039 2039 HOH HOH . C 3 HOH A 40 2040 2040 HOH HOH . C 3 HOH A 41 2041 2041 HOH HOH . C 3 HOH A 42 2042 2042 HOH HOH . C 3 HOH A 43 2043 2043 HOH HOH . C 3 HOH A 44 2044 2044 HOH HOH . C 3 HOH A 45 2045 2045 HOH HOH . C 3 HOH A 46 2046 2046 HOH HOH . C 3 HOH A 47 2047 2047 HOH HOH . C 3 HOH A 48 2048 2048 HOH HOH . C 3 HOH A 49 2049 2049 HOH HOH . C 3 HOH A 50 2050 2050 HOH HOH . C 3 HOH A 51 2051 2051 HOH HOH . C 3 HOH A 52 2052 2052 HOH HOH . C 3 HOH A 53 2053 2053 HOH HOH . C 3 HOH A 54 2054 2054 HOH HOH . C 3 HOH A 55 2055 2055 HOH HOH . C 3 HOH A 56 2056 2056 HOH HOH . C 3 HOH A 57 2057 2057 HOH HOH . C 3 HOH A 58 2058 2058 HOH HOH . C 3 HOH A 59 2059 2059 HOH HOH . C 3 HOH A 60 2060 2060 HOH HOH . C 3 HOH A 61 2061 2061 HOH HOH . C 3 HOH A 62 2062 2062 HOH HOH . C 3 HOH A 63 2063 2063 HOH HOH . C 3 HOH A 64 2064 2064 HOH HOH . C 3 HOH A 65 2065 2065 HOH HOH . C 3 HOH A 66 2066 2066 HOH HOH . C 3 HOH A 67 2067 2067 HOH HOH . C 3 HOH A 68 2068 2068 HOH HOH . C 3 HOH A 69 2069 2069 HOH HOH . C 3 HOH A 70 2070 2070 HOH HOH . C 3 HOH A 71 2071 2071 HOH HOH . C 3 HOH A 72 2072 2072 HOH HOH . C 3 HOH A 73 2073 2073 HOH HOH . C 3 HOH A 74 2074 2074 HOH HOH . C 3 HOH A 75 2075 2075 HOH HOH . C 3 HOH A 76 2076 2076 HOH HOH . C 3 HOH A 77 2077 2077 HOH HOH . C 3 HOH A 78 2078 2078 HOH HOH . C 3 HOH A 79 2079 2079 HOH HOH . C 3 HOH A 80 2080 2080 HOH HOH . C 3 HOH A 81 2081 2081 HOH HOH . C 3 HOH A 82 2082 2082 HOH HOH . C 3 HOH A 83 2083 2083 HOH HOH . C 3 HOH A 84 2084 2084 HOH HOH . C 3 HOH A 85 2085 2085 HOH HOH . C 3 HOH A 86 2086 2086 HOH HOH . C 3 HOH A 87 2087 2087 HOH HOH . C 3 HOH A 88 2088 2088 HOH HOH . C 3 HOH A 89 2089 2089 HOH HOH . C 3 HOH A 90 2090 2090 HOH HOH . C 3 HOH A 91 2091 2091 HOH HOH . C 3 HOH A 92 2092 2092 HOH HOH . C 3 HOH A 93 2093 2093 HOH HOH . C 3 HOH A 94 2094 2094 HOH HOH . C 3 HOH A 95 2095 2095 HOH HOH . C 3 HOH A 96 2096 2096 HOH HOH . C 3 HOH A 97 2097 2097 HOH HOH . C 3 HOH A 98 2098 2098 HOH HOH . C 3 HOH A 99 2099 2099 HOH HOH . C 3 HOH A 100 2100 2100 HOH HOH . C 3 HOH A 101 2101 2101 HOH HOH . C 3 HOH A 102 2102 2102 HOH HOH . C 3 HOH A 103 2103 2103 HOH HOH . C 3 HOH A 104 2104 2104 HOH HOH . C 3 HOH A 105 2105 2105 HOH HOH . C 3 HOH A 106 2106 2106 HOH HOH . C 3 HOH A 107 2107 2107 HOH HOH . C 3 HOH A 108 2108 2108 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 C OSV . . . B 2 -11.07 -12.033 20.367 1 25.26 ? C OSV 1279 A 1 HETATM 2 N N OSV . . . B 2 -10.845 -11.147 19.655 1 22.9 ? N OSV 1279 A 1 HETATM 3 S S OSV . . . B 2 -11.461 -13.343 21.451 1 30.62 ? S OSV 1279 A 1 HETATM 4 RU RU OSV . . . B 2 -11.688 -9.871 18.293 1 23.85 ? RU OSV 1279 A 1 HETATM 5 C C6 OSV . . . B 2 -14.607 -8.964 18.281 1 28.9 ? C6 OSV 1279 A 1 HETATM 6 C C7 OSV . . . B 2 -13.912 -8.113 17.215 1 26.35 ? C7 OSV 1279 A 1 HETATM 7 C C8 OSV . . . B 2 -11.536 -7.184 17.128 1 32.32 ? C8 OSV 1279 A 1 HETATM 8 C C9 OSV . . . B 2 -11.228 -6.897 18.633 1 29.75 ? C9 OSV 1279 A 1 HETATM 9 C C10 OSV . . . B 2 -11.799 -8.188 20.832 1 29.94 ? C10 OSV 1279 A 1 HETATM 10 C C11 OSV . . . B 2 -13.269 -8.537 20.543 1 28.98 ? C11 OSV 1279 A 1 HETATM 11 S S16 OSV . . . B 2 -13.392 -9.576 19.248 1 27.97 ? S16 OSV 1279 A 1 HETATM 12 S S17 OSV . . . B 2 -12.346 -8.638 16.956 1 26.07 ? S17 OSV 1279 A 1 HETATM 13 S S18 OSV . . . B 2 -10.984 -8.347 19.423 1 28.22 ? S18 OSV 1279 A 1 HETATM 14 C CAA OSV . . . B 2 -14.837 -17.504 15.261 1 33.42 ? CAA OSV 1279 A 1 HETATM 15 C CAB OSV . . . B 2 -14.683 -15.832 13.132 1 30.47 ? CAB OSV 1279 A 1 HETATM 16 O OAC OSV . . . B 2 -7.529 -12.056 12.659 1 31.72 ? OAC OSV 1279 A 1 HETATM 17 O OAD OSV . . . B 2 -11.235 -14.583 12.652 1 28.25 ? OAD OSV 1279 A 1 HETATM 18 F F1 OSV . . . B 2 -6.624 -8.524 16.078 1 41.08 ? F1 OSV 1279 A 1 HETATM 19 C CAF OSV . . . B 2 -15.077 -13.696 16.899 1 32.23 ? CAF OSV 1279 A 1 HETATM 20 C CAG OSV . . . B 2 -14.251 -12.699 17.352 1 31.28 ? CAG OSV 1279 A 1 HETATM 21 C CAH OSV . . . B 2 -8.671 -9.075 17.129 1 31.35 ? CAH OSV 1279 A 1 HETATM 22 C CAI OSV . . . B 2 -7.963 -10.272 15.124 1 31.77 ? CAI OSV 1279 A 1 HETATM 23 C CAJ OSV . . . B 2 -13.519 -14.158 15.078 1 32.01 ? CAJ OSV 1279 A 1 HETATM 24 N NAK OSV . . . B 2 -9.876 -9.866 17.122 1 26.5 ? NAK OSV 1279 A 1 HETATM 25 N NAL OSV . . . B 2 -9.271 -13.47 12.383 1 32.24 ? NAL OSV 1279 A 1 HETATM 26 N NAM OSV . . . B 2 -12.19 -11.568 16.967 1 27.74 ? NAM OSV 1279 A 1 HETATM 27 O OAN OSV . . . B 2 -15.634 -15.433 15.459 1 38.54 ? OAN OSV 1279 A 1 HETATM 28 C CAO OSV . . . B 2 -7.739 -9.283 16.114 1 35.94 ? CAO OSV 1279 A 1 HETATM 29 C CAP OSV . . . B 2 -14.707 -14.449 15.807 1 35.56 ? CAP OSV 1279 A 1 HETATM 30 C CAQ OSV . . . B 2 -8.621 -12.506 13.033 1 32 ? CAQ OSV 1279 A 1 HETATM 31 C CAR OSV . . . B 2 -10.422 -13.723 13.039 1 32.54 ? CAR OSV 1279 A 1 HETATM 32 C CAS OSV . . . B 2 -13.077 -12.465 16.68 1 30.59 ? CAS OSV 1279 A 1 HETATM 33 C CAT OSV . . . B 2 -12.676 -13.173 15.531 1 29.3 ? CAT OSV 1279 A 1 HETATM 34 C CAU OSV . . . B 2 -9.109 -11.076 15.141 1 26.23 ? CAU OSV 1279 A 1 HETATM 35 C CAV OSV . . . B 2 -10.043 -10.869 16.135 1 25.97 ? CAV OSV 1279 A 1 HETATM 36 C CAW OSV . . . B 2 -11.185 -11.642 16.126 1 27.6 ? CAW OSV 1279 A 1 HETATM 37 C CAX OSV . . . B 2 -9.352 -12.081 14.172 1 29.8 ? CAX OSV 1279 A 1 HETATM 38 C CAY OSV . . . B 2 -10.518 -12.879 14.176 1 28.06 ? CAY OSV 1279 A 1 HETATM 39 C CAZ OSV . . . B 2 -11.453 -12.641 15.155 1 27.41 ? CAZ OSV 1279 A 1 HETATM 40 C CBA OSV . . . B 2 -15.427 -16.406 14.363 1 38.34 ? CBA OSV 1279 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 40 #