data_8YT4 # _model_server_result.job_id sUcPwAAW4zfNaxnun8vs1g _model_server_result.datetime_utc '2024-10-11 03:13:29' _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 8yt4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8YT4 # _exptl.entry_id 8YT4 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 94.971 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHATE ION' _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 8YT4 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YT4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 ? 60-meric 60 'complete icosahedral assembly' 1 ? monomeric 1 'icosahedral asymmetric unit' 2 ? pentameric 5 'icosahedral pentamer' 3 ? hexameric 6 'icosahedral 23 hexamer' 4 ? monomeric 1 'icosahedral asymmetric unit, std point frame' 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 (1-60) A,B,C 2 1 A,B,C 3 (1-5) A,B,C 4 (1,2,6,10,23,24) A,B,C 5 P # 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] P 'transform to point frame' ? ? 0.500001 0.809017 -0.309017 0.309017 -0.500001 -0.809017 -0.809017 0.309017 -0.500001 -159.35499 159.35499 159.35502 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.5 0.809017 0.309017 -0.809017 0.309017 0.5 0.309017 -0.499999 0.809017 -98.48675 159.35508 60.86803 3 'point symmetry operation' ? ? -0.309018 0.5 0.809016 -0.5 -0.809017 0.309017 0.809017 -0.309016 0.500001 0.00017 318.70997 -0.00021 4 'point symmetry operation' ? ? -0.309018 -0.5 0.809017 0.5 -0.809017 -0.309016 0.809016 0.309017 0.500001 159.35518 257.84163 -98.48687 5 'point symmetry operation' ? ? 0.5 -0.809017 0.309017 0.809017 0.309017 -0.499999 0.309017 0.5 0.809017 159.35508 60.86804 -98.48674 6 'point symmetry operation' ? ? 0.309016 -0.5 0.809018 -0.5 -0.809017 -0.309017 0.809018 -0.309017 -0.499999 60.86829 417.19685 159.35478 7 'point symmetry operation' ? ? 0.809016 -0.309018 0.5 0.309017 -0.5 -0.809017 0.500001 0.809017 -0.309016 0.00014 318.70997 -0.00018 8 'point symmetry operation' ? ? 0.809017 0.309017 0.5 0.309017 0.5 -0.809017 -0.5 0.809017 0.309017 -98.48676 159.35507 60.86807 9 'point symmetry operation' ? ? 0.309017 0.500001 0.809016 -0.5 0.809017 -0.309018 -0.809017 -0.309017 0.5 -98.48687 159.35521 257.84166 10 'point symmetry operation' ? ? -0.000001 0.000001 1 -1 0 -0.000001 0 -1 0.000001 -0.00003 318.71019 318.70979 11 'point symmetry operation' ? ? -0.809017 -0.309018 -0.5 -0.309018 -0.499999 0.809018 -0.5 0.809018 0.309015 417.19686 159.35481 60.86837 12 'point symmetry operation' ? ? -0.309016 -0.500001 -0.809017 0.499999 -0.809017 0.309018 -0.809018 -0.309016 0.499999 417.19674 159.35492 257.84196 13 'point symmetry operation' ? ? 0.000001 0 -1 1 -0.000001 0.000001 -0.000001 -1 0 318.70983 0.00001 318.71017 14 'point symmetry operation' ? ? -0.309017 0.5 -0.809017 0.500001 0.809017 0.309017 0.809017 -0.309018 -0.5 257.8417 -98.48684 159.3552 15 'point symmetry operation' ? ? -0.809017 0.309017 -0.5 -0.309017 0.500001 0.809017 0.5 0.809016 -0.309018 318.71003 -0.00016 0.0002 16 'point symmetry operation' ? ? -0.499999 0.809017 -0.309018 0.809017 0.309016 -0.5 -0.309018 -0.5 -0.809017 159.35482 60.86835 417.19687 17 'point symmetry operation' ? ? -1 0.000001 0 0.000001 1 -0.000001 0 -0.000001 -1 318.70984 0.00004 318.7102 18 'point symmetry operation' ? ? -0.5 -0.809017 -0.309016 -0.809017 0.309018 0.499999 -0.309016 0.499999 -0.809018 417.19673 159.35496 257.84198 19 'point symmetry operation' ? ? 0.309017 -0.500001 -0.809016 -0.500001 -0.809016 0.309017 -0.809016 0.309017 -0.500001 318.70996 318.71001 318.71002 20 'point symmetry operation' ? ? 0.309018 0.499999 -0.809017 0.499999 -0.809018 -0.309016 -0.809017 -0.309016 -0.500001 159.3549 257.84194 417.19676 21 'point symmetry operation' ? ? -0.5 0.809018 0.309016 -0.809017 -0.309018 -0.5 -0.309018 -0.499999 0.809018 60.86833 417.19686 159.35478 22 'point symmetry operation' ? ? -0.809018 -0.309016 0.499999 -0.309016 -0.500001 -0.809017 0.499999 -0.809017 0.309019 257.84192 417.19676 159.35488 23 'point symmetry operation' ? ? -0.000001 -1 0 0.000001 0 -1 1 -0.000001 0.000001 318.71014 318.70984 -0.00001 24 'point symmetry operation' ? ? 0.809017 -0.309018 -0.5 -0.309016 0.5 -0.809017 0.500001 0.809016 0.309017 159.35518 257.84167 -98.48686 25 'point symmetry operation' ? ? 0.5 0.809016 -0.309018 -0.809017 0.309017 -0.5 -0.309016 0.500001 0.809017 0.00017 318.71 -0.00018 26 'point symmetry operation' ? ? -0.309017 -0.5 -0.809017 -0.499999 0.809017 -0.309018 0.809018 0.309016 -0.5 417.19686 159.35485 60.86835 27 'point symmetry operation' ? ? 0 -0.000001 -1 -1 0.000001 0 0.000001 1 -0.000001 318.71017 318.70985 0.00002 28 'point symmetry operation' ? ? -0.309016 0.499999 -0.809018 -0.500001 -0.809017 -0.309016 -0.809017 0.309018 0.499999 257.84194 417.19676 159.35492 29 'point symmetry operation' ? ? -0.809016 0.309017 -0.500001 0.309017 -0.500001 -0.809016 -0.500001 -0.809016 0.309017 318.70999 318.71001 318.70999 30 'point symmetry operation' ? ? -0.809017 -0.309016 -0.5 0.309018 0.499999 -0.809017 0.499999 -0.809018 -0.309016 417.19675 159.35495 257.84194 31 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 0 -0.00003 0.00002 32 'point symmetry operation' ? ? 0.309017 -0.499999 0.809017 0.5 0.809017 0.309017 -0.809017 0.309017 0.5 60.86805 -98.48675 159.35512 33 'point symmetry operation' ? ? 0.809017 -0.309016 0.500001 -0.309018 0.5 0.809016 -0.5 -0.809017 0.309017 -0.00019 0.00018 318.71 34 'point symmetry operation' ? ? 0.809016 0.309017 0.500001 -0.309018 -0.5 0.809017 0.5 -0.809017 -0.309016 -98.48688 159.35517 257.84164 35 'point symmetry operation' ? ? 0.309017 0.5 0.809017 0.5 -0.809017 0.309017 0.809017 0.309017 -0.499999 -98.48675 159.35504 60.86804 36 'point symmetry operation' ? ? 0.809018 -0.309017 -0.499999 0.309016 -0.5 0.809018 -0.5 -0.809017 -0.309018 159.35478 60.86833 417.19686 37 'point symmetry operation' ? ? 0.500001 0.809017 -0.309016 0.809017 -0.309018 0.5 0.309017 -0.5 -0.809017 -0.00016 0.00015 318.71 38 'point symmetry operation' ? ? -0.5 0.809017 0.309017 0.809017 0.309017 0.5 0.309017 0.5 -0.809017 60.86809 -98.48677 159.35511 39 'point symmetry operation' ? ? -0.809017 -0.309017 0.5 0.309017 0.500001 0.809016 -0.5 0.809017 -0.309018 257.84168 -98.48685 159.35524 40 'point symmetry operation' ? ? 0 -1 0.000001 -0.000001 0.000001 1 -1 0 -0.000001 318.70981 0.00002 318.71021 41 'point symmetry operation' ? ? -0.5 -0.809017 -0.309017 0.809018 -0.309018 -0.499999 0.309016 -0.5 0.809018 417.19685 159.35481 60.86833 42 'point symmetry operation' ? ? 0.309017 -0.5 -0.809017 0.500001 0.809017 -0.309017 0.809016 -0.309018 0.5 318.71 -0.00016 0.00017 43 'point symmetry operation' ? ? 0.309017 0.5 -0.809017 -0.499999 0.809017 0.309017 0.809017 0.309017 0.5 159.35511 60.86806 -98.48675 44 'point symmetry operation' ? ? -0.5 0.809017 -0.309018 -0.809017 -0.309016 0.5 0.309017 0.500001 0.809016 159.35521 257.84166 -98.48686 45 'point symmetry operation' ? ? -1 0 -0.000001 0 -1 0.000001 -0.000001 0.000001 1 318.71017 318.70981 0 46 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0.00003 -0.00002 0 47 'point symmetry operation' ? ? -0.809017 0.309017 0.5 0.309017 -0.499999 0.809017 0.5 0.809017 0.309017 159.35511 60.86802 -98.48674 48 'point symmetry operation' ? ? -0.5 -0.809017 0.309017 0.809017 -0.309016 0.500001 -0.309018 0.5 0.809016 318.71 -0.00019 0.0002 49 'point symmetry operation' ? ? 0.5 -0.809017 -0.309016 0.809016 0.309017 0.500001 -0.309018 -0.5 0.809017 257.84166 -98.48686 159.35521 50 'point symmetry operation' ? ? 0.809017 0.309017 -0.5 0.309017 0.5 0.809017 0.5 -0.809017 0.309017 60.86807 -98.48676 159.35508 51 'point symmetry operation' ? ? 0.809018 0.309016 -0.5 -0.309017 -0.5 -0.809017 -0.499999 0.809018 -0.309018 60.8683 417.19685 159.35482 52 'point symmetry operation' ? ? 0.000001 1 -0.000001 0 -0.000001 -1 -1 0.000001 0 0 318.71018 318.70983 53 'point symmetry operation' ? ? -0.809017 0.309018 0.499999 -0.309016 0.499999 -0.809018 -0.5 -0.809017 -0.309016 159.3549 257.84198 417.19674 54 'point symmetry operation' ? ? -0.500001 -0.809016 0.309017 -0.809016 0.309017 -0.500001 0.309017 -0.500001 -0.809016 318.70996 318.71004 318.70999 55 'point symmetry operation' ? ? 0.499999 -0.809018 -0.309016 -0.809017 -0.309016 -0.500001 0.309018 0.499999 -0.809017 257.8419 417.19677 159.35492 56 'point symmetry operation' ? ? -0.309017 -0.499999 0.809018 -0.5 0.809017 0.309016 -0.809017 -0.309018 -0.5 159.35479 60.86837 417.19688 57 'point symmetry operation' ? ? 0.499999 -0.809017 0.309018 -0.809018 -0.309016 0.499999 -0.309016 -0.500001 -0.809017 159.35486 257.84197 417.19675 58 'point symmetry operation' ? ? 1 -0.000001 0.000001 -0.000001 -1 0 0.000001 0 -1 -0.00004 318.71015 318.70982 59 'point symmetry operation' ? ? 0.500001 0.809017 0.309017 0.809017 -0.309018 -0.5 -0.309016 0.5 -0.809017 -98.48686 159.35517 257.84168 60 'point symmetry operation' ? ? -0.309017 0.500001 0.809017 0.5 0.809017 -0.309018 -0.809017 0.309017 -0.5 -0.00016 0.00018 318.71003 # _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 'O4 P -3' _chem_comp.formula_weight 94.971 _chem_comp.id PO4 _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHATE ION' _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 P O1 PO4 doub 260 n n P O2 PO4 sing 261 n n P O3 PO4 sing 262 n n P O4 PO4 sing 263 n n # _atom_sites.entry_id 8YT4 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 PO4 A 1 201 154 PO4 PO4 . C 3 HOH A 1 301 242 HOH HOH . C 3 HOH A 2 302 236 HOH HOH . C 3 HOH A 3 303 197 HOH HOH . C 3 HOH A 4 304 164 HOH HOH . C 3 HOH A 5 305 156 HOH HOH . C 3 HOH A 6 306 247 HOH HOH . C 3 HOH A 7 307 245 HOH HOH . C 3 HOH A 8 308 191 HOH HOH . C 3 HOH A 9 309 227 HOH HOH . C 3 HOH A 10 310 235 HOH HOH . C 3 HOH A 11 311 240 HOH HOH . C 3 HOH A 12 312 208 HOH HOH . C 3 HOH A 13 313 211 HOH HOH . C 3 HOH A 14 314 209 HOH HOH . C 3 HOH A 15 315 189 HOH HOH . C 3 HOH A 16 316 233 HOH HOH . C 3 HOH A 17 317 177 HOH HOH . C 3 HOH A 18 318 173 HOH HOH . C 3 HOH A 19 319 194 HOH HOH . C 3 HOH A 20 320 217 HOH HOH . C 3 HOH A 21 321 230 HOH HOH . C 3 HOH A 22 322 204 HOH HOH . C 3 HOH A 23 323 165 HOH HOH . C 3 HOH A 24 324 172 HOH HOH . C 3 HOH A 25 325 174 HOH HOH . C 3 HOH A 26 326 169 HOH HOH . C 3 HOH A 27 327 239 HOH HOH . C 3 HOH A 28 328 248 HOH HOH . C 3 HOH A 29 329 201 HOH HOH . C 3 HOH A 30 330 246 HOH HOH . C 3 HOH A 31 331 200 HOH HOH . C 3 HOH A 32 332 186 HOH HOH . C 3 HOH A 33 333 244 HOH HOH . C 3 HOH A 34 334 215 HOH HOH . C 3 HOH A 35 335 213 HOH HOH . C 3 HOH A 36 336 243 HOH HOH . C 3 HOH A 37 337 232 HOH HOH . C 3 HOH A 38 338 170 HOH HOH . C 3 HOH A 39 339 176 HOH HOH . C 3 HOH A 40 340 234 HOH HOH . C 3 HOH A 41 341 179 HOH HOH . C 3 HOH A 42 342 237 HOH HOH . C 3 HOH A 43 343 171 HOH HOH . C 3 HOH A 44 344 206 HOH HOH . C 3 HOH A 45 345 187 HOH HOH . C 3 HOH A 46 346 159 HOH HOH . C 3 HOH A 47 347 241 HOH HOH . C 3 HOH A 48 348 193 HOH HOH . C 3 HOH A 49 349 238 HOH HOH . C 3 HOH A 50 350 218 HOH HOH . C 3 HOH A 51 351 219 HOH HOH . C 3 HOH A 52 352 216 HOH HOH . C 3 HOH A 53 353 231 HOH HOH . C 3 HOH A 54 354 205 HOH HOH . C 3 HOH A 55 355 192 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 P P PO4 . . . B 2 140.772 176.771 120.562 1 19.16 ? P PO4 201 A 1 HETATM 2 O O1 PO4 . . . B 2 141.566 176.563 119.258 1 23.09 ? O1 PO4 201 A 1 HETATM 3 O O2 PO4 . . . B 2 139.692 177.828 120.335 1 22.1 ? O2 PO4 201 A 1 HETATM 4 O O3 PO4 . . . B 2 141.732 177.216 121.661 1 21.34 ? O3 PO4 201 A 1 HETATM 5 O O4 PO4 . . . B 2 140.128 175.457 120.947 1 20.67 ? O4 PO4 201 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 5 #