data_8JRV # _model_server_result.job_id JYGyJgrEHHbv9OP3OERDdg _model_server_result.datetime_utc '2024-12-21 16:04:55' _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 8jrv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":701}' # _entry.id 8JRV # _exptl.entry_id 8JRV _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 746.566 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' _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 8JRV _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JRV _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 239 R CYS 224 1_555 A SG CYS 309 R CYS 294 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 D SG CYS 522 H CYS 25 1_555 D SG CYS 596 H CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 E SG CYS 400 L CYS 24 1_555 E SG CYS 465 L CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A C GLU 461 R GLU 1356 1_555 A N SEP 462 R SEP 1357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C SEP 462 R SEP 1357 1_555 A N CYS 463 R CYS 1358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C THR 464 R THR 1359 1_555 A N TPO 465 R TPO 1360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 A C TPO 465 R TPO 1360 1_555 A N ALA 466 R ALA 1361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C ALA 466 R ALA 1361 1_555 A N SEP 467 R SEP 1362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 A C SEP 467 R SEP 1362 1_555 A N SEP 468 R SEP 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 A C SEP 468 R SEP 1363 1_555 A N SEP 469 R SEP 1364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 A C SEP 469 R SEP 1364 1_555 A N LEU 470 R LEU 1365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _chem_comp.formula 'C25 H49 O19 P3' _chem_comp.formula_weight 746.566 _chem_comp.id PIO _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate' # 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 O1 PIO sing 258 n n C1 C2 PIO sing 259 n n C1 C6 PIO sing 260 n n C1 H1 PIO sing 261 n n O1 P1 PIO sing 262 n n P1 O11 PIO sing 263 n n O11 H11 PIO sing 264 n n P1 O12 PIO doub 265 n n P1 O13 PIO sing 266 n n C2 O2 PIO sing 267 n n C2 C3 PIO sing 268 n n C2 H2 PIO sing 269 n n O2 HO2 PIO sing 270 n n C3 O3 PIO sing 271 n n C3 C4 PIO sing 272 n n C3 H3 PIO sing 273 n n O3 HO3 PIO sing 274 n n C4 O4 PIO sing 275 n n C4 C5 PIO sing 276 n n C4 H4 PIO sing 277 n n O4 P4 PIO sing 278 n n P4 O41 PIO sing 279 n n O41 H41 PIO sing 280 n n P4 O42 PIO doub 281 n n P4 O43 PIO sing 282 n n O43 H43 PIO sing 283 n n C5 O5 PIO sing 284 n n C5 C6 PIO sing 285 n n C5 H5 PIO sing 286 n n O5 P5 PIO sing 287 n n P5 O51 PIO sing 288 n n O51 H51 PIO sing 289 n n P5 O52 PIO sing 290 n n O52 H52 PIO sing 291 n n P5 O53 PIO doub 292 n n C6 O6 PIO sing 293 n n C6 H6 PIO sing 294 n n O6 HO6 PIO sing 295 n n O13 C1C PIO sing 296 n n C1A O1A PIO doub 297 n n C1A C2A PIO sing 298 n n C1A O2C PIO sing 299 n n C1B O1B PIO doub 300 n n C1B C2B PIO sing 301 n n C1B O3C PIO sing 302 n n C1C C2C PIO sing 303 n n C1C H1C PIO sing 304 n n C1C H1CA PIO sing 305 n n C2A C3A PIO sing 306 n n C2A H2A PIO sing 307 n n C2A H2AA PIO sing 308 n n C2B C3B PIO sing 309 n n C2B H2B PIO sing 310 n n C2B H2BA PIO sing 311 n n C2C O2C PIO sing 312 n n C2C C3C PIO sing 313 n n C2C H2C PIO sing 314 n n C3A C4A PIO sing 315 n n C3A H3A PIO sing 316 n n C3A H3AA PIO sing 317 n n C3B C4B PIO sing 318 n n C3B H3B PIO sing 319 n n C3B H3BA PIO sing 320 n n C3C O3C PIO sing 321 n n C3C H3C PIO sing 322 n n C3C H3CA PIO sing 323 n n C4A C5A PIO sing 324 n n C4A H4A PIO sing 325 n n C4A H4AA PIO sing 326 n n C4B C5B PIO sing 327 n n C4B H4B PIO sing 328 n n C4B H4BA PIO sing 329 n n C5A C6A PIO sing 330 n n C5A H5A PIO sing 331 n n C5A H5AA PIO sing 332 n n C5B C6B PIO sing 333 n n C5B H5B PIO sing 334 n n C5B H5BA PIO sing 335 n n C6A C7A PIO sing 336 n n C6A H6A PIO sing 337 n n C6A H6AA PIO sing 338 n n C6B C7B PIO sing 339 n n C6B H6B PIO sing 340 n n C6B H6BA PIO sing 341 n n C7A C8A PIO sing 342 n n C7A H7A PIO sing 343 n n C7A H7AA PIO sing 344 n n C7B C8B PIO sing 345 n n C7B H7B PIO sing 346 n n C7B H7BA PIO sing 347 n n C8A H8A PIO sing 348 n n C8A H8AA PIO sing 349 n n C8A H8AB PIO sing 350 n n C8B H8B PIO sing 351 n n C8B H8BA PIO sing 352 n n C8B H8BB PIO sing 353 n n # _atom_sites.entry_id 8JRV _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 # _pdbx_nonpoly_scheme.asym_id G _pdbx_nonpoly_scheme.entity_id 5 _pdbx_nonpoly_scheme.mon_id PIO _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 701 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id PIO _pdbx_nonpoly_scheme.auth_mon_id PIO _pdbx_nonpoly_scheme.pdb_ins_code . # 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 PIO . . . G 5 136.698 141.669 137.543 1 117.94 ? C1 PIO 701 A 1 HETATM 2 O O1 PIO . . . G 5 137.06 141.592 138.932 1 117.94 ? O1 PIO 701 A 1 HETATM 3 P P1 PIO . . . G 5 137.447 140.111 139.364 1 117.94 ? P1 PIO 701 A 1 HETATM 4 C C2 PIO . . . G 5 137.143 143.039 137.057 1 117.94 ? C2 PIO 701 A 1 HETATM 5 O O2 PIO . . . G 5 138.376 143.404 137.674 1 117.94 ? O2 PIO 701 A 1 HETATM 6 C C3 PIO . . . G 5 136.09 144.086 137.378 1 117.94 ? C3 PIO 701 A 1 HETATM 7 O O3 PIO . . . G 5 135.83 144.102 138.781 1 117.94 ? O3 PIO 701 A 1 HETATM 8 C C4 PIO . . . G 5 134.834 143.765 136.597 1 117.94 ? C4 PIO 701 A 1 HETATM 9 O O4 PIO . . . G 5 135.067 144.141 135.23 1 117.94 ? O4 PIO 701 A 1 HETATM 10 P P4 PIO . . . G 5 135.227 145.729 134.817 1 117.94 ? P4 PIO 701 A 1 HETATM 11 C C5 PIO . . . G 5 134.725 142.292 136.347 1 117.94 ? C5 PIO 701 A 1 HETATM 12 O O5 PIO . . . G 5 133.34 142.03 136.027 1 117.94 ? O5 PIO 701 A 1 HETATM 13 P P5 PIO . . . G 5 131.875 142.257 136.759 1 117.94 ? P5 PIO 701 A 1 HETATM 14 C C6 PIO . . . G 5 135.192 141.51 137.543 1 117.94 ? C6 PIO 701 A 1 HETATM 15 O O6 PIO . . . G 5 134.81 140.144 137.429 1 117.94 ? O6 PIO 701 A 1 HETATM 16 O O11 PIO . . . G 5 136.541 139.005 138.941 1 117.94 ? O11 PIO 701 A 1 HETATM 17 O O12 PIO . . . G 5 138.843 139.898 138.915 1 117.94 ? O12 PIO 701 A 1 HETATM 18 O O13 PIO . . . G 5 137.303 140.497 140.899 1 117.94 ? O13 PIO 701 A 1 HETATM 19 C C1A PIO . . . G 5 140.291 143.475 140.962 1 117.94 ? C1A PIO 701 A 1 HETATM 20 O O1A PIO . . . G 5 139.624 144.155 140.226 1 117.94 ? O1A PIO 701 A 1 HETATM 21 C C1B PIO . . . G 5 137.642 144.782 143.537 1 117.94 ? C1B PIO 701 A 1 HETATM 22 O O1B PIO . . . G 5 138.736 144.891 144.025 1 117.94 ? O1B PIO 701 A 1 HETATM 23 C C1C PIO . . . G 5 138.513 140.6 141.669 1 117.94 ? C1C PIO 701 A 1 HETATM 24 C C2A PIO . . . G 5 141.777 143.347 140.956 1 117.94 ? C2A PIO 701 A 1 HETATM 25 C C2B PIO . . . G 5 136.464 145.496 144.196 1 117.94 ? C2B PIO 701 A 1 HETATM 26 C C2C PIO . . . G 5 138.482 142.102 141.66 1 117.94 ? C2C PIO 701 A 1 HETATM 27 O O2C PIO . . . G 5 139.772 142.706 141.93 1 117.94 ? O2C PIO 701 A 1 HETATM 28 C C3A PIO . . . G 5 142.276 142.873 142.271 1 117.94 ? C3A PIO 701 A 1 HETATM 29 C C3B PIO . . . G 5 136.778 146.954 144.52 1 117.94 ? C3B PIO 701 A 1 HETATM 30 C C3C PIO . . . G 5 137.45 142.632 142.62 1 117.94 ? C3C PIO 701 A 1 HETATM 31 O O3C PIO . . . G 5 137.441 144.012 142.387 1 117.94 ? O3C PIO 701 A 1 HETATM 32 O O41 PIO . . . G 5 134.489 146.589 135.815 1 117.94 ? O41 PIO 701 A 1 HETATM 33 O O42 PIO . . . G 5 134.643 145.948 133.441 1 117.94 ? O42 PIO 701 A 1 HETATM 34 O O43 PIO . . . G 5 136.689 146.107 134.803 1 117.94 ? O43 PIO 701 A 1 HETATM 35 C C4A PIO . . . G 5 143.646 142.203 142.201 1 117.94 ? C4A PIO 701 A 1 HETATM 36 C C4B PIO . . . G 5 135.936 147.485 145.678 1 117.94 ? C4B PIO 701 A 1 HETATM 37 O O51 PIO . . . G 5 130.823 142.434 135.69 1 117.94 ? O51 PIO 701 A 1 HETATM 38 O O52 PIO . . . G 5 131.515 141.046 137.587 1 117.94 ? O52 PIO 701 A 1 HETATM 39 O O53 PIO . . . G 5 131.887 143.487 137.635 1 117.94 ? O53 PIO 701 A 1 HETATM 40 C C5A PIO . . . G 5 143.56 140.758 141.714 1 117.94 ? C5A PIO 701 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 454 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #