data_3SYQ # _model_server_result.job_id rTTDPaAuxIf9KurhrvIseA _model_server_result.datetime_utc '2025-01-10 17:43:59' _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 3syq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 3SYQ # _exptl.entry_id 3SYQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 746.566 _entity.id 2 _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 3SYQ _cell.length_a 87.605 _cell.length_b 208.491 _cell.length_c 117.376 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SYQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -58.688 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _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 85 A CYS 134 1_555 A SG CYS 117 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 85 B CYS 134 1_555 B SG CYS 117 B CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 A O THR 105 A THR 154 1_555 F K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc2 A OG1 THR 105 A THR 154 1_555 G K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc3 A O THR 105 A THR 154 1_555 G K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc4 A O ILE 106 A ILE 155 1_555 E K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc5 A O ILE 106 A ILE 155 1_555 F K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc6 A O GLY 107 A GLY 156 1_555 D K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? metalc ? metalc7 A O GLY 107 A GLY 156 1_555 E K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.915 ? metalc ? metalc8 A O TYR 108 A TYR 157 1_555 D K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.461 ? metalc ? metalc9 D K K . A K 501 1_555 B O GLY 107 B GLY 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.111 ? metalc ? metalc10 D K K . A K 501 1_555 B O TYR 108 B TYR 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.247 ? metalc ? metalc11 E K K . A K 502 1_555 B O ILE 106 B ILE 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.003 ? metalc ? metalc12 E K K . A K 502 1_555 B O GLY 107 B GLY 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? metalc ? metalc13 F K K . A K 503 1_555 B O THR 105 B THR 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.122 ? metalc ? metalc14 F K K . A K 503 1_555 B O ILE 106 B ILE 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc15 G K K . A K 504 1_555 B O THR 105 B THR 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc16 G K K . A K 504 1_555 B OG1 THR 105 B THR 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.011 ? # _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 3SYQ _atom_sites.fract_transf_matrix[1][1] 0.011415 _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] 0.004796 _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] 0.00852 _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 2 PIO A 1 400 400 PIO PT5 . D 3 K A 1 501 501 K K . E 3 K A 1 502 502 K K . F 3 K A 1 503 503 K K . G 3 K A 1 504 504 K K . # 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 . . . C 2 -16.762 48.942 -12.734 1 164.73 ? C1 PIO 400 A 1 HETATM 2 O O1 PIO . . . C 2 -16.484 50.032 -11.843 1 164.91 ? O1 PIO 400 A 1 HETATM 3 P P1 PIO . . . C 2 -17.147 51.492 -12.066 1 165.11 ? P1 PIO 400 A 1 HETATM 4 C C2 PIO . . . C 2 -18.265 48.619 -12.754 1 164.74 ? C2 PIO 400 A 1 HETATM 5 O O2 PIO . . . C 2 -18.732 48.321 -11.43 1 164.91 ? O2 PIO 400 A 1 HETATM 6 C C3 PIO . . . C 2 -18.57 47.469 -13.719 1 164.54 ? C3 PIO 400 A 1 HETATM 7 O O3 PIO . . . C 2 -19.964 47.141 -13.662 1 164.81 ? O3 PIO 400 A 1 HETATM 8 C C4 PIO . . . C 2 -17.716 46.242 -13.384 1 164.09 ? C4 PIO 400 A 1 HETATM 9 O O4 PIO . . . C 2 -18.004 45.183 -14.292 1 163.08 ? O4 PIO 400 A 1 HETATM 10 P P4 PIO . . . C 2 -18.781 43.859 -13.802 1 162.15 ? P4 PIO 400 A 1 HETATM 11 C C5 PIO . . . C 2 -16.224 46.581 -13.418 1 164.25 ? C5 PIO 400 A 1 HETATM 12 O O5 PIO . . . C 2 -15.442 45.423 -13.114 1 164.2 ? O5 PIO 400 A 1 HETATM 13 P P5 PIO . . . C 2 -14.482 44.692 -14.19 1 163.91 ? P5 PIO 400 A 1 HETATM 14 C C6 PIO . . . C 2 -15.907 47.703 -12.431 1 164.47 ? C6 PIO 400 A 1 HETATM 15 O O6 PIO . . . C 2 -14.52 48.018 -12.557 1 164.47 ? O6 PIO 400 A 1 HETATM 16 O O11 PIO . . . C 2 -16.111 52.55 -11.776 1 165.32 ? O11 PIO 400 A 1 HETATM 17 O O12 PIO . . . C 2 -18.429 51.504 -11.267 1 165.41 ? O12 PIO 400 A 1 HETATM 18 O O13 PIO . . . C 2 -17.502 51.538 -13.65 1 164.84 ? O13 PIO 400 A 1 HETATM 19 C C1A PIO . . . C 2 -21.037 51.63 -15.484 1 164.16 ? C1A PIO 400 A 1 HETATM 20 C C1B PIO . . . C 2 -16.967 54.109 -17.772 1 163.75 ? C1B PIO 400 A 1 HETATM 21 C C1C PIO . . . C 2 -17.916 52.72 -14.343 1 164.45 ? C1C PIO 400 A 1 HETATM 22 C C2C PIO . . . C 2 -18.759 52.37 -15.575 1 164.34 ? C2C PIO 400 A 1 HETATM 23 O O2C PIO . . . C 2 -19.638 51.278 -15.291 1 164.25 ? O2C PIO 400 A 1 HETATM 24 C C3C PIO . . . C 2 -17.859 52.008 -16.757 1 164.17 ? C3C PIO 400 A 1 HETATM 25 O O3C PIO . . . C 2 -17.927 53.016 -17.765 1 163.96 ? O3C PIO 400 A 1 HETATM 26 O O41 PIO . . . C 2 -17.822 42.748 -14.151 1 161.84 ? O41 PIO 400 A 1 HETATM 27 O O42 PIO . . . C 2 -19.006 44.017 -12.317 1 162.06 ? O42 PIO 400 A 1 HETATM 28 O O43 PIO . . . C 2 -20.047 43.899 -14.623 1 162.11 ? O43 PIO 400 A 1 HETATM 29 O O51 PIO . . . C 2 -13.092 45.071 -13.735 1 163.76 ? O51 PIO 400 A 1 HETATM 30 O O52 PIO . . . C 2 -14.812 43.23 -14.009 1 163.89 ? O52 PIO 400 A 1 HETATM 31 O O53 PIO . . . C 2 -14.872 45.237 -15.547 1 163.86 ? O53 PIO 400 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #