data_3SPI # _model_server_result.job_id izzqOI3KzHTKc8o9fmRwNg _model_server_result.datetime_utc '2024-11-23 23:23:33' _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 3spi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":400}' # _entry.id 3SPI # _exptl.entry_id 3SPI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 746.566 _entity.id 3 _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 3SPI _cell.length_a 83.326 _cell.length_b 83.326 _cell.length_c 184.809 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SPI _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _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 _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_445 -x-1,-y-1,z -1 0 0 0 -1 0 0 0 1 -83.326 -83.326 0 3 'crystal symmetry operation' 3_455 -y-1,x,z 0 -1 0 1 0 0 0 0 1 -83.326 0 0 4 'crystal symmetry operation' 4_545 y,-x-1,z 0 1 0 -1 0 0 0 0 1 0 -83.326 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id F _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 88 A CYS 123 1_555 A SG CYS 120 A CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc1 A O THR 108 A THR 143 1_555 D K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc2 A O THR 108 A THR 143 1_555 E K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? metalc ? metalc3 A OG1 THR 108 A THR 143 1_555 E K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc4 A O ILE 109 A ILE 144 1_555 C K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc5 A O ILE 109 A ILE 144 1_555 D K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc6 A O GLY 110 A GLY 145 1_555 B K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? metalc ? metalc7 A O GLY 110 A GLY 145 1_555 C K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? metalc ? metalc8 A O TYR 111 A TYR 146 1_555 B K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? # _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 3SPI _atom_sites.fract_transf_matrix[1][1] 0.012001 _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] 0.012001 _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] 0.005411 _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 K A 1 501 501 K K . C 2 K A 1 502 502 K K . D 2 K A 1 503 503 K K . E 2 K A 1 504 504 K K . F 3 PIO A 1 400 400 PIO PIO . # 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 . . . F 3 -31.606 -22.559 31.096 1 146.47 ? C1 PIO 400 A 1 HETATM 2 O O1 PIO . . . F 3 -32.34 -22.236 32.281 1 146.23 ? O1 PIO 400 A 1 HETATM 3 P P1 PIO . . . F 3 -31.615 -21.881 33.68 1 118.15 ? P1 PIO 400 A 1 HETATM 4 C C2 PIO . . . F 3 -30.711 -21.417 30.653 1 146.47 ? C2 PIO 400 A 1 HETATM 5 O O2 PIO . . . F 3 -31.506 -20.34 30.147 1 146.26 ? O2 PIO 400 A 1 HETATM 6 C C3 PIO . . . F 3 -29.813 -21.951 29.552 1 146.81 ? C3 PIO 400 A 1 HETATM 7 O O3 PIO . . . F 3 -28.845 -20.96 29.193 1 146.76 ? O3 PIO 400 A 1 HETATM 8 C C4 PIO . . . F 3 -30.645 -22.332 28.331 1 147.24 ? C4 PIO 400 A 1 HETATM 9 O O4 PIO . . . F 3 -29.791 -22.966 27.379 1 147.51 ? O4 PIO 400 A 1 HETATM 10 P P4 PIO . . . F 3 -29.707 -22.448 25.855 1 141.95 ? P4 PIO 400 A 1 HETATM 11 C C5 PIO . . . F 3 -31.795 -23.282 28.68 1 147.17 ? C5 PIO 400 A 1 HETATM 12 O O5 PIO . . . F 3 -32.684 -23.32 27.561 1 147.41 ? O5 PIO 400 A 1 HETATM 13 P P5 PIO . . . F 3 -33.853 -24.421 27.418 1 109.43 ? P5 PIO 400 A 1 HETATM 14 C C6 PIO . . . F 3 -32.556 -22.872 29.946 1 146.77 ? C6 PIO 400 A 1 HETATM 15 O O6 PIO . . . F 3 -33.45 -23.917 30.346 1 146.7 ? O6 PIO 400 A 1 HETATM 16 O O11 PIO . . . F 3 -30.284 -21.219 33.415 1 118.48 ? O11 PIO 400 A 1 HETATM 17 O O12 PIO . . . F 3 -32.636 -21.165 34.531 1 118.3 ? O12 PIO 400 A 1 HETATM 18 O O13 PIO . . . F 3 -31.321 -23.303 34.384 1 124.97 ? O13 PIO 400 A 1 HETATM 19 C C1A PIO . . . F 3 -30.675 -26.793 35.477 1 124.4 ? C1A PIO 400 A 1 HETATM 20 O O1A PIO . . . F 3 -29.898 -26.865 34.539 1 124.72 ? O1A PIO 400 A 1 HETATM 21 C C1B PIO . . . F 3 -32.298 -23.451 39.092 1 124.97 ? C1B PIO 400 A 1 HETATM 22 O O1B PIO . . . F 3 -33.399 -22.95 39.249 1 125.12 ? O1B PIO 400 A 1 HETATM 23 C C1C PIO . . . F 3 -30.097 -23.469 35.104 1 124.95 ? C1C PIO 400 A 1 HETATM 24 C C2A PIO . . . F 3 -31.091 -28.041 36.223 1 123.58 ? C2A PIO 400 A 1 HETATM 25 C C2B PIO . . . F 3 -31.447 -23.819 40.285 1 124.63 ? C2B PIO 400 A 1 HETATM 26 C C2C PIO . . . F 3 -30.171 -24.568 36.164 1 124.92 ? C2C PIO 400 A 1 HETATM 27 O O2C PIO . . . F 3 -31.212 -25.492 35.848 1 124.71 ? O2C PIO 400 A 1 HETATM 28 C C3A PIO . . . F 3 -30.675 -27.971 37.688 1 122.79 ? C3A PIO 400 A 1 HETATM 29 C C3B PIO . . . F 3 -32.29 -24.586 41.297 1 124.28 ? C3B PIO 400 A 1 HETATM 30 C C3C PIO . . . F 3 -30.424 -23.948 37.535 1 125.05 ? C3C PIO 400 A 1 HETATM 31 O O3C PIO . . . F 3 -31.811 -23.692 37.741 1 125.05 ? O3C PIO 400 A 1 HETATM 32 O O41 PIO . . . F 3 -28.783 -21.257 25.94 1 142.11 ? O41 PIO 400 A 1 HETATM 33 O O42 PIO . . . F 3 -31.131 -22.104 25.49 1 141.84 ? O42 PIO 400 A 1 HETATM 34 O O43 PIO . . . F 3 -29.125 -23.621 25.103 1 141.92 ? O43 PIO 400 A 1 HETATM 35 C C4A PIO . . . F 3 -31.186 -29.192 38.446 1 122.2 ? C4A PIO 400 A 1 HETATM 36 C C4B PIO . . . F 3 -31.431 -25.111 42.442 1 124.16 ? C4B PIO 400 A 1 HETATM 37 O O51 PIO . . . F 3 -34.097 -24.492 25.929 1 109.54 ? O51 PIO 400 A 1 HETATM 38 O O52 PIO . . . F 3 -33.258 -25.672 28.018 1 109.38 ? O52 PIO 400 A 1 HETATM 39 O O53 PIO . . . F 3 -35.01 -23.837 28.193 1 109.54 ? O53 PIO 400 A 1 HETATM 40 C C5A PIO . . . F 3 -30.765 -29.159 39.911 1 121.85 ? C5A PIO 400 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #