data_3SPG # _model_server_result.job_id 3SbCZZQArj7TauNeh-SW-Q _model_server_result.datetime_utc '2024-10-18 21:25:20' _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 3spg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":400}' # _entry.id 3SPG # _exptl.entry_id 3SPG _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 3SPG _cell.length_a 81.865 _cell.length_b 81.865 _cell.length_c 183.102 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SPG _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,G,H,I _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 -81.865 -81.865 0 3 'crystal symmetry operation' 3_455 -y-1,x,z 0 -1 0 1 0 0 0 0 1 -81.865 0 0 4 'crystal symmetry operation' 4_545 y,-x-1,z 0 1 0 -1 0 0 0 0 1 0 -81.865 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id H _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc1 I O HOH . A HOH 27 1_555 F K K . A K 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.181 ? metalc ? metalc2 I O HOH . A HOH 30 1_555 F K K . A K 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.294 ? metalc ? metalc3 A O THR 108 A THR 143 1_555 D K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? metalc ? metalc4 A OG1 THR 108 A THR 143 1_555 E K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc5 A O THR 108 A THR 143 1_555 E K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc6 A O ILE 109 A ILE 144 1_555 C K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc7 A O ILE 109 A ILE 144 1_555 D K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc8 A O GLY 110 A GLY 145 1_555 B K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc9 A O GLY 110 A GLY 145 1_555 C K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc10 A O TYR 111 A TYR 146 1_555 B K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? # _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 260 n n C1 C2 PIO sing 261 n n C1 C6 PIO sing 262 n n C1 H1 PIO sing 263 n n O1 P1 PIO sing 264 n n P1 O11 PIO sing 265 n n O11 H11 PIO sing 266 n n P1 O12 PIO doub 267 n n P1 O13 PIO sing 268 n n C2 O2 PIO sing 269 n n C2 C3 PIO sing 270 n n C2 H2 PIO sing 271 n n O2 HO2 PIO sing 272 n n C3 O3 PIO sing 273 n n C3 C4 PIO sing 274 n n C3 H3 PIO sing 275 n n O3 HO3 PIO sing 276 n n C4 O4 PIO sing 277 n n C4 C5 PIO sing 278 n n C4 H4 PIO sing 279 n n O4 P4 PIO sing 280 n n P4 O41 PIO sing 281 n n O41 H41 PIO sing 282 n n P4 O42 PIO doub 283 n n P4 O43 PIO sing 284 n n O43 H43 PIO sing 285 n n C5 O5 PIO sing 286 n n C5 C6 PIO sing 287 n n C5 H5 PIO sing 288 n n O5 P5 PIO sing 289 n n P5 O51 PIO sing 290 n n O51 H51 PIO sing 291 n n P5 O52 PIO sing 292 n n O52 H52 PIO sing 293 n n P5 O53 PIO doub 294 n n C6 O6 PIO sing 295 n n C6 H6 PIO sing 296 n n O6 HO6 PIO sing 297 n n O13 C1C PIO sing 298 n n C1A O1A PIO doub 299 n n C1A C2A PIO sing 300 n n C1A O2C PIO sing 301 n n C1B O1B PIO doub 302 n n C1B C2B PIO sing 303 n n C1B O3C PIO sing 304 n n C1C C2C PIO sing 305 n n C1C H1C PIO sing 306 n n C1C H1CA PIO sing 307 n n C2A C3A PIO sing 308 n n C2A H2A PIO sing 309 n n C2A H2AA PIO sing 310 n n C2B C3B PIO sing 311 n n C2B H2B PIO sing 312 n n C2B H2BA PIO sing 313 n n C2C O2C PIO sing 314 n n C2C C3C PIO sing 315 n n C2C H2C PIO sing 316 n n C3A C4A PIO sing 317 n n C3A H3A PIO sing 318 n n C3A H3AA PIO sing 319 n n C3B C4B PIO sing 320 n n C3B H3B PIO sing 321 n n C3B H3BA PIO sing 322 n n C3C O3C PIO sing 323 n n C3C H3C PIO sing 324 n n C3C H3CA PIO sing 325 n n C4A C5A PIO sing 326 n n C4A H4A PIO sing 327 n n C4A H4AA PIO sing 328 n n C4B C5B PIO sing 329 n n C4B H4B PIO sing 330 n n C4B H4BA PIO sing 331 n n C5A C6A PIO sing 332 n n C5A H5A PIO sing 333 n n C5A H5AA PIO sing 334 n n C5B C6B PIO sing 335 n n C5B H5B PIO sing 336 n n C5B H5BA PIO sing 337 n n C6A C7A PIO sing 338 n n C6A H6A PIO sing 339 n n C6A H6AA PIO sing 340 n n C6B C7B PIO sing 341 n n C6B H6B PIO sing 342 n n C6B H6BA PIO sing 343 n n C7A C8A PIO sing 344 n n C7A H7A PIO sing 345 n n C7A H7AA PIO sing 346 n n C7B C8B PIO sing 347 n n C7B H7B PIO sing 348 n n C7B H7BA PIO sing 349 n n C8A H8A PIO sing 350 n n C8A H8AA PIO sing 351 n n C8A H8AB PIO sing 352 n n C8B H8B PIO sing 353 n n C8B H8BA PIO sing 354 n n C8B H8BB PIO sing 355 n n # _atom_sites.entry_id 3SPG _atom_sites.fract_transf_matrix[1][1] 0.012215 _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] 0.012215 _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] 0.005461 _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 2 K A 1 506 506 K K . G 2 K A 1 510 510 K K . H 3 PIO A 1 400 400 PIO PIO . I 4 HOH A 1 1 1 HOH HOH . I 4 HOH A 2 2 2 HOH HOH . I 4 HOH A 3 3 3 HOH HOH . I 4 HOH A 4 4 4 HOH HOH . I 4 HOH A 5 5 5 HOH HOH . I 4 HOH A 6 6 6 HOH HOH . I 4 HOH A 7 7 7 HOH HOH . I 4 HOH A 8 8 8 HOH HOH . I 4 HOH A 9 9 9 HOH HOH . I 4 HOH A 10 10 10 HOH HOH . I 4 HOH A 11 11 11 HOH HOH . I 4 HOH A 12 12 12 HOH HOH . I 4 HOH A 13 13 13 HOH HOH . I 4 HOH A 14 14 14 HOH HOH . I 4 HOH A 15 15 15 HOH HOH . I 4 HOH A 16 16 16 HOH HOH . I 4 HOH A 17 17 17 HOH HOH . I 4 HOH A 18 18 18 HOH HOH . I 4 HOH A 19 19 19 HOH HOH . I 4 HOH A 20 20 20 HOH HOH . I 4 HOH A 21 21 21 HOH HOH . I 4 HOH A 22 22 22 HOH HOH . I 4 HOH A 23 23 23 HOH HOH . I 4 HOH A 24 24 24 HOH HOH . I 4 HOH A 25 25 25 HOH HOH . I 4 HOH A 26 26 26 HOH HOH . I 4 HOH A 27 27 27 HOH HOH . I 4 HOH A 28 28 28 HOH HOH . I 4 HOH A 29 29 29 HOH HOH . I 4 HOH A 30 30 30 HOH HOH . I 4 HOH A 31 31 31 HOH HOH . I 4 HOH A 32 32 32 HOH HOH . I 4 HOH A 33 33 33 HOH HOH . I 4 HOH A 34 34 34 HOH HOH . I 4 HOH A 35 35 35 HOH HOH . I 4 HOH A 36 379 37 HOH HOH . I 4 HOH A 37 380 38 HOH HOH . I 4 HOH A 38 381 39 HOH HOH . I 4 HOH A 39 382 40 HOH HOH . I 4 HOH A 40 383 41 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 C1 PIO . . . H 3 -31.699 -21.833 9.399 1 102.21 ? C1 PIO 400 A 1 HETATM 2 O O1 PIO . . . H 3 -32.438 -21.368 10.529 1 102.76 ? O1 PIO 400 A 1 HETATM 3 P P1 PIO . . . H 3 -31.785 -20.984 11.954 1 87.84 ? P1 PIO 400 A 1 HETATM 4 C C2 PIO . . . H 3 -30.708 -20.799 8.886 1 102.95 ? C2 PIO 400 A 1 HETATM 5 O O2 PIO . . . H 3 -31.397 -19.604 8.498 1 102.77 ? O2 PIO 400 A 1 HETATM 6 C C3 PIO . . . H 3 -29.966 -21.385 7.691 1 103.02 ? C3 PIO 400 A 1 HETATM 7 O O3 PIO . . . H 3 -28.984 -20.447 7.236 1 102.84 ? O3 PIO 400 A 1 HETATM 8 C C4 PIO . . . H 3 -30.931 -21.7 6.553 1 102.78 ? C4 PIO 400 A 1 HETATM 9 O O4 PIO . . . H 3 -30.231 -22.369 5.501 1 105 ? O4 PIO 400 A 1 HETATM 10 P P4 PIO . . . H 3 -30.109 -21.708 4.027 1 111.83 ? P4 PIO 400 A 1 HETATM 11 C C5 PIO . . . H 3 -32.095 -22.586 6.996 1 100.87 ? C5 PIO 400 A 1 HETATM 12 O O5 PIO . . . H 3 -33.054 -22.553 5.938 1 98.97 ? O5 PIO 400 A 1 HETATM 13 P P5 PIO . . . H 3 -34.229 -23.646 5.772 1 106.66 ? P5 PIO 400 A 1 HETATM 14 C C6 PIO . . . H 3 -32.724 -22.115 8.313 1 100.93 ? C6 PIO 400 A 1 HETATM 15 O O6 PIO . . . H 3 -33.63 -23.087 8.839 1 99.29 ? O6 PIO 400 A 1 HETATM 16 O O11 PIO . . . H 3 -30.523 -20.185 11.712 1 89.2 ? O11 PIO 400 A 1 HETATM 17 O O12 PIO . . . H 3 -32.914 -20.369 12.743 1 86.3 ? O12 PIO 400 A 1 HETATM 18 O O13 PIO . . . H 3 -31.394 -22.397 12.645 1 105.95 ? O13 PIO 400 A 1 HETATM 19 C C1A PIO . . . H 3 -30.462 -25.847 14.234 1 111.06 ? C1A PIO 400 A 1 HETATM 20 O O1A PIO . . . H 3 -29.669 -26.026 13.324 1 111.79 ? O1A PIO 400 A 1 HETATM 21 C C1B PIO . . . H 3 -32.438 -22.77 17.437 1 111.13 ? C1B PIO 400 A 1 HETATM 22 O O1B PIO . . . H 3 -33.58 -22.389 17.637 1 112.32 ? O1B PIO 400 A 1 HETATM 23 C C1C PIO . . . H 3 -30.128 -22.575 13.294 1 106.76 ? C1C PIO 400 A 1 HETATM 24 C C2A PIO . . . H 3 -30.789 -26.968 15.19 1 111.65 ? C2A PIO 400 A 1 HETATM 25 C C2B PIO . . . H 3 -31.577 -23.187 18.606 1 110.92 ? C2B PIO 400 A 1 HETATM 26 C C2C PIO . . . H 3 -30.17 -23.484 14.534 1 108.77 ? C2C PIO 400 A 1 HETATM 27 O O2C PIO . . . H 3 -31.106 -24.55 14.371 1 110.07 ? O2C PIO 400 A 1 HETATM 28 C C3A PIO . . . H 3 -29.991 -26.8 16.476 1 112.42 ? C3A PIO 400 A 1 HETATM 29 C C3B PIO . . . H 3 -32.483 -23.667 19.738 1 110.46 ? C3B PIO 400 A 1 HETATM 30 C C3C PIO . . . H 3 -30.549 -22.684 15.78 1 109.41 ? C3C PIO 400 A 1 HETATM 31 O O3C PIO . . . H 3 -31.941 -22.825 16.067 1 110.29 ? O3C PIO 400 A 1 HETATM 32 O O41 PIO . . . H 3 -28.926 -20.78 4.203 1 111.05 ? O41 PIO 400 A 1 HETATM 33 O O42 PIO . . . H 3 -31.435 -21.016 3.771 1 109.83 ? O42 PIO 400 A 1 HETATM 34 O O43 PIO . . . H 3 -29.837 -22.884 3.112 1 112.13 ? O43 PIO 400 A 1 HETATM 35 C C4B PIO . . . H 3 -31.75 -24.593 20.707 1 109.72 ? C4B PIO 400 A 1 HETATM 36 O O51 PIO . . . H 3 -34.724 -23.455 4.357 1 107.06 ? O51 PIO 400 A 1 HETATM 37 O O52 PIO . . . H 3 -33.549 -24.978 6.001 1 106.6 ? O52 PIO 400 A 1 HETATM 38 O O53 PIO . . . H 3 -35.251 -23.248 6.812 1 106.12 ? O53 PIO 400 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #