data_4KFM # _model_server_result.job_id 6FRbmIcBoFLSK3SLCny13w _model_server_result.datetime_utc '2025-01-25 08:44:22' _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 4kfm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 4KFM # _exptl.entry_id 4KFM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 746.566 _entity.id 4 _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 4KFM _cell.length_a 127.308 _cell.length_b 127.308 _cell.length_c 309.392 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KFM _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _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 -127.308 -127.308 0 3 'crystal symmetry operation' 3_455 -y-1,x,z 0 -1 0 1 0 0 0 0 1 -127.308 0 0 4 'crystal symmetry operation' 4_545 y,-x-1,z 0 1 0 -1 0 0 0 0 1 0 -127.308 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc1 A O THR 105 A THR 154 1_555 G K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? metalc ? metalc2 A OG1 THR 105 A THR 154 1_555 H K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? metalc ? metalc3 A O THR 105 A THR 154 1_555 H K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.122 ? metalc ? metalc4 A O ILE 106 A ILE 155 1_555 F K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.01 ? metalc ? metalc5 A O GLY 107 A GLY 156 1_555 E K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.404 ? metalc ? metalc6 A OD2 ASP 179 A ASP 228 1_555 J NA NA . A NA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc7 A O ARG 181 A ARG 230 1_555 J NA NA . A NA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.917 ? # _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 340 n n C1 C2 PIO sing 341 n n C1 C6 PIO sing 342 n n C1 H1 PIO sing 343 n n O1 P1 PIO sing 344 n n P1 O11 PIO sing 345 n n O11 H11 PIO sing 346 n n P1 O12 PIO doub 347 n n P1 O13 PIO sing 348 n n C2 O2 PIO sing 349 n n C2 C3 PIO sing 350 n n C2 H2 PIO sing 351 n n O2 HO2 PIO sing 352 n n C3 O3 PIO sing 353 n n C3 C4 PIO sing 354 n n C3 H3 PIO sing 355 n n O3 HO3 PIO sing 356 n n C4 O4 PIO sing 357 n n C4 C5 PIO sing 358 n n C4 H4 PIO sing 359 n n O4 P4 PIO sing 360 n n P4 O41 PIO sing 361 n n O41 H41 PIO sing 362 n n P4 O42 PIO doub 363 n n P4 O43 PIO sing 364 n n O43 H43 PIO sing 365 n n C5 O5 PIO sing 366 n n C5 C6 PIO sing 367 n n C5 H5 PIO sing 368 n n O5 P5 PIO sing 369 n n P5 O51 PIO sing 370 n n O51 H51 PIO sing 371 n n P5 O52 PIO sing 372 n n O52 H52 PIO sing 373 n n P5 O53 PIO doub 374 n n C6 O6 PIO sing 375 n n C6 H6 PIO sing 376 n n O6 HO6 PIO sing 377 n n O13 C1C PIO sing 378 n n C1A O1A PIO doub 379 n n C1A C2A PIO sing 380 n n C1A O2C PIO sing 381 n n C1B O1B PIO doub 382 n n C1B C2B PIO sing 383 n n C1B O3C PIO sing 384 n n C1C C2C PIO sing 385 n n C1C H1C PIO sing 386 n n C1C H1CA PIO sing 387 n n C2A C3A PIO sing 388 n n C2A H2A PIO sing 389 n n C2A H2AA PIO sing 390 n n C2B C3B PIO sing 391 n n C2B H2B PIO sing 392 n n C2B H2BA PIO sing 393 n n C2C O2C PIO sing 394 n n C2C C3C PIO sing 395 n n C2C H2C PIO sing 396 n n C3A C4A PIO sing 397 n n C3A H3A PIO sing 398 n n C3A H3AA PIO sing 399 n n C3B C4B PIO sing 400 n n C3B H3B PIO sing 401 n n C3B H3BA PIO sing 402 n n C3C O3C PIO sing 403 n n C3C H3C PIO sing 404 n n C3C H3CA PIO sing 405 n n C4A C5A PIO sing 406 n n C4A H4A PIO sing 407 n n C4A H4AA PIO sing 408 n n C4B C5B PIO sing 409 n n C4B H4B PIO sing 410 n n C4B H4BA PIO sing 411 n n C5A C6A PIO sing 412 n n C5A H5A PIO sing 413 n n C5A H5AA PIO sing 414 n n C5B C6B PIO sing 415 n n C5B H5B PIO sing 416 n n C5B H5BA PIO sing 417 n n C6A C7A PIO sing 418 n n C6A H6A PIO sing 419 n n C6A H6AA PIO sing 420 n n C6B C7B PIO sing 421 n n C6B H6B PIO sing 422 n n C6B H6BA PIO sing 423 n n C7A C8A PIO sing 424 n n C7A H7A PIO sing 425 n n C7A H7AA PIO sing 426 n n C7B C8B PIO sing 427 n n C7B H7B PIO sing 428 n n C7B H7BA PIO sing 429 n n C8A H8A PIO sing 430 n n C8A H8AA PIO sing 431 n n C8A H8AB PIO sing 432 n n C8B H8B PIO sing 433 n n C8B H8BA PIO sing 434 n n C8B H8BB PIO sing 435 n n # _atom_sites.entry_id 4KFM _atom_sites.fract_transf_matrix[1][1] 0.007855 _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] 0.007855 _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] 0.003232 _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 D 4 PIO A 1 401 400 PIO PIO . E 5 K A 1 402 501 K K . F 5 K A 1 403 502 K K . G 5 K A 1 404 503 K K . H 5 K A 1 405 504 K K . I 5 K A 1 406 505 K K . J 6 NA A 1 407 600 NA NA . K 7 LMT A 1 408 700 LMT LMT . # 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 . . . D 4 -52.999 -43.121 -63.457 1 133.74 ? C1 PIO 401 A 1 HETATM 2 O O1 PIO . . . D 4 -52.095 -42.999 -64.558 1 130.57 ? O1 PIO 401 A 1 HETATM 3 P P1 PIO . . . D 4 -52.51 -42.177 -65.881 1 131.62 ? P1 PIO 401 A 1 HETATM 4 C C2 PIO . . . D 4 -52.739 -42.011 -62.448 1 135.16 ? C2 PIO 401 A 1 HETATM 5 O O2 PIO . . . D 4 -51.386 -42.079 -61.992 1 134.95 ? O2 PIO 401 A 1 HETATM 6 C C3 PIO . . . D 4 -53.69 -42.128 -61.261 1 135.26 ? C3 PIO 401 A 1 HETATM 7 O O3 PIO . . . D 4 -53.35 -41.152 -60.275 1 133.63 ? O3 PIO 401 A 1 HETATM 8 C C4 PIO . . . D 4 -53.632 -43.499 -60.606 1 135.38 ? C4 PIO 401 A 1 HETATM 9 O O4 PIO . . . D 4 -54.7 -43.586 -59.668 1 142.72 ? O4 PIO 401 A 1 HETATM 10 P P4 PIO . . . D 4 -54.438 -43.423 -58.089 1 152.31 ? P4 PIO 401 A 1 HETATM 11 C C5 PIO . . . D 4 -53.757 -44.651 -61.594 1 134.2 ? C5 PIO 401 A 1 HETATM 12 O O5 PIO . . . D 4 -53.395 -45.86 -60.922 1 134.64 ? O5 PIO 401 A 1 HETATM 13 P P5 PIO . . . D 4 -54.462 -46.96 -60.429 1 133.1 ? P5 PIO 401 A 1 HETATM 14 C C6 PIO . . . D 4 -52.834 -44.48 -62.794 1 135.09 ? C6 PIO 401 A 1 HETATM 15 O O6 PIO . . . D 4 -53.109 -45.508 -63.745 1 138.26 ? O6 PIO 401 A 1 HETATM 16 O O11 PIO . . . D 4 -51.696 -42.673 -67.046 1 124.3 ? O11 PIO 401 A 1 HETATM 17 O O12 PIO . . . D 4 -52.458 -40.714 -65.537 1 142.73 ? O12 PIO 401 A 1 HETATM 18 O O13 PIO . . . D 4 -54.066 -42.562 -66.102 1 129.66 ? O13 PIO 401 A 1 HETATM 19 C C1A PIO . . . D 4 -57.275 -44.144 -68.563 1 95.09 ? C1A PIO 401 A 1 HETATM 20 C C1B PIO . . . D 4 -53.794 -42.277 -71.181 1 108.44 ? C1B PIO 401 A 1 HETATM 21 C C1C PIO . . . D 4 -54.989 -41.7 -66.777 1 124.9 ? C1C PIO 401 A 1 HETATM 22 C C2C PIO . . . D 4 -55.644 -42.409 -67.971 1 123.62 ? C2C PIO 401 A 1 HETATM 23 O O2C PIO . . . D 4 -56.541 -43.441 -67.514 1 114.78 ? O2C PIO 401 A 1 HETATM 24 C C3C PIO . . . D 4 -54.557 -42.976 -68.9 1 127.91 ? C3C PIO 401 A 1 HETATM 25 O O3C PIO . . . D 4 -54.036 -41.973 -69.774 1 120.74 ? O3C PIO 401 A 1 HETATM 26 O O41 PIO . . . D 4 -55.674 -44.008 -57.444 1 152.75 ? O41 PIO 401 A 1 HETATM 27 O O42 PIO . . . D 4 -53.187 -44.232 -57.84 1 149.95 ? O42 PIO 401 A 1 HETATM 28 O O43 PIO . . . D 4 -54.255 -41.937 -57.895 1 143.9 ? O43 PIO 401 A 1 HETATM 29 O O51 PIO . . . D 4 -53.633 -48.221 -60.333 1 127.83 ? O51 PIO 401 A 1 HETATM 30 O O52 PIO . . . D 4 -54.956 -46.459 -59.092 1 133.87 ? O52 PIO 401 A 1 HETATM 31 O O53 PIO . . . D 4 -55.517 -46.938 -61.511 1 132.42 ? O53 PIO 401 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 31 #