data_4QK4 # _model_server_result.job_id 5Ksk0kgnuKOAAU2NHZctiw _model_server_result.datetime_utc '2024-11-18 13:39:43' _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 4qk4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 4QK4 # _exptl.entry_id 4QK4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'SMILES string: CCCCCCCCCCCCCCCC(=O)OCC(CO[P](O)(=O)OC1C(O)C(O)C (O[P](O)(O)=O)C(O[P](O)(O)=O)C1O)OC(=O)CCCCCCCCCCCCCCC' _entity.formula_weight 970.992 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-3-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate' _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 4QK4 _cell.length_a 75 _cell.length_b 75 _cell.length_c 138.63 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4QK4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C41 H81 O19 P3' _chem_comp.formula_weight 970.992 _chem_comp.id PIK _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-3-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'PI(4,5)P2 dipalmitoyl (16:0,16:0)' # 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 CA2 CA3 PIK sing 269 n n CA2 CA1 PIK sing 270 n n OA1 CA1 PIK sing 271 n n OA1 C9 PIK sing 272 n n CA3 CA4 PIK sing 273 n n O3 C3 PIK sing 274 n n OB2 CB1 PIK doub 275 n n CA1 OA2 PIK doub 276 n n O41 P4 PIK doub 277 n n C9 C8 PIK sing 278 n n OB1 CB1 PIK sing 279 n n OB1 C8 PIK sing 280 n n CB1 CB2 PIK sing 281 n n CA4 CA5 PIK sing 282 n n CA5 CA6 PIK sing 283 n n C3 C2 PIK sing 284 n n C3 C4 PIK sing 285 n n C8 C7 PIK sing 286 n n P4 O42 PIK sing 287 n n P4 O4 PIK sing 288 n n P4 O43 PIK sing 289 n n O2 C2 PIK sing 290 n n C2 C1 PIK sing 291 n n CB3 CB2 PIK sing 292 n n CB3 CB4 PIK sing 293 n n O4 C4 PIK sing 294 n n C7 O13 PIK sing 295 n n O13 P1 PIK sing 296 n n C4 C5 PIK sing 297 n n CA6 CA7 PIK sing 298 n n CB5 CB4 PIK sing 299 n n CB5 CB6 PIK sing 300 n n CA7 CA8 PIK sing 301 n n C1 O1 PIK sing 302 n n C1 C6 PIK sing 303 n n O11 P1 PIK doub 304 n n O1 P1 PIK sing 305 n n P1 O12 PIK sing 306 n n CB6 CB7 PIK sing 307 n n C5 C6 PIK sing 308 n n C5 O5 PIK sing 309 n n CA9 CA8 PIK sing 310 n n CA9 CAA PIK sing 311 n n C6 O6 PIK sing 312 n n O5 P5 PIK sing 313 n n CB7 CB8 PIK sing 314 n n CAB CAA PIK sing 315 n n CAB CAC PIK sing 316 n n O53 P5 PIK doub 317 n n P5 O52 PIK sing 318 n n P5 O51 PIK sing 319 n n CB8 CB9 PIK sing 320 n n CAC CAD PIK sing 321 n n CAD CAE PIK sing 322 n n CB9 CBA PIK sing 323 n n CBC CBB PIK sing 324 n n CBC CBD PIK sing 325 n n CBB CBA PIK sing 326 n n CBD CBE PIK sing 327 n n CAE CAF PIK sing 328 n n CBE CBF PIK sing 329 n n CAF CAG PIK sing 330 n n CBF CBG PIK sing 331 n n O12 H1 PIK sing 332 n n CBG H2 PIK sing 333 n n CBG H3 PIK sing 334 n n CBG H4 PIK sing 335 n n CBF H5 PIK sing 336 n n CBF H6 PIK sing 337 n n CBE H7 PIK sing 338 n n CBE H8 PIK sing 339 n n CBD H9 PIK sing 340 n n CBD H10 PIK sing 341 n n CBC H11 PIK sing 342 n n CBC H12 PIK sing 343 n n CBB H13 PIK sing 344 n n CBB H14 PIK sing 345 n n CBA H15 PIK sing 346 n n CBA H16 PIK sing 347 n n CB9 H17 PIK sing 348 n n CB9 H18 PIK sing 349 n n CB8 H19 PIK sing 350 n n CB8 H20 PIK sing 351 n n CB7 H21 PIK sing 352 n n CB7 H22 PIK sing 353 n n CB6 H23 PIK sing 354 n n CB6 H24 PIK sing 355 n n CB5 H25 PIK sing 356 n n CB5 H26 PIK sing 357 n n CB4 H27 PIK sing 358 n n CB4 H28 PIK sing 359 n n CB3 H29 PIK sing 360 n n CB3 H30 PIK sing 361 n n CB2 H31 PIK sing 362 n n CB2 H32 PIK sing 363 n n C8 H33 PIK sing 364 n n C7 H34 PIK sing 365 n n C7 H35 PIK sing 366 n n C1 H36 PIK sing 367 n n C2 H37 PIK sing 368 n n C3 H38 PIK sing 369 n n C4 H39 PIK sing 370 n n C5 H40 PIK sing 371 n n C6 H41 PIK sing 372 n n O2 H42 PIK sing 373 n n O3 H43 PIK sing 374 n n O6 H44 PIK sing 375 n n O42 H45 PIK sing 376 n n O43 H46 PIK sing 377 n n O51 H47 PIK sing 378 n n O52 H48 PIK sing 379 n n C9 H49 PIK sing 380 n n C9 H50 PIK sing 381 n n CA2 H51 PIK sing 382 n n CA2 H52 PIK sing 383 n n CA3 H53 PIK sing 384 n n CA3 H54 PIK sing 385 n n CA4 H55 PIK sing 386 n n CA4 H56 PIK sing 387 n n CA5 H57 PIK sing 388 n n CA5 H58 PIK sing 389 n n CA6 H59 PIK sing 390 n n CA6 H60 PIK sing 391 n n CA7 H61 PIK sing 392 n n CA7 H62 PIK sing 393 n n CA8 H63 PIK sing 394 n n CA8 H64 PIK sing 395 n n CA9 H65 PIK sing 396 n n CA9 H66 PIK sing 397 n n CAA H67 PIK sing 398 n n CAA H68 PIK sing 399 n n CAB H69 PIK sing 400 n n CAB H70 PIK sing 401 n n CAC H71 PIK sing 402 n n CAC H72 PIK sing 403 n n CAD H73 PIK sing 404 n n CAD H74 PIK sing 405 n n CAE H75 PIK sing 406 n n CAE H76 PIK sing 407 n n CAF H77 PIK sing 408 n n CAF H78 PIK sing 409 n n CAG H79 PIK sing 410 n n CAG H80 PIK sing 411 n n CAG H81 PIK sing 412 n n # _atom_sites.entry_id 4QK4 _atom_sites.fract_transf_matrix[1][1] 0.013333 _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] 0.013333 _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] 0.007213 _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 3 PIK A 1 501 1 PIK PIJ . D 4 EDO A 1 502 501 EDO EDO . E 4 EDO A 1 503 502 EDO EDO . F 4 EDO A 1 504 503 EDO EDO . G 4 EDO A 1 505 504 EDO EDO . H 4 EDO A 1 506 505 EDO EDO . I 5 HOH A 1 601 506 HOH HOH . I 5 HOH A 2 602 507 HOH HOH . I 5 HOH A 3 603 508 HOH HOH . I 5 HOH A 4 604 509 HOH HOH . I 5 HOH A 5 605 510 HOH HOH . I 5 HOH A 6 606 511 HOH HOH . I 5 HOH A 7 607 512 HOH HOH . I 5 HOH A 8 608 513 HOH HOH . I 5 HOH A 9 609 514 HOH HOH . I 5 HOH A 10 610 515 HOH HOH . I 5 HOH A 11 611 516 HOH HOH . I 5 HOH A 12 612 517 HOH HOH . I 5 HOH A 13 613 518 HOH HOH . I 5 HOH A 14 614 519 HOH HOH . I 5 HOH A 15 615 520 HOH HOH . I 5 HOH A 16 616 521 HOH HOH . I 5 HOH A 17 617 522 HOH HOH . I 5 HOH A 18 618 523 HOH HOH . I 5 HOH A 19 619 524 HOH HOH . I 5 HOH A 20 620 525 HOH HOH . I 5 HOH A 21 621 526 HOH HOH . I 5 HOH A 22 622 527 HOH HOH . I 5 HOH A 23 623 528 HOH HOH . I 5 HOH A 24 624 529 HOH HOH . I 5 HOH A 25 625 530 HOH HOH . I 5 HOH A 26 626 531 HOH HOH . I 5 HOH A 27 627 532 HOH HOH . I 5 HOH A 28 628 533 HOH HOH . I 5 HOH A 29 629 534 HOH HOH . I 5 HOH A 30 630 535 HOH HOH . I 5 HOH A 31 631 536 HOH HOH . I 5 HOH A 32 632 537 HOH HOH . I 5 HOH A 33 633 538 HOH HOH . I 5 HOH A 34 634 539 HOH HOH . I 5 HOH A 35 635 540 HOH HOH . I 5 HOH A 36 636 541 HOH HOH . I 5 HOH A 37 637 542 HOH HOH . I 5 HOH A 38 638 543 HOH HOH . I 5 HOH A 39 639 544 HOH HOH . I 5 HOH A 40 640 545 HOH HOH . I 5 HOH A 41 641 546 HOH HOH . I 5 HOH A 42 642 547 HOH HOH . I 5 HOH A 43 643 548 HOH HOH . I 5 HOH A 44 644 549 HOH HOH . I 5 HOH A 45 645 550 HOH HOH . I 5 HOH A 46 646 551 HOH HOH . I 5 HOH A 47 647 552 HOH HOH . I 5 HOH A 48 648 553 HOH HOH . I 5 HOH A 49 649 554 HOH HOH . I 5 HOH A 50 650 555 HOH HOH . I 5 HOH A 51 651 556 HOH HOH . I 5 HOH A 52 652 557 HOH HOH . I 5 HOH A 53 653 558 HOH HOH . I 5 HOH A 54 654 559 HOH HOH . I 5 HOH A 55 655 560 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 P P1 PIK . . . C 3 -24.035 46.574 -12.017 1 52.79 ? P1 PIK 501 A 1 HETATM 2 O O11 PIK . . . C 3 -25.423 46.068 -12.306 1 76.64 ? O11 PIK 501 A 1 HETATM 3 O O12 PIK . . . C 3 -23.591 46.071 -10.67 1 47.57 ? O12 PIK 501 A 1 HETATM 4 O O13 PIK . . . C 3 -23.043 46.044 -13.144 1 70.47 ? O13 PIK 501 A 1 HETATM 5 C CBG PIK . . . C 3 -18.731 37.03 -3.989 1 87.44 ? CBG PIK 501 A 1 HETATM 6 C CBF PIK . . . C 3 -18.226 38.048 -4.98 1 79.09 ? CBF PIK 501 A 1 HETATM 7 C CBE PIK . . . C 3 -18.531 37.615 -6.444 1 38.44 ? CBE PIK 501 A 1 HETATM 8 C CBD PIK . . . C 3 -19.438 38.621 -7.159 1 69.66 ? CBD PIK 501 A 1 HETATM 9 C CBC PIK . . . C 3 -20.788 37.955 -7.628 1 57.62 ? CBC PIK 501 A 1 HETATM 10 C CBB PIK . . . C 3 -22.008 38.852 -7.372 1 46.43 ? CBB PIK 501 A 1 HETATM 11 C CBA PIK . . . C 3 -23.24 38.053 -6.918 1 62 ? CBA PIK 501 A 1 HETATM 12 C CB9 PIK . . . C 3 -24.376 38.078 -7.942 1 60.73 ? CB9 PIK 501 A 1 HETATM 13 C CB8 PIK . . . C 3 -23.893 37.828 -9.382 1 69.78 ? CB8 PIK 501 A 1 HETATM 14 C CB7 PIK . . . C 3 -25.015 37.309 -10.294 1 67.73 ? CB7 PIK 501 A 1 HETATM 15 C CB6 PIK . . . C 3 -24.504 36.954 -11.723 1 55.26 ? CB6 PIK 501 A 1 HETATM 16 C CB5 PIK . . . C 3 -24.992 37.945 -12.794 1 72.57 ? CB5 PIK 501 A 1 HETATM 17 C CB4 PIK . . . C 3 -24.78 39.436 -12.393 1 49.32 ? CB4 PIK 501 A 1 HETATM 18 C CB3 PIK . . . C 3 -24.524 40.35 -13.624 1 73.66 ? CB3 PIK 501 A 1 HETATM 19 C CB2 PIK . . . C 3 -23.12 41.009 -13.593 1 33.42 ? CB2 PIK 501 A 1 HETATM 20 C CB1 PIK . . . C 3 -23.034 42.246 -14.506 1 65.21 ? CB1 PIK 501 A 1 HETATM 21 O OB2 PIK . . . C 3 -23.898 42.421 -15.352 1 60.39 ? OB2 PIK 501 A 1 HETATM 22 O OB1 PIK . . . C 3 -21.748 42.934 -14.636 1 71.75 ? OB1 PIK 501 A 1 HETATM 23 C C8 PIK . . . C 3 -21.652 44.262 -14.038 1 61.96 ? C8 PIK 501 A 1 HETATM 24 C C7 PIK . . . C 3 -22.978 44.624 -13.345 1 66.16 ? C7 PIK 501 A 1 HETATM 25 C C1 PIK . . . C 3 -25.282 48.793 -12.337 1 102.26 ? C1 PIK 501 A 1 HETATM 26 C C2 PIK . . . C 3 -25.248 49.343 -13.753 1 93.07 ? C2 PIK 501 A 1 HETATM 27 C C3 PIK . . . C 3 -26.612 49.898 -14.091 1 103.84 ? C3 PIK 501 A 1 HETATM 28 C C4 PIK . . . C 3 -27 50.991 -13.099 1 118.52 ? C4 PIK 501 A 1 HETATM 29 C C5 PIK . . . C 3 -26.999 50.447 -11.681 1 119.52 ? C5 PIK 501 A 1 HETATM 30 C C6 PIK . . . C 3 -25.623 49.901 -11.354 1 98.12 ? C6 PIK 501 A 1 HETATM 31 O O1 PIK . . . C 3 -24.052 48.158 -12.021 1 117.7 ? O1 PIK 501 A 1 HETATM 32 O O2 PIK . . . C 3 -24.313 50.386 -13.808 1 98.34 ? O2 PIK 501 A 1 HETATM 33 O O3 PIK . . . C 3 -26.633 50.389 -15.429 1 98.12 ? O3 PIK 501 A 1 HETATM 34 O O4 PIK . . . C 3 -28.265 51.54 -13.443 1 130.33 ? O4 PIK 501 A 1 HETATM 35 O O5 PIK . . . C 3 -27.355 51.431 -10.783 1 135.64 ? O5 PIK 501 A 1 HETATM 36 O O6 PIK . . . C 3 -25.573 49.421 -9.997 1 82.87 ? O6 PIK 501 A 1 HETATM 37 P P4 PIK . . . C 3 -28.332 53.038 -13.853 1 160.29 ? P4 PIK 501 A 1 HETATM 38 O O41 PIK . . . C 3 -27.799 53.193 -15.253 1 162.36 ? O41 PIK 501 A 1 HETATM 39 O O42 PIK . . . C 3 -29.763 53.509 -13.805 1 164.21 ? O42 PIK 501 A 1 HETATM 40 O O43 PIK . . . C 3 -27.496 53.86 -12.899 1 158.45 ? O43 PIK 501 A 1 HETATM 41 P P5 PIK . . . C 3 -28.327 51.052 -9.593 1 121.36 ? P5 PIK 501 A 1 HETATM 42 O O51 PIK . . . C 3 -27.523 50.813 -8.344 1 108.63 ? O51 PIK 501 A 1 HETATM 43 O O52 PIK . . . C 3 -29.301 52.188 -9.354 1 139.3 ? O52 PIK 501 A 1 HETATM 44 O O53 PIK . . . C 3 -29.092 49.796 -9.947 1 108.79 ? O53 PIK 501 A 1 HETATM 45 C C9 PIK . . . C 3 -21.208 45.275 -15.115 1 37.62 ? C9 PIK 501 A 1 HETATM 46 O OA1 PIK . . . C 3 -20.182 44.659 -15.942 1 82.1 ? OA1 PIK 501 A 1 HETATM 47 C CA1 PIK . . . C 3 -18.946 44.312 -15.266 1 52.29 ? CA1 PIK 501 A 1 HETATM 48 O OA2 PIK . . . C 3 -18.595 44.926 -14.262 1 48.76 ? OA2 PIK 501 A 1 HETATM 49 C CA2 PIK . . . C 3 -17.923 43.373 -15.975 1 55.49 ? CA2 PIK 501 A 1 HETATM 50 C CA3 PIK . . . C 3 -18.304 41.893 -15.853 1 39.94 ? CA3 PIK 501 A 1 HETATM 51 C CA4 PIK . . . C 3 -18.614 41.466 -14.42 1 54.86 ? CA4 PIK 501 A 1 HETATM 52 C CA5 PIK . . . C 3 -18.991 39.985 -14.346 1 58.72 ? CA5 PIK 501 A 1 HETATM 53 C CA6 PIK . . . C 3 -18.656 39.351 -13.008 1 54.87 ? CA6 PIK 501 A 1 HETATM 54 C CA7 PIK . . . C 3 -19.681 38.256 -12.615 1 46.14 ? CA7 PIK 501 A 1 HETATM 55 C CA8 PIK . . . C 3 -19.222 37.433 -11.402 1 45.67 ? CA8 PIK 501 A 1 HETATM 56 C CA9 PIK . . . C 3 -19.824 36.008 -11.404 1 49.56 ? CA9 PIK 501 A 1 HETATM 57 C CAA PIK . . . C 3 -19.819 35.362 -10.019 1 42.64 ? CAA PIK 501 A 1 HETATM 58 C CAB PIK . . . C 3 -20.54 34.016 -10.02 1 34.96 ? CAB PIK 501 A 1 HETATM 59 C CAC PIK . . . C 3 -20.935 33.561 -8.603 1 45.17 ? CAC PIK 501 A 1 HETATM 60 C CAD PIK . . . C 3 -21.963 34.492 -7.98 1 46.34 ? CAD PIK 501 A 1 HETATM 61 C CAE PIK . . . C 3 -22.889 33.767 -6.989 1 45.29 ? CAE PIK 501 A 1 HETATM 62 C CAF PIK . . . C 3 -23.357 34.667 -5.852 1 56.04 ? CAF PIK 501 A 1 HETATM 63 C CAG PIK . . . C 3 -24.306 33.953 -4.9 1 62.11 ? CAG PIK 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 63 #