data_8VT9 # _model_server_result.job_id 59wM3JiE0QdUHjqBIp-bkw _model_server_result.datetime_utc '2024-12-21 17:18:10' _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 8vt9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":502}' # _entry.id 8VT9 # _exptl.entry_id 8VT9 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 1047.088 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate' _entity.pdbx_number_of_molecules 4 _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 8VT9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VT9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA _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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 O N N ? 3 X N N ? 3 GA N N # _chem_comp.formula 'C47 H85 O19 P3' _chem_comp.formula_weight 1047.088 _chem_comp.id PT5 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Phosphatidylinositol 4,5-bisphosphate;PtdIns(4,5)P2' # 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 C23 C24 PT5 sing 450 n n C23 C22 PT5 sing 451 n n C22 C21 PT5 doub 452 e n C21 C20 PT5 sing 453 n n C20 C19 PT5 sing 454 n n C19 C18 PT5 doub 455 z n C16 C17 PT5 sing 456 n n C16 C15 PT5 doub 457 z n C18 C17 PT5 sing 458 n n C15 C14 PT5 sing 459 n n C14 C13 PT5 sing 460 n n C13 C12 PT5 sing 461 n n O17 C10 PT5 doub 462 n n O52 P5 PT5 doub 463 n n O6 C6 PT5 sing 464 n n C12 C10 PT5 sing 465 n n O53 P5 PT5 sing 466 n n C10 O16 PT5 sing 467 n n P5 O5 PT5 sing 468 n n P5 O51 PT5 sing 469 n n O5 C5 PT5 sing 470 n n C5 C6 PT5 sing 471 n n C5 C4 PT5 sing 472 n n C6 C1 PT5 sing 473 n n C1 C2 PT5 sing 474 n n C1 O1 PT5 sing 475 n n O16 C8 PT5 sing 476 n n C7 O13 PT5 sing 477 n n C7 C8 PT5 sing 478 n n C2 O2 PT5 sing 479 n n C2 C3 PT5 sing 480 n n O13 P1 PT5 sing 481 n n C8 C9 PT5 sing 482 n n O4 C4 PT5 sing 483 n n O4 P4 PT5 sing 484 n n C4 C3 PT5 sing 485 n n C3 O3 PT5 sing 486 n n O1 P1 PT5 sing 487 n n O42 P4 PT5 doub 488 n n P1 O11 PT5 doub 489 n n P1 O12 PT5 sing 490 n n P4 O41 PT5 sing 491 n n P4 O43 PT5 sing 492 n n C9 O18 PT5 sing 493 n n C31 C11 PT5 sing 494 n n C31 C32 PT5 sing 495 n n O18 C11 PT5 sing 496 n n C11 O19 PT5 doub 497 n n C32 C33 PT5 sing 498 n n C33 C34 PT5 sing 499 n n C34 C35 PT5 sing 500 n n C35 C36 PT5 sing 501 n n C36 C37 PT5 sing 502 n n C37 C38 PT5 sing 503 n n C40 C39 PT5 sing 504 n n C39 C38 PT5 sing 505 n n O12 H1 PT5 sing 506 n n O6 H2 PT5 sing 507 n n C1 H3 PT5 sing 508 n n C6 H4 PT5 sing 509 n n C2 H5 PT5 sing 510 n n O2 H6 PT5 sing 511 n n C3 H7 PT5 sing 512 n n O3 H8 PT5 sing 513 n n C4 H9 PT5 sing 514 n n O41 H10 PT5 sing 515 n n O43 H11 PT5 sing 516 n n C5 H12 PT5 sing 517 n n O51 H13 PT5 sing 518 n n O53 H14 PT5 sing 519 n n C7 H15 PT5 sing 520 n n C7 H16 PT5 sing 521 n n C8 H17 PT5 sing 522 n n C9 H18 PT5 sing 523 n n C9 H19 PT5 sing 524 n n C12 H20 PT5 sing 525 n n C12 H21 PT5 sing 526 n n C13 H22 PT5 sing 527 n n C13 H23 PT5 sing 528 n n C14 H24 PT5 sing 529 n n C14 H25 PT5 sing 530 n n C15 H26 PT5 sing 531 n n C16 H28 PT5 sing 532 n n C17 H30 PT5 sing 533 n n C17 H31 PT5 sing 534 n n C18 H32 PT5 sing 535 n n C19 H33 PT5 sing 536 n n C20 H34 PT5 sing 537 n n C20 H35 PT5 sing 538 n n C21 H36 PT5 sing 539 n n C22 H38 PT5 sing 540 n n C23 H40 PT5 sing 541 n n C23 H41 PT5 sing 542 n n C24 H42 PT5 sing 543 n n C31 H45 PT5 sing 544 n n C31 H46 PT5 sing 545 n n C32 H47 PT5 sing 546 n n C32 H48 PT5 sing 547 n n C33 H49 PT5 sing 548 n n C33 H50 PT5 sing 549 n n C34 H51 PT5 sing 550 n n C34 H52 PT5 sing 551 n n C35 H53 PT5 sing 552 n n C35 H54 PT5 sing 553 n n C36 H55 PT5 sing 554 n n C36 H56 PT5 sing 555 n n C37 H57 PT5 sing 556 n n C37 H58 PT5 sing 557 n n C38 H59 PT5 sing 558 n n C38 H60 PT5 sing 559 n n C39 H61 PT5 sing 560 n n C39 H62 PT5 sing 561 n n C40 H63 PT5 sing 562 n n C40 H64 PT5 sing 563 n n C24 C25 PT5 doub 564 n n C25 C26 PT5 sing 565 n n C26 C27 PT5 sing 566 n n C27 C28 PT5 sing 567 n n C28 C29 PT5 sing 568 n n C29 C30 PT5 sing 569 n n C40 C41 PT5 sing 570 n n C41 C42 PT5 sing 571 n n C42 C43 PT5 sing 572 n n C43 C44 PT5 sing 573 n n C44 C45 PT5 sing 574 n n C45 C46 PT5 sing 575 n n C46 C47 PT5 sing 576 n n C25 H27 PT5 sing 577 n n C26 H29 PT5 sing 578 n n C26 H37 PT5 sing 579 n n C27 H39 PT5 sing 580 n n C27 H43 PT5 sing 581 n n C28 H44 PT5 sing 582 n n C28 H65 PT5 sing 583 n n C29 H66 PT5 sing 584 n n C29 H67 PT5 sing 585 n n C30 H68 PT5 sing 586 n n C30 H69 PT5 sing 587 n n C30 H70 PT5 sing 588 n n C41 H71 PT5 sing 589 n n C41 H72 PT5 sing 590 n n C42 H73 PT5 sing 591 n n C42 H74 PT5 sing 592 n n C43 H75 PT5 sing 593 n n C43 H76 PT5 sing 594 n n C44 H77 PT5 sing 595 n n C44 H78 PT5 sing 596 n n C45 H79 PT5 sing 597 n n C45 H80 PT5 sing 598 n n C46 H81 PT5 sing 599 n n C46 H82 PT5 sing 600 n n C47 H83 PT5 sing 601 n n C47 H84 PT5 sing 602 n n C47 H85 PT5 sing 603 n n # _atom_sites.entry_id 8VT9 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 E 2 CMP A 1 501 500 CMP CMP . F 3 PT5 A 1 502 600 PT5 PT5 . G 4 PCW A 1 503 601 PCW PCW . H 4 PCW A 1 504 602 PCW PCW . I 4 PCW A 1 505 603 PCW PCW . J 4 PCW A 1 506 604 PCW PCW . K 4 PCW A 1 507 605 PCW PCW . L 4 PCW A 1 508 606 PCW PCW . M 4 PCW A 1 509 607 PCW PCW . N 2 CMP B 1 501 500 CMP CMP . O 3 PT5 B 1 502 600 PT5 PT5 . P 4 PCW B 1 503 601 PCW PCW . Q 4 PCW B 1 504 602 PCW PCW . R 4 PCW B 1 505 603 PCW PCW . S 4 PCW B 1 506 604 PCW PCW . T 4 PCW B 1 507 605 PCW PCW . U 4 PCW B 1 508 606 PCW PCW . V 4 PCW B 1 509 607 PCW PCW . W 2 CMP C 1 501 500 CMP CMP . X 3 PT5 C 1 502 600 PT5 PT5 . Y 4 PCW C 1 503 601 PCW PCW . Z 4 PCW C 1 504 602 PCW PCW . AA 4 PCW C 1 505 603 PCW PCW . BA 4 PCW C 1 506 604 PCW PCW . CA 4 PCW C 1 507 605 PCW PCW . DA 4 PCW C 1 508 606 PCW PCW . EA 4 PCW C 1 509 607 PCW PCW . FA 2 CMP D 1 501 500 CMP CMP . GA 3 PT5 D 1 502 600 PT5 PT5 . HA 4 PCW D 1 503 601 PCW PCW . IA 4 PCW D 1 504 602 PCW PCW . JA 4 PCW D 1 505 603 PCW PCW . KA 4 PCW D 1 506 604 PCW PCW . LA 4 PCW D 1 507 605 PCW PCW . MA 4 PCW D 1 508 606 PCW PCW . NA 4 PCW D 1 509 607 PCW PCW . # 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 O O12 PT5 . . . O 3 123.341 148.393 142.029 1 111.6 -1 O12 PT5 502 B 1 HETATM 2 P P1 PT5 . . . O 3 122.658 147.074 141.742 1 111.6 ? P1 PT5 502 B 1 HETATM 3 O O13 PT5 . . . O 3 123.788 145.845 141.553 1 111.6 ? O13 PT5 502 B 1 HETATM 4 O O11 PT5 . . . O 3 121.757 146.718 142.903 1 111.6 ? O11 PT5 502 B 1 HETATM 5 O O6 PT5 . . . O 3 123.381 148.526 138.395 1 111.6 ? O6 PT5 502 B 1 HETATM 6 O O1 PT5 . . . O 3 121.759 147.165 140.337 1 111.6 ? O1 PT5 502 B 1 HETATM 7 C C1 PT5 . . . O 3 121.428 148.415 139.765 1 111.6 ? C1 PT5 502 B 1 HETATM 8 C C6 PT5 . . . O 3 121.969 148.461 138.336 1 111.6 ? C6 PT5 502 B 1 HETATM 9 C C2 PT5 . . . O 3 119.898 148.565 139.817 1 111.6 ? C2 PT5 502 B 1 HETATM 10 O O2 PT5 . . . O 3 119.313 147.432 139.231 1 111.6 ? O2 PT5 502 B 1 HETATM 11 C C3 PT5 . . . O 3 119.423 149.81 139.062 1 111.6 ? C3 PT5 502 B 1 HETATM 12 O O3 PT5 . . . O 3 118.011 149.825 139.052 1 111.6 ? O3 PT5 502 B 1 HETATM 13 C C4 PT5 . . . O 3 119.926 149.812 137.621 1 111.6 ? C4 PT5 502 B 1 HETATM 14 O O4 PT5 . . . O 3 119.538 151.022 137.023 1 111.6 ? O4 PT5 502 B 1 HETATM 15 P P4 PT5 . . . O 3 118.413 150.91 135.818 1 111.6 ? P4 PT5 502 B 1 HETATM 16 O O41 PT5 . . . O 3 117.615 149.64 136.013 1 111.6 ? O41 PT5 502 B 1 HETATM 17 O O42 PT5 . . . O 3 119.107 150.877 134.477 1 111.6 -1 O42 PT5 502 B 1 HETATM 18 O O43 PT5 . . . O 3 117.477 152.097 135.884 1 111.6 ? O43 PT5 502 B 1 HETATM 19 C C5 PT5 . . . O 3 121.454 149.677 137.544 1 111.6 ? C5 PT5 502 B 1 HETATM 20 O O5 PT5 . . . O 3 121.816 149.523 136.205 1 111.6 ? O5 PT5 502 B 1 HETATM 21 P P5 PT5 . . . O 3 122.783 150.667 135.535 1 111.6 ? P5 PT5 502 B 1 HETATM 22 O O52 PT5 . . . O 3 123.163 151.674 136.593 1 111.6 ? O52 PT5 502 B 1 HETATM 23 O O51 PT5 . . . O 3 122.053 151.365 134.411 1 111.6 -1 O51 PT5 502 B 1 HETATM 24 O O53 PT5 . . . O 3 124.03 150.005 134.999 1 111.6 ? O53 PT5 502 B 1 HETATM 25 C C7 PT5 . . . O 3 123.503 144.895 140.555 1 111.6 ? C7 PT5 502 B 1 HETATM 26 C C8 PT5 . . . O 3 123.328 143.509 141.17 1 111.6 ? C8 PT5 502 B 1 HETATM 27 C C9 PT5 . . . O 3 122.845 143.597 142.636 1 111.6 ? C9 PT5 502 B 1 HETATM 28 O O16 PT5 . . . O 3 122.383 142.77 140.412 1 111.6 ? O16 PT5 502 B 1 HETATM 29 C C10 PT5 . . . O 3 122.558 141.326 140.554 1 111.6 ? C10 PT5 502 B 1 HETATM 30 O O17 PT5 . . . O 3 121.598 140.626 140.742 1 111.6 ? O17 PT5 502 B 1 HETATM 31 O O18 PT5 . . . O 3 123.92 143.18 143.503 1 111.6 ? O18 PT5 502 B 1 HETATM 32 C C11 PT5 . . . O 3 124.11 141.741 143.605 1 111.6 ? C11 PT5 502 B 1 HETATM 33 O O19 PT5 . . . O 3 125.193 141.277 143.472 1 111.6 ? O19 PT5 502 B 1 HETATM 34 C C12 PT5 . . . O 3 124.017 140.692 140.46 1 111.6 ? C12 PT5 502 B 1 HETATM 35 C C13 PT5 . . . O 3 124.064 139.222 140.995 1 111.6 ? C13 PT5 502 B 1 HETATM 36 C C14 PT5 . . . O 3 123.227 138.246 140.078 1 111.6 ? C14 PT5 502 B 1 HETATM 37 C C15 PT5 . . . O 3 122.154 137.514 140.941 1 111.6 ? C15 PT5 502 B 1 HETATM 38 C C16 PT5 . . . O 3 121.049 137.183 140.193 1 111.6 ? C16 PT5 502 B 1 HETATM 39 C C17 PT5 . . . O 3 119.907 136.44 140.982 1 111.6 ? C17 PT5 502 B 1 HETATM 40 C C18 PT5 . . . O 3 120.232 136.514 142.505 1 111.6 ? C18 PT5 502 B 1 HETATM 41 C C19 PT5 . . . O 3 119.133 136.305 143.298 1 111.6 ? C19 PT5 502 B 1 HETATM 42 C C20 PT5 . . . O 3 119.428 136.368 144.835 1 111.6 ? C20 PT5 502 B 1 HETATM 43 C C21 PT5 . . . O 3 119.448 134.899 145.411 1 111.6 ? C21 PT5 502 B 1 HETATM 44 C C22 PT5 . . . O 3 119.411 134.854 146.758 1 111.6 ? C22 PT5 502 B 1 HETATM 45 C C23 PT5 . . . O 3 119.359 135.506 148.186 1 111.6 ? C23 PT5 502 B 1 HETATM 46 C C24 PT5 . . . O 3 119.491 134.365 149.27 1 111.6 ? C24 PT5 502 B 1 HETATM 47 C C31 PT5 . . . O 3 122.901 140.781 143.889 1 111.6 ? C31 PT5 502 B 1 HETATM 48 C C32 PT5 . . . O 3 122.544 140.729 145.422 1 111.6 ? C32 PT5 502 B 1 HETATM 49 C C33 PT5 . . . O 3 122.754 139.313 146.049 1 111.6 ? C33 PT5 502 B 1 HETATM 50 C C34 PT5 . . . O 3 122.418 139.319 147.571 1 111.6 ? C34 PT5 502 B 1 HETATM 51 C C35 PT5 . . . O 3 123.06 138.132 148.344 1 111.6 ? C35 PT5 502 B 1 HETATM 52 C C36 PT5 . . . O 3 122.25 137.768 149.601 1 111.6 ? C36 PT5 502 B 1 HETATM 53 C C37 PT5 . . . O 3 123.109 137.132 150.692 1 111.6 ? C37 PT5 502 B 1 HETATM 54 C C38 PT5 . . . O 3 122.297 136.187 151.568 1 111.6 ? C38 PT5 502 B 1 HETATM 55 C C39 PT5 . . . O 3 122.814 136.115 152.981 1 111.6 ? C39 PT5 502 B 1 HETATM 56 C C40 PT5 . . . O 3 122.94 134.684 153.463 1 111.6 ? C40 PT5 502 B 1 HETATM 57 C C25 PT5 . . . O 3 119.241 134.637 150.597 1 111.6 ? C25 PT5 502 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 57 #