data_8VT9
#
_model_server_result.job_id            L75LS4P48GpHs5ZQeWZySg 
_model_server_result.datetime_utc      '2024-12-21 16:53:45' 
_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":"X","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 . . . X 3 148.383 157.241 142.038 1 111.6 -1 O12 PT5 502 C 1 
HETATM 2 P P1 PT5 . . . X 3 147.063 157.924 141.752 1 111.6 ? P1 PT5 502 C 1 
HETATM 3 O O13 PT5 . . . X 3 145.834 156.794 141.563 1 111.6 ? O13 PT5 502 C 1 
HETATM 4 O O11 PT5 . . . X 3 146.708 158.825 142.913 1 111.6 ? O11 PT5 502 C 1 
HETATM 5 O O6 PT5 . . . X 3 148.515 157.202 138.404 1 111.6 ? O6 PT5 502 C 1 
HETATM 6 O O1 PT5 . . . X 3 147.153 158.823 140.347 1 111.6 ? O1 PT5 502 C 1 
HETATM 7 C C1 PT5 . . . X 3 148.403 159.154 139.774 1 111.6 ? C1 PT5 502 C 1 
HETATM 8 C C6 PT5 . . . X 3 148.449 158.613 138.345 1 111.6 ? C6 PT5 502 C 1 
HETATM 9 C C2 PT5 . . . X 3 148.553 160.684 139.827 1 111.6 ? C2 PT5 502 C 1 
HETATM 10 O O2 PT5 . . . X 3 147.42 161.269 139.241 1 111.6 ? O2 PT5 502 C 1 
HETATM 11 C C3 PT5 . . . X 3 149.798 161.16 139.072 1 111.6 ? C3 PT5 502 C 1 
HETATM 12 O O3 PT5 . . . X 3 149.813 162.571 139.061 1 111.6 ? O3 PT5 502 C 1 
HETATM 13 C C4 PT5 . . . X 3 149.8 160.657 137.63 1 111.6 ? C4 PT5 502 C 1 
HETATM 14 O O4 PT5 . . . X 3 151.009 161.045 137.031 1 111.6 ? O4 PT5 502 C 1 
HETATM 15 P P4 PT5 . . . X 3 150.896 162.17 135.827 1 111.6 ? P4 PT5 502 C 1 
HETATM 16 O O41 PT5 . . . X 3 149.626 162.968 136.022 1 111.6 ? O41 PT5 502 C 1 
HETATM 17 O O42 PT5 . . . X 3 150.863 161.476 134.485 1 111.6 -1 O42 PT5 502 C 1 
HETATM 18 O O43 PT5 . . . X 3 152.083 163.107 135.892 1 111.6 ? O43 PT5 502 C 1 
HETATM 19 C C5 PT5 . . . X 3 149.664 159.128 137.553 1 111.6 ? C5 PT5 502 C 1 
HETATM 20 O O5 PT5 . . . X 3 149.51 158.767 136.213 1 111.6 ? O5 PT5 502 C 1 
HETATM 21 P P5 PT5 . . . X 3 150.654 157.801 135.543 1 111.6 ? P5 PT5 502 C 1 
HETATM 22 O O52 PT5 . . . X 3 151.662 157.42 136.601 1 111.6 ? O52 PT5 502 C 1 
HETATM 23 O O51 PT5 . . . X 3 151.351 158.53 134.42 1 111.6 -1 O51 PT5 502 C 1 
HETATM 24 O O53 PT5 . . . X 3 149.992 156.553 135.007 1 111.6 ? O53 PT5 502 C 1 
HETATM 25 C C7 PT5 . . . X 3 144.884 157.079 140.566 1 111.6 ? C7 PT5 502 C 1 
HETATM 26 C C8 PT5 . . . X 3 143.498 157.253 141.181 1 111.6 ? C8 PT5 502 C 1 
HETATM 27 C C9 PT5 . . . X 3 143.586 157.736 142.647 1 111.6 ? C9 PT5 502 C 1 
HETATM 28 O O16 PT5 . . . X 3 142.759 158.198 140.424 1 111.6 ? O16 PT5 502 C 1 
HETATM 29 C C10 PT5 . . . X 3 141.315 158.023 140.565 1 111.6 ? C10 PT5 502 C 1 
HETATM 30 O O17 PT5 . . . X 3 140.615 158.983 140.754 1 111.6 ? O17 PT5 502 C 1 
HETATM 31 O O18 PT5 . . . X 3 143.17 156.661 143.513 1 111.6 ? O18 PT5 502 C 1 
HETATM 32 C C11 PT5 . . . X 3 141.732 156.47 143.616 1 111.6 ? C11 PT5 502 C 1 
HETATM 33 O O19 PT5 . . . X 3 141.267 155.387 143.483 1 111.6 ? O19 PT5 502 C 1 
HETATM 34 C C12 PT5 . . . X 3 140.681 156.564 140.472 1 111.6 ? C12 PT5 502 C 1 
HETATM 35 C C13 PT5 . . . X 3 139.211 156.516 141.007 1 111.6 ? C13 PT5 502 C 1 
HETATM 36 C C14 PT5 . . . X 3 138.235 157.353 140.09 1 111.6 ? C14 PT5 502 C 1 
HETATM 37 C C15 PT5 . . . X 3 137.502 158.426 140.954 1 111.6 ? C15 PT5 502 C 1 
HETATM 38 C C16 PT5 . . . X 3 137.172 159.531 140.207 1 111.6 ? C16 PT5 502 C 1 
HETATM 39 C C17 PT5 . . . X 3 136.428 160.673 140.995 1 111.6 ? C17 PT5 502 C 1 
HETATM 40 C C18 PT5 . . . X 3 136.503 160.348 142.519 1 111.6 ? C18 PT5 502 C 1 
HETATM 41 C C19 PT5 . . . X 3 136.294 161.447 143.312 1 111.6 ? C19 PT5 502 C 1 
HETATM 42 C C20 PT5 . . . X 3 136.358 161.152 144.849 1 111.6 ? C20 PT5 502 C 1 
HETATM 43 C C21 PT5 . . . X 3 134.889 161.131 145.425 1 111.6 ? C21 PT5 502 C 1 
HETATM 44 C C22 PT5 . . . X 3 134.844 161.168 146.772 1 111.6 ? C22 PT5 502 C 1 
HETATM 45 C C23 PT5 . . . X 3 135.497 161.22 148.2 1 111.6 ? C23 PT5 502 C 1 
HETATM 46 C C24 PT5 . . . X 3 134.356 161.087 149.285 1 111.6 ? C24 PT5 502 C 1 
HETATM 47 C C31 PT5 . . . X 3 140.771 157.679 143.901 1 111.6 ? C31 PT5 502 C 1 
HETATM 48 C C32 PT5 . . . X 3 140.72 158.035 145.434 1 111.6 ? C32 PT5 502 C 1 
HETATM 49 C C33 PT5 . . . X 3 139.304 157.826 146.061 1 111.6 ? C33 PT5 502 C 1 
HETATM 50 C C34 PT5 . . . X 3 139.311 158.161 147.584 1 111.6 ? C34 PT5 502 C 1 
HETATM 51 C C35 PT5 . . . X 3 138.124 157.519 148.356 1 111.6 ? C35 PT5 502 C 1 
HETATM 52 C C36 PT5 . . . X 3 137.76 158.329 149.614 1 111.6 ? C36 PT5 502 C 1 
HETATM 53 C C37 PT5 . . . X 3 137.125 157.469 150.705 1 111.6 ? C37 PT5 502 C 1 
HETATM 54 C C38 PT5 . . . X 3 136.18 158.281 151.581 1 111.6 ? C38 PT5 502 C 1 
HETATM 55 C C39 PT5 . . . X 3 136.109 157.764 152.994 1 111.6 ? C39 PT5 502 C 1 
HETATM 56 C C40 PT5 . . . X 3 134.678 157.637 153.477 1 111.6 ? C40 PT5 502 C 1 
HETATM 57 C C25 PT5 . . . X 3 134.629 161.337 150.612 1 111.6 ? C25 PT5 502 C 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           57 
#