data_8VT9
#
_model_server_result.job_id            9j8yC3BwOR1pZyqiETInxg 
_model_server_result.datetime_utc      '2024-12-21 17:13:17' 
_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":"GA","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 . . . GA 3 157.238 132.196 142.034 1 111.6 -1 O12 PT5 502 D 1 
HETATM 2 P P1 PT5 . . . GA 3 157.921 133.514 141.747 1 111.6 ? P1 PT5 502 D 1 
HETATM 3 O O13 PT5 . . . GA 3 156.792 134.744 141.558 1 111.6 ? O13 PT5 502 D 1 
HETATM 4 O O11 PT5 . . . GA 3 158.822 133.87 142.908 1 111.6 ? O11 PT5 502 D 1 
HETATM 5 O O6 PT5 . . . GA 3 157.199 132.063 138.399 1 111.6 ? O6 PT5 502 D 1 
HETATM 6 O O1 PT5 . . . GA 3 158.821 133.424 140.342 1 111.6 ? O1 PT5 502 D 1 
HETATM 7 C C1 PT5 . . . GA 3 159.151 132.174 139.77 1 111.6 ? C1 PT5 502 D 1 
HETATM 8 C C6 PT5 . . . GA 3 158.61 132.128 138.341 1 111.6 ? C6 PT5 502 D 1 
HETATM 9 C C2 PT5 . . . GA 3 160.681 132.023 139.822 1 111.6 ? C2 PT5 502 D 1 
HETATM 10 O O2 PT5 . . . GA 3 161.267 133.155 139.237 1 111.6 ? O2 PT5 502 D 1 
HETATM 11 C C3 PT5 . . . GA 3 161.156 130.778 139.068 1 111.6 ? C3 PT5 502 D 1 
HETATM 12 O O3 PT5 . . . GA 3 162.568 130.762 139.057 1 111.6 ? O3 PT5 502 D 1 
HETATM 13 C C4 PT5 . . . GA 3 160.653 130.776 137.626 1 111.6 ? C4 PT5 502 D 1 
HETATM 14 O O4 PT5 . . . GA 3 161.041 129.566 137.028 1 111.6 ? O4 PT5 502 D 1 
HETATM 15 P P4 PT5 . . . GA 3 162.166 129.678 135.824 1 111.6 ? P4 PT5 502 D 1 
HETATM 16 O O41 PT5 . . . GA 3 162.964 130.948 136.019 1 111.6 ? O41 PT5 502 D 1 
HETATM 17 O O42 PT5 . . . GA 3 161.472 129.711 134.482 1 111.6 -1 O42 PT5 502 D 1 
HETATM 18 O O43 PT5 . . . GA 3 163.102 128.491 135.889 1 111.6 ? O43 PT5 502 D 1 
HETATM 19 C C5 PT5 . . . GA 3 159.125 130.912 137.549 1 111.6 ? C5 PT5 502 D 1 
HETATM 20 O O5 PT5 . . . GA 3 158.764 131.066 136.209 1 111.6 ? O5 PT5 502 D 1 
HETATM 21 P P5 PT5 . . . GA 3 157.797 129.923 135.539 1 111.6 ? P5 PT5 502 D 1 
HETATM 22 O O52 PT5 . . . GA 3 157.416 128.915 136.597 1 111.6 ? O52 PT5 502 D 1 
HETATM 23 O O51 PT5 . . . GA 3 158.526 129.225 134.416 1 111.6 -1 O51 PT5 502 D 1 
HETATM 24 O O53 PT5 . . . GA 3 156.55 130.586 135.003 1 111.6 ? O53 PT5 502 D 1 
HETATM 25 C C7 PT5 . . . GA 3 157.078 135.694 140.56 1 111.6 ? C7 PT5 502 D 1 
HETATM 26 C C8 PT5 . . . GA 3 157.253 137.08 141.176 1 111.6 ? C8 PT5 502 D 1 
HETATM 27 C C9 PT5 . . . GA 3 157.736 136.992 142.642 1 111.6 ? C9 PT5 502 D 1 
HETATM 28 O O16 PT5 . . . GA 3 158.199 137.818 140.418 1 111.6 ? O16 PT5 502 D 1 
HETATM 29 C C10 PT5 . . . GA 3 158.024 139.263 140.56 1 111.6 ? C10 PT5 502 D 1 
HETATM 30 O O17 PT5 . . . GA 3 158.985 139.962 140.748 1 111.6 ? O17 PT5 502 D 1 
HETATM 31 O O18 PT5 . . . GA 3 156.661 137.409 143.508 1 111.6 ? O18 PT5 502 D 1 
HETATM 32 C C11 PT5 . . . GA 3 156.471 138.848 143.61 1 111.6 ? C11 PT5 502 D 1 
HETATM 33 O O19 PT5 . . . GA 3 155.388 139.312 143.478 1 111.6 ? O19 PT5 502 D 1 
HETATM 34 C C12 PT5 . . . GA 3 156.566 139.898 140.466 1 111.6 ? C12 PT5 502 D 1 
HETATM 35 C C13 PT5 . . . GA 3 156.518 141.367 141 1 111.6 ? C13 PT5 502 D 1 
HETATM 36 C C14 PT5 . . . GA 3 157.356 142.343 140.084 1 111.6 ? C14 PT5 502 D 1 
HETATM 37 C C15 PT5 . . . GA 3 158.429 143.075 140.948 1 111.6 ? C15 PT5 502 D 1 
HETATM 38 C C16 PT5 . . . GA 3 159.534 143.405 140.2 1 111.6 ? C16 PT5 502 D 1 
HETATM 39 C C17 PT5 . . . GA 3 160.677 144.148 140.989 1 111.6 ? C17 PT5 502 D 1 
HETATM 40 C C18 PT5 . . . GA 3 160.352 144.074 142.512 1 111.6 ? C18 PT5 502 D 1 
HETATM 41 C C19 PT5 . . . GA 3 161.451 144.282 143.306 1 111.6 ? C19 PT5 502 D 1 
HETATM 42 C C20 PT5 . . . GA 3 161.155 144.219 144.842 1 111.6 ? C20 PT5 502 D 1 
HETATM 43 C C21 PT5 . . . GA 3 161.136 145.688 145.419 1 111.6 ? C21 PT5 502 D 1 
HETATM 44 C C22 PT5 . . . GA 3 161.173 145.732 146.765 1 111.6 ? C22 PT5 502 D 1 
HETATM 45 C C23 PT5 . . . GA 3 161.224 145.08 148.194 1 111.6 ? C23 PT5 502 D 1 
HETATM 46 C C24 PT5 . . . GA 3 161.092 146.221 149.278 1 111.6 ? C24 PT5 502 D 1 
HETATM 47 C C31 PT5 . . . GA 3 157.68 139.807 143.895 1 111.6 ? C31 PT5 502 D 1 
HETATM 48 C C32 PT5 . . . GA 3 158.037 139.859 145.428 1 111.6 ? C32 PT5 502 D 1 
HETATM 49 C C33 PT5 . . . GA 3 157.828 141.275 146.055 1 111.6 ? C33 PT5 502 D 1 
HETATM 50 C C34 PT5 . . . GA 3 158.163 141.268 147.578 1 111.6 ? C34 PT5 502 D 1 
HETATM 51 C C35 PT5 . . . GA 3 157.522 142.456 148.35 1 111.6 ? C35 PT5 502 D 1 
HETATM 52 C C36 PT5 . . . GA 3 158.332 142.819 149.608 1 111.6 ? C36 PT5 502 D 1 
HETATM 53 C C37 PT5 . . . GA 3 157.472 143.455 150.698 1 111.6 ? C37 PT5 502 D 1 
HETATM 54 C C38 PT5 . . . GA 3 158.285 144.4 151.575 1 111.6 ? C38 PT5 502 D 1 
HETATM 55 C C39 PT5 . . . GA 3 157.767 144.472 152.988 1 111.6 ? C39 PT5 502 D 1 
HETATM 56 C C40 PT5 . . . GA 3 157.642 145.903 153.47 1 111.6 ? C40 PT5 502 D 1 
HETATM 57 C C25 PT5 . . . GA 3 161.342 145.949 150.605 1 111.6 ? C25 PT5 502 D 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           57 
#