data_8JF2
#
_model_server_result.job_id            '_m5Oq48D-JuhxYYue56sIw' 
_model_server_result.datetime_utc      '2025-03-06 03:24:22' 
_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          8jf2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":502}' 
#
_entry.id    8JF2 
#
_exptl.entry_id    8JF2 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              751.023 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE' 
_entity.pdbx_number_of_molecules    6 
_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            8JF2 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8JF2 
_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    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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,OA 
_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 I N N 
? 3 O N N 
? 3 X N N 
? 3 Y N N 
? 3 GA N N 
? 3 HA N N 
#
_chem_comp.formula           'C40 H79 O10 P' 
_chem_comp.formula_weight    751.023 
_chem_comp.id                PGT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'PHOSPHATIDYLGLYCEROL;1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)' 
#
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
C48 C47 PGT sing 436 n n 
C48 H481 PGT sing 437 n n 
C48 H482 PGT sing 438 n n 
C48 H483 PGT sing 439 n n 
C47 C46 PGT sing 440 n n 
C47 H471 PGT sing 441 n n 
C47 H472 PGT sing 442 n n 
C46 C45 PGT sing 443 n n 
C46 H461 PGT sing 444 n n 
C46 H462 PGT sing 445 n n 
C45 C44 PGT sing 446 n n 
C45 H451 PGT sing 447 n n 
C45 H452 PGT sing 448 n n 
C44 C43 PGT sing 449 n n 
C44 H441 PGT sing 450 n n 
C44 H442 PGT sing 451 n n 
C43 C42 PGT sing 452 n n 
C43 H431 PGT sing 453 n n 
C43 H432 PGT sing 454 n n 
C42 C41 PGT sing 455 n n 
C42 H421 PGT sing 456 n n 
C42 H422 PGT sing 457 n n 
C41 C40 PGT sing 458 n n 
C41 H411 PGT sing 459 n n 
C41 H412 PGT sing 460 n n 
C40 C39 PGT sing 461 n n 
C40 H401 PGT sing 462 n n 
C40 H402 PGT sing 463 n n 
C39 C38 PGT sing 464 n n 
C39 H391 PGT sing 465 n n 
C39 H392 PGT sing 466 n n 
C38 C37 PGT sing 467 n n 
C38 H381 PGT sing 468 n n 
C38 H382 PGT sing 469 n n 
C37 C36 PGT sing 470 n n 
C37 H371 PGT sing 471 n n 
C37 H372 PGT sing 472 n n 
C36 C35 PGT sing 473 n n 
C36 H361 PGT sing 474 n n 
C36 H362 PGT sing 475 n n 
C35 C34 PGT sing 476 n n 
C35 H351 PGT sing 477 n n 
C35 H352 PGT sing 478 n n 
C34 C33 PGT sing 479 n n 
C34 H341 PGT sing 480 n n 
C34 H342 PGT sing 481 n n 
C33 C32 PGT sing 482 n n 
C33 H331 PGT sing 483 n n 
C33 H332 PGT sing 484 n n 
C32 C31 PGT sing 485 n n 
C32 H321 PGT sing 486 n n 
C32 H322 PGT sing 487 n n 
C31 O31 PGT doub 488 n n 
C31 O2 PGT sing 489 n n 
O2 C2 PGT sing 490 n n 
C2 C1 PGT sing 491 n n 
C2 C3 PGT sing 492 n n 
C2 H2 PGT sing 493 n n 
C1 O3P PGT sing 494 n n 
C1 H11 PGT sing 495 n n 
C1 H12 PGT sing 496 n n 
O3P P PGT sing 497 n n 
P O1P PGT doub 498 n n 
P O2P PGT sing 499 n n 
P O4P PGT sing 500 n n 
O2P HO2P PGT sing 501 n n 
O4P C4 PGT sing 502 n n 
C4 C5 PGT sing 503 n n 
C4 H41 PGT sing 504 n n 
C4 H42 PGT sing 505 n n 
C5 O5 PGT sing 506 n n 
C5 C6 PGT sing 507 n n 
C5 H5 PGT sing 508 n n 
O5 HO5 PGT sing 509 n n 
C6 O6 PGT sing 510 n n 
C6 H61 PGT sing 511 n n 
C6 H62 PGT sing 512 n n 
O6 HO6 PGT sing 513 n n 
C3 O3 PGT sing 514 n n 
C3 H31 PGT sing 515 n n 
C3 H32 PGT sing 516 n n 
O3 C11 PGT sing 517 n n 
C11 O11 PGT doub 518 n n 
C11 C12 PGT sing 519 n n 
C12 C13 PGT sing 520 n n 
C12 H121 PGT sing 521 n n 
C12 H122 PGT sing 522 n n 
C13 C14 PGT sing 523 n n 
C13 H131 PGT sing 524 n n 
C13 H132 PGT sing 525 n n 
C14 C15 PGT sing 526 n n 
C14 H141 PGT sing 527 n n 
C14 H142 PGT sing 528 n n 
C15 C16 PGT sing 529 n n 
C15 H151 PGT sing 530 n n 
C15 H152 PGT sing 531 n n 
C16 C17 PGT sing 532 n n 
C16 H161 PGT sing 533 n n 
C16 H162 PGT sing 534 n n 
C17 C18 PGT sing 535 n n 
C17 H171 PGT sing 536 n n 
C17 H172 PGT sing 537 n n 
C18 C19 PGT sing 538 n n 
C18 H181 PGT sing 539 n n 
C18 H182 PGT sing 540 n n 
C19 C20 PGT sing 541 n n 
C19 H191 PGT sing 542 n n 
C19 H192 PGT sing 543 n n 
C20 C21 PGT sing 544 n n 
C20 H201 PGT sing 545 n n 
C20 H202 PGT sing 546 n n 
C21 C22 PGT sing 547 n n 
C21 H211 PGT sing 548 n n 
C21 H212 PGT sing 549 n n 
C22 C23 PGT sing 550 n n 
C22 H221 PGT sing 551 n n 
C22 H222 PGT sing 552 n n 
C23 C24 PGT sing 553 n n 
C23 H231 PGT sing 554 n n 
C23 H232 PGT sing 555 n n 
C24 C25 PGT sing 556 n n 
C24 H241 PGT sing 557 n n 
C24 H242 PGT sing 558 n n 
C25 C26 PGT sing 559 n n 
C25 H251 PGT sing 560 n n 
C25 H252 PGT sing 561 n n 
C26 H261 PGT sing 562 n n 
C26 H262 PGT sing 563 n n 
C26 H263 PGT sing 564 n n 
#
_atom_sites.entry_id                     8JF2 
_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
I 3 PGT A 1 601 601 PGT PGT . 
J 4 LMT A 1 602 5 LMT LMT . 
K 4 LMT A 1 603 17 LMT LMT . 
L 4 LMT A 1 604 18 LMT LMT . 
M 4 LMT A 1 605 19 LMT LMT . 
N 5 DGA B 1 501 603 DGA DGA . 
O 3 PGT B 1 502 502 PGT PGT . 
P 4 LMT B 1 503 2 LMT LMT . 
Q 4 LMT B 1 504 4 LMT LMT . 
R 4 LMT B 1 505 11 LMT LMT . 
S 4 LMT B 1 506 12 LMT LMT . 
T 4 LMT B 1 507 13 LMT LMT . 
U 4 LMT B 1 508 14 LMT LMT . 
V 4 LMT B 1 509 21 LMT LMT . 
W 4 LMT B 1 510 23 LMT LMT . 
X 3 PGT B 1 511 114 PGT PGT . 
Y 3 PGT C 1 501 502 PGT PGT . 
Z 5 DGA C 1 502 505 DGA DGA . 
AA 4 LMT C 1 503 9 LMT LMT . 
BA 4 LMT C 1 504 10 LMT LMT . 
CA 4 LMT C 1 505 16 LMT LMT . 
DA 4 LMT C 1 506 20 LMT LMT . 
EA 4 LMT C 1 507 22 LMT LMT . 
FA 4 LMT C 1 508 25 LMT LMT . 
GA 3 PGT C 1 509 115 PGT PGT . 
HA 3 PGT D 1 601 601 PGT PGT . 
IA 4 LMT D 1 602 1 LMT LMT . 
JA 4 LMT D 1 603 3 LMT LMT . 
KA 4 LMT D 1 604 6 LMT LMT . 
LA 4 LMT D 1 605 7 LMT LMT . 
MA 4 LMT D 1 606 8 LMT LMT . 
NA 4 LMT D 1 607 15 LMT LMT . 
OA 4 LMT D 1 608 24 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 C48 PGT . . . O 3 191.577 149.741 124.415 1 89.84 ? C48 PGT 502 B 1 
HETATM 2 C C47 PGT . . . O 3 190.349 148.877 124.161 1 89.84 ? C47 PGT 502 B 1 
HETATM 3 C C46 PGT . . . O 3 189.627 148.475 125.441 1 89.84 ? C46 PGT 502 B 1 
HETATM 4 C C45 PGT . . . O 3 188.379 149.303 125.72 1 89.84 ? C45 PGT 502 B 1 
HETATM 5 C C44 PGT . . . O 3 187.165 148.848 124.921 1 89.84 ? C44 PGT 502 B 1 
HETATM 6 C C43 PGT . . . O 3 185.867 149.526 125.345 1 89.84 ? C43 PGT 502 B 1 
HETATM 7 C C42 PGT . . . O 3 185.741 150.961 124.848 1 89.84 ? C42 PGT 502 B 1 
HETATM 8 C C41 PGT . . . O 3 184.385 151.591 125.144 1 89.84 ? C41 PGT 502 B 1 
HETATM 9 C C40 PGT . . . O 3 184.161 151.884 126.621 1 89.84 ? C40 PGT 502 B 1 
HETATM 10 C C39 PGT . . . O 3 182.863 152.629 126.887 1 89.84 ? C39 PGT 502 B 1 
HETATM 11 C C38 PGT . . . O 3 181.656 151.715 127.026 1 89.84 ? C38 PGT 502 B 1 
HETATM 12 C C37 PGT . . . O 3 180.346 152.482 127.08 1 89.84 ? C37 PGT 502 B 1 
HETATM 13 C C36 PGT . . . O 3 179.234 151.72 127.782 1 89.84 ? C36 PGT 502 B 1 
HETATM 14 C C35 PGT . . . O 3 179.515 151.529 129.262 1 89.84 ? C35 PGT 502 B 1 
HETATM 15 C C34 PGT . . . O 3 178.525 150.611 129.962 1 89.84 ? C34 PGT 502 B 1 
HETATM 16 C C33 PGT . . . O 3 178.94 150.322 131.397 1 89.84 ? C33 PGT 502 B 1 
HETATM 17 C C32 PGT . . . O 3 178.108 149.214 132.013 1 89.84 ? C32 PGT 502 B 1 
HETATM 18 C C31 PGT . . . O 3 178.828 147.898 132.101 1 89.84 ? C31 PGT 502 B 1 
HETATM 19 O O31 PGT . . . O 3 179.992 147.742 131.832 1 89.84 ? O31 PGT 502 B 1 
HETATM 20 O O2 PGT . . . O 3 178.036 146.909 132.526 1 89.84 ? O2 PGT 502 B 1 
HETATM 21 C C2 PGT . . . O 3 176.617 146.935 132.311 1 89.84 ? C2 PGT 502 B 1 
HETATM 22 C C1 PGT . . . O 3 175.87 146.758 133.616 1 89.84 ? C1 PGT 502 B 1 
HETATM 23 O O3P PGT . . . O 3 176.216 147.751 134.545 1 89.84 ? O3P PGT 502 B 1 
HETATM 24 P P PGT . . . O 3 176.572 147.29 136.073 1 89.84 ? P PGT 502 B 1 
HETATM 25 O O1P PGT . . . O 3 176.559 148.477 136.983 1 89.84 ? O1P PGT 502 B 1 
HETATM 26 O O2P PGT . . . O 3 175.772 146.085 136.449 1 89.84 ? O2P PGT 502 B 1 
HETATM 27 O O4P PGT . . . O 3 178.117 146.893 135.687 1 89.84 ? O4P PGT 502 B 1 
HETATM 28 C C4 PGT . . . O 3 179.052 147.93 135.485 1 89.84 ? C4 PGT 502 B 1 
HETATM 29 C C5 PGT . . . O 3 179.751 148.261 136.798 1 89.84 ? C5 PGT 502 B 1 
HETATM 30 O O5 PGT . . . O 3 178.902 148.921 137.706 1 89.84 ? O5 PGT 502 B 1 
HETATM 31 C C6 PGT . . . O 3 181.016 149.058 136.53 1 89.84 ? C6 PGT 502 B 1 
HETATM 32 O O6 PGT . . . O 3 181.103 150.102 137.467 1 89.84 ? O6 PGT 502 B 1 
HETATM 33 C C3 PGT . . . O 3 176.283 145.904 131.263 1 89.84 ? C3 PGT 502 B 1 
HETATM 34 O O3 PGT . . . O 3 175.995 146.549 130.036 1 89.84 ? O3 PGT 502 B 1 
HETATM 35 C C11 PGT . . . O 3 174.768 146.439 129.558 1 89.84 ? C11 PGT 502 B 1 
HETATM 36 O O11 PGT . . . O 3 173.832 146.065 130.215 1 89.84 ? O11 PGT 502 B 1 
HETATM 37 C C12 PGT . . . O 3 174.718 146.837 128.117 1 89.84 ? C12 PGT 502 B 1 
HETATM 38 C C13 PGT . . . O 3 176.088 146.747 127.472 1 89.84 ? C13 PGT 502 B 1 
HETATM 39 C C14 PGT . . . O 3 176.152 147.504 126.159 1 89.84 ? C14 PGT 502 B 1 
HETATM 40 C C15 PGT . . . O 3 177.572 147.855 125.754 1 89.84 ? C15 PGT 502 B 1 
HETATM 41 C C16 PGT . . . O 3 177.607 148.926 124.679 1 89.84 ? C16 PGT 502 B 1 
HETATM 42 C C17 PGT . . . O 3 178.989 149.116 124.077 1 89.84 ? C17 PGT 502 B 1 
HETATM 43 C C18 PGT . . . O 3 178.993 150.078 122.902 1 89.84 ? C18 PGT 502 B 1 
HETATM 44 C C19 PGT . . . O 3 180.393 150.377 122.397 1 89.84 ? C19 PGT 502 B 1 
HETATM 45 C C20 PGT . . . O 3 181.206 149.121 122.144 1 89.84 ? C20 PGT 502 B 1 
HETATM 46 C C21 PGT . . . O 3 182.696 149.402 122.038 1 89.84 ? C21 PGT 502 B 1 
HETATM 47 C C22 PGT . . . O 3 183.019 150.524 121.061 1 89.84 ? C22 PGT 502 B 1 
HETATM 48 C C23 PGT . . . O 3 182.651 150.2 119.619 1 89.84 ? C23 PGT 502 B 1 
HETATM 49 C C24 PGT . . . O 3 183.821 150.33 118.657 1 89.84 ? C24 PGT 502 B 1 
HETATM 50 C C25 PGT . . . O 3 183.66 151.491 117.69 1 89.84 ? C25 PGT 502 B 1 
HETATM 51 C C26 PGT . . . O 3 182.322 151.455 116.972 1 89.84 ? C26 PGT 502 B 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           51 
#