data_6VXZ
#
_model_server_result.job_id            Wh5zbfkaNKiajvA0KDhcyQ 
_model_server_result.datetime_utc      '2025-08-31 08:13:27' 
_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          6vxz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"EA","auth_seq_id":506}' 
#
_entry.id    6VXZ 
#
_exptl.entry_id    6VXZ 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              749.007 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate' 
_entity.pdbx_number_of_molecules    24 
_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            6VXZ 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VXZ 
_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 
_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 G N N 
? 3 H N N 
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 M N N 
? 3 N N N 
? 3 O N N 
? 3 P N N 
? 3 Q N N 
? 3 R N N 
? 3 T N N 
? 3 U N N 
? 3 V N N 
? 3 W N N 
? 3 X N N 
? 3 Y N N 
? 3 AA N N 
? 3 BA N N 
? 3 CA N N 
? 3 DA N N 
? 3 EA N N 
? 3 FA N N 
#
_chem_comp.formula           'C40 H77 O10 P' 
_chem_comp.formula_weight    749.007 
_chem_comp.id                PGW 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)];PHOSPHATIDYLGLYCEROL 
#
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
CAD C05 PGW sing 272 n n 
CAD HAD PGW sing 273 n n 
CAD HADA PGW sing 274 n n 
OAE CAD PGW sing 275 n n 
OAE HOAE PGW sing 276 n n 
OAF C05 PGW sing 277 n n 
OAF HOAF PGW sing 278 n n 
P O13 PGW sing 279 n n 
P O11 PGW sing 280 n n 
C01 O03 PGW sing 281 n n 
C01 C02 PGW sing 282 n n 
C01 H01 PGW sing 283 n n 
C01 H01A PGW sing 284 n n 
C1 C2 PGW sing 285 n n 
O01 C1 PGW sing 286 n n 
C02 O01 PGW sing 287 n n 
C02 H02 PGW sing 288 n n 
C2 C3 PGW sing 289 n n 
C2 H2 PGW sing 290 n n 
C2 H2A PGW sing 291 n n 
O02 C1 PGW doub 292 n n 
C03 C02 PGW sing 293 n n 
C03 H03 PGW sing 294 n n 
C03 H03A PGW sing 295 n n 
C3 C4 PGW sing 296 n n 
C3 H3 PGW sing 297 n n 
C3 H3A PGW sing 298 n n 
C04 C05 PGW sing 299 n n 
C04 O12 PGW sing 300 n n 
C04 H04 PGW sing 301 n n 
C04 H04A PGW sing 302 n n 
C4 C5 PGW sing 303 n n 
C4 H4 PGW sing 304 n n 
C4 H4A PGW sing 305 n n 
O04 C19 PGW doub 306 n n 
C05 H05 PGW sing 307 n n 
C5 C6 PGW sing 308 n n 
C5 H5 PGW sing 309 n n 
C5 H5A PGW sing 310 n n 
C06 C07 PGW sing 311 n n 
C06 H06 PGW sing 312 n n 
C06 H06A PGW sing 313 n n 
C6 C7 PGW sing 314 n n 
C6 H6 PGW sing 315 n n 
C6 H6A PGW sing 316 n n 
C07 H07 PGW sing 317 n n 
C07 H07A PGW sing 318 n n 
C7 C8 PGW sing 319 n n 
C7 H7 PGW sing 320 n n 
C7 H7A PGW sing 321 n n 
C08 C07 PGW sing 322 n n 
C08 H08 PGW sing 323 n n 
C08 H08A PGW sing 324 n n 
C8 C9 PGW sing 325 n n 
C8 H8 PGW sing 326 n n 
C8 H8A PGW sing 327 n n 
C09 C08 PGW sing 328 n n 
C09 C11 PGW sing 329 n n 
C09 H09 PGW sing 330 n n 
C09 H09A PGW sing 331 n n 
C9 C10 PGW doub 332 z n 
C10 C06 PGW sing 333 n n 
C11 H11 PGW sing 334 n n 
C11 H11A PGW sing 335 n n 
O11 C03 PGW sing 336 n n 
C12 C11 PGW sing 337 n n 
C12 H12 PGW sing 338 n n 
C12 H12A PGW sing 339 n n 
O12 P PGW sing 340 n n 
C13 C12 PGW sing 341 n n 
C13 C14 PGW sing 342 n n 
C13 H13 PGW sing 343 n n 
C13 H13A PGW sing 344 n n 
O13 HO13 PGW sing 345 n n 
C14 H14 PGW sing 346 n n 
C14 H14A PGW sing 347 n n 
C14 H14B PGW sing 348 n n 
O14 P PGW doub 349 n n 
C15 C16 PGW sing 350 n n 
C15 H15 PGW sing 351 n n 
C15 H15A PGW sing 352 n n 
C16 H16 PGW sing 353 n n 
C16 H16A PGW sing 354 n n 
C17 C16 PGW sing 355 n n 
C17 C18 PGW sing 356 n n 
C17 H17 PGW sing 357 n n 
C17 H17A PGW sing 358 n n 
C18 C28 PGW sing 359 n n 
C18 H18 PGW sing 360 n n 
C18 H18A PGW sing 361 n n 
C19 O03 PGW sing 362 n n 
C19 C20 PGW sing 363 n n 
C20 C21 PGW sing 364 n n 
C20 H20 PGW sing 365 n n 
C20 H20A PGW sing 366 n n 
C21 C22 PGW sing 367 n n 
C21 H21 PGW sing 368 n n 
C21 H21A PGW sing 369 n n 
C22 C23 PGW sing 370 n n 
C22 H22 PGW sing 371 n n 
C22 H22A PGW sing 372 n n 
C23 C24 PGW sing 373 n n 
C23 H23 PGW sing 374 n n 
C23 H23A PGW sing 375 n n 
C24 C25 PGW sing 376 n n 
C24 H24 PGW sing 377 n n 
C24 H24A PGW sing 378 n n 
C25 C26 PGW sing 379 n n 
C25 H25 PGW sing 380 n n 
C25 H25A PGW sing 381 n n 
C26 C27 PGW sing 382 n n 
C26 H26 PGW sing 383 n n 
C26 H26A PGW sing 384 n n 
C27 C15 PGW sing 385 n n 
C27 H27 PGW sing 386 n n 
C27 H27A PGW sing 387 n n 
C28 H28 PGW sing 388 n n 
C28 H28A PGW sing 389 n n 
C29 H29 PGW sing 390 n n 
C29 H29A PGW sing 391 n n 
C29 H29B PGW sing 392 n n 
C30 C28 PGW sing 393 n n 
C30 C29 PGW sing 394 n n 
C30 H30 PGW sing 395 n n 
C30 H30A PGW sing 396 n n 
C9 H9 PGW sing 397 n n 
C10 H10 PGW sing 398 n n 
#
_atom_sites.entry_id                     6VXZ 
_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 1 501 501 CMP CMP . 
F 3 PGW A 1 502 502 PGW PGW . 
G 3 PGW A 1 503 503 PGW PGW . 
H 3 PGW A 1 504 504 PGW PGW . 
I 3 PGW A 1 505 505 PGW PGW . 
J 3 PGW A 1 506 506 PGW PGW . 
K 3 PGW A 1 507 507 PGW PGW . 
L 2 CMP B 1 501 501 CMP CMP . 
M 3 PGW B 1 502 502 PGW PGW . 
N 3 PGW B 1 503 503 PGW PGW . 
O 3 PGW B 1 504 504 PGW PGW . 
P 3 PGW B 1 505 505 PGW PGW . 
Q 3 PGW B 1 506 506 PGW PGW . 
R 3 PGW B 1 507 507 PGW PGW . 
S 2 CMP C 1 501 501 CMP CMP . 
T 3 PGW C 1 502 502 PGW PGW . 
U 3 PGW C 1 503 503 PGW PGW . 
V 3 PGW C 1 504 504 PGW PGW . 
W 3 PGW C 1 505 505 PGW PGW . 
X 3 PGW C 1 506 506 PGW PGW . 
Y 3 PGW C 1 507 507 PGW PGW . 
Z 2 CMP D 1 501 501 CMP CMP . 
AA 3 PGW D 1 502 502 PGW PGW . 
BA 3 PGW D 1 503 503 PGW PGW . 
CA 3 PGW D 1 504 504 PGW PGW . 
DA 3 PGW D 1 505 505 PGW PGW . 
EA 3 PGW D 1 506 506 PGW PGW . 
FA 3 PGW D 1 507 507 PGW PGW . 
#
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 P PGW . . . EA 3 136.499 126.397 140.267 1 33.13 ? P PGW 506 D 1 
HETATM 2 C C01 PGW . . . EA 3 135.768 123.174 142.979 1 33.13 ? C01 PGW 506 D 1 
HETATM 3 C C1 PGW . . . EA 3 134.972 125.008 144.699 1 33.13 ? C1 PGW 506 D 1 
HETATM 4 O O01 PGW . . . EA 3 134.259 125 143.562 1 33.13 ? O01 PGW 506 D 1 
HETATM 5 C C02 PGW . . . EA 3 134.566 123.99 142.559 1 33.13 ? C02 PGW 506 D 1 
HETATM 6 C C2 PGW . . . EA 3 134.131 124.745 145.916 1 33.13 ? C2 PGW 506 D 1 
HETATM 7 O O02 PGW . . . EA 3 136.156 125.212 144.713 1 33.13 ? O02 PGW 506 D 1 
HETATM 8 C C03 PGW . . . EA 3 134.741 124.675 141.223 1 33.13 ? C03 PGW 506 D 1 
HETATM 9 C C3 PGW . . . EA 3 134.937 124.479 147.148 1 33.13 ? C3 PGW 506 D 1 
HETATM 10 O O03 PGW . . . EA 3 135.438 121.774 142.851 1 33.13 ? O03 PGW 506 D 1 
HETATM 11 C C4 PGW . . . EA 3 134.736 123.072 147.686 1 33.13 ? C4 PGW 506 D 1 
HETATM 12 O O04 PGW . . . EA 3 137.32 120.582 142.858 1 33.13 ? O04 PGW 506 D 1 
HETATM 13 C C5 PGW . . . EA 3 135.94 122.504 148.395 1 33.13 ? C5 PGW 506 D 1 
HETATM 14 C C6 PGW . . . EA 3 135.972 122.774 149.878 1 33.13 ? C6 PGW 506 D 1 
HETATM 15 C C7 PGW . . . EA 3 136.604 121.662 150.703 1 33.13 ? C7 PGW 506 D 1 
HETATM 16 C C8 PGW . . . EA 3 137.098 122.095 152.048 1 33.13 ? C8 PGW 506 D 1 
HETATM 17 C C9 PGW . . . EA 3 138.265 123.03 151.974 1 33.13 ? C9 PGW 506 D 1 
HETATM 18 C C10 PGW . . . EA 3 139.432 122.845 152.535 1 33.13 ? C10 PGW 506 D 1 
HETATM 19 O O11 PGW . . . EA 3 136.135 125.054 141.066 1 33.13 ? O11 PGW 506 D 1 
HETATM 20 O O12 PGW . . . EA 3 135.063 127.078 140.034 1 33.13 ? O12 PGW 506 D 1 
HETATM 21 O O13 PGW . . . EA 3 137.045 126.011 138.92 1 33.13 ? O13 PGW 506 D 1 
HETATM 22 O O14 PGW . . . EA 3 137.308 127.277 141.18 1 33.13 ? O14 PGW 506 D 1 
HETATM 23 C C15 PGW . . . EA 3 139.581 117.8 152.202 1 33.13 ? C15 PGW 506 D 1 
HETATM 24 C C16 PGW . . . EA 3 139.539 118.181 153.661 1 33.13 ? C16 PGW 506 D 1 
HETATM 25 C C19 PGW . . . EA 3 136.295 120.915 143.393 1 33.13 ? C19 PGW 506 D 1 
HETATM 26 C C20 PGW . . . EA 3 135.817 120.432 144.733 1 33.13 ? C20 PGW 506 D 1 
HETATM 27 C C21 PGW . . . EA 3 136.188 119.011 145.02 1 33.13 ? C21 PGW 506 D 1 
HETATM 28 C C22 PGW . . . EA 3 136.78 118.83 146.407 1 33.13 ? C22 PGW 506 D 1 
HETATM 29 C C23 PGW . . . EA 3 138.201 118.322 146.412 1 33.13 ? C23 PGW 506 D 1 
HETATM 30 C C24 PGW . . . EA 3 138.806 118.191 147.788 1 33.13 ? C24 PGW 506 D 1 
HETATM 31 C C25 PGW . . . EA 3 137.883 118.595 148.91 1 33.13 ? C25 PGW 506 D 1 
HETATM 32 C C26 PGW . . . EA 3 138.059 117.796 150.176 1 33.13 ? C26 PGW 506 D 1 
HETATM 33 C C27 PGW . . . EA 3 138.629 118.581 151.331 1 33.13 ? C27 PGW 506 D 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           33 
#