data_6YE4
#
_model_server_result.job_id            RyaMqtt5zUdDgz1bWJ7t0A 
_model_server_result.datetime_utc      '2025-03-06 09:42:46' 
_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          6ye4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":301}' 
#
_entry.id    6YE4 
#
_exptl.entry_id    6YE4 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              751.023 
_entity.id                          2 
_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    5 
_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            6YE4 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YE4 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J 
_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
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J 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 222 n n 
C48 H481 PGT sing 223 n n 
C48 H482 PGT sing 224 n n 
C48 H483 PGT sing 225 n n 
C47 C46 PGT sing 226 n n 
C47 H471 PGT sing 227 n n 
C47 H472 PGT sing 228 n n 
C46 C45 PGT sing 229 n n 
C46 H461 PGT sing 230 n n 
C46 H462 PGT sing 231 n n 
C45 C44 PGT sing 232 n n 
C45 H451 PGT sing 233 n n 
C45 H452 PGT sing 234 n n 
C44 C43 PGT sing 235 n n 
C44 H441 PGT sing 236 n n 
C44 H442 PGT sing 237 n n 
C43 C42 PGT sing 238 n n 
C43 H431 PGT sing 239 n n 
C43 H432 PGT sing 240 n n 
C42 C41 PGT sing 241 n n 
C42 H421 PGT sing 242 n n 
C42 H422 PGT sing 243 n n 
C41 C40 PGT sing 244 n n 
C41 H411 PGT sing 245 n n 
C41 H412 PGT sing 246 n n 
C40 C39 PGT sing 247 n n 
C40 H401 PGT sing 248 n n 
C40 H402 PGT sing 249 n n 
C39 C38 PGT sing 250 n n 
C39 H391 PGT sing 251 n n 
C39 H392 PGT sing 252 n n 
C38 C37 PGT sing 253 n n 
C38 H381 PGT sing 254 n n 
C38 H382 PGT sing 255 n n 
C37 C36 PGT sing 256 n n 
C37 H371 PGT sing 257 n n 
C37 H372 PGT sing 258 n n 
C36 C35 PGT sing 259 n n 
C36 H361 PGT sing 260 n n 
C36 H362 PGT sing 261 n n 
C35 C34 PGT sing 262 n n 
C35 H351 PGT sing 263 n n 
C35 H352 PGT sing 264 n n 
C34 C33 PGT sing 265 n n 
C34 H341 PGT sing 266 n n 
C34 H342 PGT sing 267 n n 
C33 C32 PGT sing 268 n n 
C33 H331 PGT sing 269 n n 
C33 H332 PGT sing 270 n n 
C32 C31 PGT sing 271 n n 
C32 H321 PGT sing 272 n n 
C32 H322 PGT sing 273 n n 
C31 O31 PGT doub 274 n n 
C31 O2 PGT sing 275 n n 
O2 C2 PGT sing 276 n n 
C2 C1 PGT sing 277 n n 
C2 C3 PGT sing 278 n n 
C2 H2 PGT sing 279 n n 
C1 O3P PGT sing 280 n n 
C1 H11 PGT sing 281 n n 
C1 H12 PGT sing 282 n n 
O3P P PGT sing 283 n n 
P O1P PGT doub 284 n n 
P O2P PGT sing 285 n n 
P O4P PGT sing 286 n n 
O2P HO2P PGT sing 287 n n 
O4P C4 PGT sing 288 n n 
C4 C5 PGT sing 289 n n 
C4 H41 PGT sing 290 n n 
C4 H42 PGT sing 291 n n 
C5 O5 PGT sing 292 n n 
C5 C6 PGT sing 293 n n 
C5 H5 PGT sing 294 n n 
O5 HO5 PGT sing 295 n n 
C6 O6 PGT sing 296 n n 
C6 H61 PGT sing 297 n n 
C6 H62 PGT sing 298 n n 
O6 HO6 PGT sing 299 n n 
C3 O3 PGT sing 300 n n 
C3 H31 PGT sing 301 n n 
C3 H32 PGT sing 302 n n 
O3 C11 PGT sing 303 n n 
C11 O11 PGT doub 304 n n 
C11 C12 PGT sing 305 n n 
C12 C13 PGT sing 306 n n 
C12 H121 PGT sing 307 n n 
C12 H122 PGT sing 308 n n 
C13 C14 PGT sing 309 n n 
C13 H131 PGT sing 310 n n 
C13 H132 PGT sing 311 n n 
C14 C15 PGT sing 312 n n 
C14 H141 PGT sing 313 n n 
C14 H142 PGT sing 314 n n 
C15 C16 PGT sing 315 n n 
C15 H151 PGT sing 316 n n 
C15 H152 PGT sing 317 n n 
C16 C17 PGT sing 318 n n 
C16 H161 PGT sing 319 n n 
C16 H162 PGT sing 320 n n 
C17 C18 PGT sing 321 n n 
C17 H171 PGT sing 322 n n 
C17 H172 PGT sing 323 n n 
C18 C19 PGT sing 324 n n 
C18 H181 PGT sing 325 n n 
C18 H182 PGT sing 326 n n 
C19 C20 PGT sing 327 n n 
C19 H191 PGT sing 328 n n 
C19 H192 PGT sing 329 n n 
C20 C21 PGT sing 330 n n 
C20 H201 PGT sing 331 n n 
C20 H202 PGT sing 332 n n 
C21 C22 PGT sing 333 n n 
C21 H211 PGT sing 334 n n 
C21 H212 PGT sing 335 n n 
C22 C23 PGT sing 336 n n 
C22 H221 PGT sing 337 n n 
C22 H222 PGT sing 338 n n 
C23 C24 PGT sing 339 n n 
C23 H231 PGT sing 340 n n 
C23 H232 PGT sing 341 n n 
C24 C25 PGT sing 342 n n 
C24 H241 PGT sing 343 n n 
C24 H242 PGT sing 344 n n 
C25 C26 PGT sing 345 n n 
C25 H251 PGT sing 346 n n 
C25 H252 PGT sing 347 n n 
C26 H261 PGT sing 348 n n 
C26 H262 PGT sing 349 n n 
C26 H263 PGT sing 350 n n 
#
_atom_sites.entry_id                     6YE4 
_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
F 2 PGT A 1 301 301 PGT PGT . 
G 2 PGT B 1 301 301 PGT PGT . 
H 2 PGT C 1 301 301 PGT PGT . 
I 2 PGT D 1 301 301 PGT PGT . 
J 2 PGT E 1 301 301 PGT PGT . 
#
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 C43 PGT . . . H 2 168.596 154.649 160.875 1 46.1 ? C43 PGT 301 C 1 
HETATM 2 C C42 PGT . . . H 2 169.606 154.114 159.883 1 46.1 ? C42 PGT 301 C 1 
HETATM 3 C C41 PGT . . . H 2 169.072 154.462 158.521 1 46.1 ? C41 PGT 301 C 1 
HETATM 4 C C40 PGT . . . H 2 169.914 153.741 157.499 1 46.1 ? C40 PGT 301 C 1 
HETATM 5 C C39 PGT . . . H 2 169.119 153.832 156.227 1 46.1 ? C39 PGT 301 C 1 
HETATM 6 C C38 PGT . . . H 2 169.535 152.649 155.426 1 46.1 ? C38 PGT 301 C 1 
HETATM 7 C C37 PGT . . . H 2 168.441 152.384 154.426 1 46.1 ? C37 PGT 301 C 1 
HETATM 8 C C36 PGT . . . H 2 168.482 153.227 153.169 1 46.1 ? C36 PGT 301 C 1 
HETATM 9 C C35 PGT . . . H 2 169.885 153.139 152.618 1 46.1 ? C35 PGT 301 C 1 
HETATM 10 C C34 PGT . . . H 2 169.832 153.562 151.177 1 46.1 ? C34 PGT 301 C 1 
HETATM 11 C C33 PGT . . . H 2 171.174 154.047 150.675 1 46.1 ? C33 PGT 301 C 1 
HETATM 12 C C32 PGT . . . H 2 172.271 153.018 150.806 1 46.1 ? C32 PGT 301 C 1 
HETATM 13 C C31 PGT . . . H 2 172.278 152.122 149.6 1 46.1 ? C31 PGT 301 C 1 
HETATM 14 O O31 PGT . . . H 2 172.39 150.986 149.814 1 46.1 ? O31 PGT 301 C 1 
HETATM 15 O O2 PGT . . . H 2 172.109 152.546 148.275 1 46.1 ? O2 PGT 301 C 1 
HETATM 16 C C2 PGT . . . H 2 173.2 152.962 147.477 1 46.1 ? C2 PGT 301 C 1 
HETATM 17 C C1 PGT . . . H 2 172.61 153.63 146.236 1 46.1 ? C1 PGT 301 C 1 
HETATM 18 O O3P PGT . . . H 2 173.09 153.074 145.047 1 46.1 ? O3P PGT 301 C 1 
HETATM 19 P P PGT . . . H 2 173.428 154.085 143.783 1 46.1 ? P PGT 301 C 1 
HETATM 20 O O1P PGT . . . H 2 172.637 155.354 143.947 1 46.1 ? O1P PGT 301 C 1 
HETATM 21 O O2P PGT . . . H 2 173.043 153.469 142.465 1 46.1 ? O2P PGT 301 C 1 
HETATM 22 O O4P PGT . . . H 2 175.05 154.392 143.741 1 46.1 ? O4P PGT 301 C 1 
HETATM 23 C C4 PGT . . . H 2 175.525 155.711 143.715 1 46.1 ? C4 PGT 301 C 1 
HETATM 24 C C5 PGT . . . H 2 176.18 156.182 145.011 1 46.1 ? C5 PGT 301 C 1 
HETATM 25 O O5 PGT . . . H 2 177.549 156.163 144.764 1 46.1 ? O5 PGT 301 C 1 
HETATM 26 C C6 PGT . . . H 2 175.903 155.265 146.194 1 46.1 ? C6 PGT 301 C 1 
HETATM 27 O O6 PGT . . . H 2 175.638 156.017 147.341 1 46.1 ? O6 PGT 301 C 1 
HETATM 28 C C3 PGT . . . H 2 174.191 151.851 147.081 1 46.1 ? C3 PGT 301 C 1 
HETATM 29 O O3 PGT . . . H 2 174.899 151.46 148.231 1 46.1 ? O3 PGT 301 C 1 
HETATM 30 C C11 PGT . . . H 2 175.705 150.325 148.162 1 46.1 ? C11 PGT 301 C 1 
HETATM 31 O O11 PGT . . . H 2 176.363 150.086 147.216 1 46.1 ? O11 PGT 301 C 1 
HETATM 32 C C12 PGT . . . H 2 175.555 149.341 149.31 1 46.1 ? C12 PGT 301 C 1 
HETATM 33 C C13 PGT . . . H 2 176.103 149.842 150.625 1 46.1 ? C13 PGT 301 C 1 
HETATM 34 C C14 PGT . . . H 2 175.324 149.111 151.702 1 46.1 ? C14 PGT 301 C 1 
HETATM 35 C C15 PGT . . . H 2 176.172 148.884 152.934 1 46.1 ? C15 PGT 301 C 1 
HETATM 36 C C16 PGT . . . H 2 175.324 148.416 154.109 1 46.1 ? C16 PGT 301 C 1 
HETATM 37 C C17 PGT . . . H 2 176.239 147.677 155.059 1 46.1 ? C17 PGT 301 C 1 
HETATM 38 C C18 PGT . . . H 2 175.692 147.649 156.477 1 46.1 ? C18 PGT 301 C 1 
HETATM 39 C C19 PGT . . . H 2 174.231 147.308 156.6 1 46.1 ? C19 PGT 301 C 1 
HETATM 40 C C20 PGT . . . H 2 173.925 147.229 158.083 1 46.1 ? C20 PGT 301 C 1 
HETATM 41 C C21 PGT . . . H 2 172.421 147.108 158.174 1 46.1 ? C21 PGT 301 C 1 
HETATM 42 C C22 PGT . . . H 2 171.886 146.845 159.568 1 46.1 ? C22 PGT 301 C 1 
HETATM 43 C C23 PGT . . . H 2 172.222 147.979 160.495 1 46.1 ? C23 PGT 301 C 1 
HETATM 44 C C24 PGT . . . H 2 171.518 147.695 161.81 1 46.1 ? C24 PGT 301 C 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           44 
#