data_8YMC
#
_model_server_result.job_id            0ZyfP4gaxD3jY2kPfNXPng 
_model_server_result.datetime_utc      '2025-08-30 17:10:15' 
_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          8ymc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    8YMC 
#
_exptl.entry_id    8YMC 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              648.891 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE' 
_entity.pdbx_number_of_molecules    2 
_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            8YMC 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YMC 
_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_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H 
_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    x,y,z 
_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
? 4 G N N 
? 4 H N N 
#
_chem_comp.formula           'C35 H69 O8 P' 
_chem_comp.formula_weight    648.891 
_chem_comp.id                LPP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE;L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT;3-SN-PHOSPHATIDIC ACID;1,2-DIPALMITOYLDISODIUM 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
P1 O2 LPP sing 241 n n 
P1 O3 LPP doub 242 n n 
P1 O4 LPP sing 243 n n 
P1 O5 LPP sing 244 n n 
O2 HO2 LPP sing 245 n n 
O4 HO4 LPP sing 246 n n 
O5 C6 LPP sing 247 n n 
C6 C7 LPP sing 248 n n 
C6 HC61 LPP sing 249 n n 
C6 HC62 LPP sing 250 n n 
C7 C8 LPP sing 251 n n 
C7 O9 LPP sing 252 n n 
C7 HC7 LPP sing 253 n n 
C8 O27 LPP sing 254 n n 
C8 HC81 LPP sing 255 n n 
C8 HC82 LPP sing 256 n n 
O9 C11 LPP sing 257 n n 
O27 C29 LPP sing 258 n n 
C11 O10 LPP doub 259 n n 
C11 C12 LPP sing 260 n n 
C12 C13 LPP sing 261 n n 
C12 H121 LPP sing 262 n n 
C12 H122 LPP sing 263 n n 
C13 C14 LPP sing 264 n n 
C13 H131 LPP sing 265 n n 
C13 H132 LPP sing 266 n n 
C14 C15 LPP sing 267 n n 
C14 H141 LPP sing 268 n n 
C14 H142 LPP sing 269 n n 
C15 C16 LPP sing 270 n n 
C15 H151 LPP sing 271 n n 
C15 H152 LPP sing 272 n n 
C16 C17 LPP sing 273 n n 
C16 H161 LPP sing 274 n n 
C16 H162 LPP sing 275 n n 
C17 C18 LPP sing 276 n n 
C17 H171 LPP sing 277 n n 
C17 H172 LPP sing 278 n n 
C18 C19 LPP sing 279 n n 
C18 H181 LPP sing 280 n n 
C18 H182 LPP sing 281 n n 
C19 C20 LPP sing 282 n n 
C19 H191 LPP sing 283 n n 
C19 H192 LPP sing 284 n n 
C20 C21 LPP sing 285 n n 
C20 H201 LPP sing 286 n n 
C20 H202 LPP sing 287 n n 
C21 C22 LPP sing 288 n n 
C21 H211 LPP sing 289 n n 
C21 H212 LPP sing 290 n n 
C22 C23 LPP sing 291 n n 
C22 H221 LPP sing 292 n n 
C22 H222 LPP sing 293 n n 
C23 C24 LPP sing 294 n n 
C23 H231 LPP sing 295 n n 
C23 H232 LPP sing 296 n n 
C24 C25 LPP sing 297 n n 
C24 H241 LPP sing 298 n n 
C24 H242 LPP sing 299 n n 
C25 C26 LPP sing 300 n n 
C25 H251 LPP sing 301 n n 
C25 H252 LPP sing 302 n n 
C26 H261 LPP sing 303 n n 
C26 H262 LPP sing 304 n n 
C26 H263 LPP sing 305 n n 
C29 O28 LPP doub 306 n n 
C29 C30 LPP sing 307 n n 
C30 C31 LPP sing 308 n n 
C30 H301 LPP sing 309 n n 
C30 H302 LPP sing 310 n n 
C31 C32 LPP sing 311 n n 
C31 H311 LPP sing 312 n n 
C31 H312 LPP sing 313 n n 
C32 C33 LPP sing 314 n n 
C32 H321 LPP sing 315 n n 
C32 H322 LPP sing 316 n n 
C33 C34 LPP sing 317 n n 
C33 H331 LPP sing 318 n n 
C33 H332 LPP sing 319 n n 
C34 C35 LPP sing 320 n n 
C34 H341 LPP sing 321 n n 
C34 H342 LPP sing 322 n n 
C35 C36 LPP sing 323 n n 
C35 H351 LPP sing 324 n n 
C35 H352 LPP sing 325 n n 
C36 C37 LPP sing 326 n n 
C36 H361 LPP sing 327 n n 
C36 H362 LPP sing 328 n n 
C37 C38 LPP sing 329 n n 
C37 H371 LPP sing 330 n n 
C37 H372 LPP sing 331 n n 
C38 C39 LPP sing 332 n n 
C38 H381 LPP sing 333 n n 
C38 H382 LPP sing 334 n n 
C39 C40 LPP sing 335 n n 
C39 H391 LPP sing 336 n n 
C39 H392 LPP sing 337 n n 
C40 C41 LPP sing 338 n n 
C40 H401 LPP sing 339 n n 
C40 H402 LPP sing 340 n n 
C41 C42 LPP sing 341 n n 
C41 H411 LPP sing 342 n n 
C41 H412 LPP sing 343 n n 
C42 C43 LPP sing 344 n n 
C42 H421 LPP sing 345 n n 
C42 H422 LPP sing 346 n n 
C43 C44 LPP sing 347 n n 
C43 H431 LPP sing 348 n n 
C43 H432 LPP sing 349 n n 
C44 H441 LPP sing 350 n n 
C44 H442 LPP sing 351 n n 
C44 H443 LPP sing 352 n n 
#
_atom_sites.entry_id                     8YMC 
_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 3 ATP A 1 301 301 ATP ATP . 
F 3 ATP B 1 301 301 ATP ATP . 
G 4 LPP C 1 401 401 LPP LPP . 
H 4 LPP D 1 401 401 LPP LPP . 
#
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 P1 LPP . . . H 4 132.324 123.647 89.253 1 167.87 ? P1 LPP 401 D 1 
HETATM 2 O O2 LPP . . . H 4 132.87 122.417 89.937 1 157.95 ? O2 LPP 401 D 1 
HETATM 3 O O3 LPP . . . H 4 133.451 124.392 88.578 1 158.51 ? O3 LPP 401 D 1 
HETATM 4 O O4 LPP . . . H 4 131.302 123.236 88.219 1 155.48 ? O4 LPP 401 D 1 
HETATM 5 O O5 LPP . . . H 4 131.614 124.624 90.373 1 157.03 ? O5 LPP 401 D 1 
HETATM 6 C C6 LPP . . . H 4 130.388 124.229 90.916 1 154.6 ? C6 LPP 401 D 1 
HETATM 7 C C7 LPP . . . H 4 130.554 123.972 92.411 1 154.63 ? C7 LPP 401 D 1 
HETATM 8 C C8 LPP . . . H 4 131.419 125.071 93.024 1 154.88 ? C8 LPP 401 D 1 
HETATM 9 O O9 LPP . . . H 4 129.298 123.984 93.027 1 156.4 ? O9 LPP 401 D 1 
HETATM 10 O O27 LPP . . . H 4 132.727 124.608 93.202 1 157.78 ? O27 LPP 401 D 1 
HETATM 11 C C11 LPP . . . H 4 128.779 122.713 93.292 1 154.78 ? C11 LPP 401 D 1 
HETATM 12 O O10 LPP . . . H 4 129.197 121.768 92.712 1 155.69 ? O10 LPP 401 D 1 
HETATM 13 C C12 LPP . . . H 4 127.671 122.544 94.328 1 152.84 ? C12 LPP 401 D 1 
HETATM 14 C C13 LPP . . . H 4 127.671 123.736 95.282 1 152.33 ? C13 LPP 401 D 1 
HETATM 15 C C14 LPP . . . H 4 128.56 123.423 96.483 1 151.66 ? C14 LPP 401 D 1 
HETATM 16 C C15 LPP . . . H 4 128.308 124.45 97.586 1 152.18 ? C15 LPP 401 D 1 
HETATM 17 C C16 LPP . . . H 4 128.276 123.74 98.937 1 151.38 ? C16 LPP 401 D 1 
HETATM 18 C C17 LPP . . . H 4 128.09 124.766 100.052 1 149.89 ? C17 LPP 401 D 1 
HETATM 19 C C18 LPP . . . H 4 127.174 124.187 101.127 1 151.69 ? C18 LPP 401 D 1 
HETATM 20 C C19 LPP . . . H 4 127.808 122.93 101.719 1 152.17 ? C19 LPP 401 D 1 
HETATM 21 C C20 LPP . . . H 4 127.177 122.629 103.076 1 153.03 ? C20 LPP 401 D 1 
HETATM 22 C C21 LPP . . . H 4 127.821 121.379 103.669 1 151.64 ? C21 LPP 401 D 1 
HETATM 23 C C22 LPP . . . H 4 127.882 121.507 105.189 1 152.04 ? C22 LPP 401 D 1 
HETATM 24 C C23 LPP . . . H 4 126.495 121.285 105.786 1 152.16 ? C23 LPP 401 D 1 
HETATM 25 C C24 LPP . . . H 4 126.614 121.163 107.303 1 152.15 ? C24 LPP 401 D 1 
HETATM 26 C C25 LPP . . . H 4 125.295 120.666 107.889 1 151.12 ? C25 LPP 401 D 1 
HETATM 27 C C26 LPP . . . H 4 124.269 121.796 107.879 1 150.74 ? C26 LPP 401 D 1 
HETATM 28 C C29 LPP . . . H 4 132.905 123.794 94.326 1 156.49 ? C29 LPP 401 D 1 
HETATM 29 O O28 LPP . . . H 4 133.601 122.839 94.252 1 154.77 ? O28 LPP 401 D 1 
HETATM 30 C C30 LPP . . . H 4 132.208 124.139 95.642 1 152.48 ? C30 LPP 401 D 1 
HETATM 31 C C31 LPP . . . H 4 132.313 122.98 96.632 1 151.52 ? C31 LPP 401 D 1 
HETATM 32 C C32 LPP . . . H 4 133.609 123.085 97.433 1 150.22 ? C32 LPP 401 D 1 
HETATM 33 C C33 LPP . . . H 4 133.292 123.34 98.906 1 152.49 ? C33 LPP 401 D 1 
HETATM 34 C C34 LPP . . . H 4 132.723 122.074 99.541 1 153.02 ? C34 LPP 401 D 1 
HETATM 35 C C35 LPP . . . H 4 133.441 121.805 100.862 1 153.28 ? C35 LPP 401 D 1 
HETATM 36 C C36 LPP . . . H 4 133.268 123 101.797 1 151.05 ? C36 LPP 401 D 1 
HETATM 37 C C37 LPP . . . H 4 131.97 122.842 102.583 1 150.57 ? C37 LPP 401 D 1 
HETATM 38 C C38 LPP . . . H 4 132.033 123.698 103.845 1 151.37 ? C38 LPP 401 D 1 
HETATM 39 C C39 LPP . . . H 4 131.372 122.946 104.998 1 152.18 ? C39 LPP 401 D 1 
HETATM 40 C C40 LPP . . . H 4 131.583 123.718 106.297 1 151.2 ? C40 LPP 401 D 1 
HETATM 41 C C41 LPP . . . H 4 131.504 122.757 107.481 1 151.07 ? C41 LPP 401 D 1 
HETATM 42 C C42 LPP . . . H 4 131.962 123.478 108.747 1 151.92 ? C42 LPP 401 D 1 
HETATM 43 C C43 LPP . . . H 4 132.08 122.476 109.893 1 151.61 ? C43 LPP 401 D 1 
HETATM 44 C C44 LPP . . . H 4 132.803 123.129 111.068 1 151.23 ? C44 LPP 401 D 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           415 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           44 
#