data_8YMC
#
_model_server_result.job_id            m9c-EAylVdQXNGGs-eQ7sQ 
_model_server_result.datetime_utc      '2025-08-30 17:09:20' 
_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":"G","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 . . . G 4 110.629 119.561 89.412 1 161.33 ? P1 LPP 401 C 1 
HETATM 2 O O2 LPP . . . G 4 110.19 120.741 90.244 1 149.92 ? O2 LPP 401 C 1 
HETATM 3 O O3 LPP . . . G 4 109.413 118.859 88.858 1 152.59 ? O3 LPP 401 C 1 
HETATM 4 O O4 LPP . . . G 4 111.495 120.043 88.273 1 151.75 ? O4 LPP 401 C 1 
HETATM 5 O O5 LPP . . . G 4 111.488 118.508 90.347 1 152.48 ? O5 LPP 401 C 1 
HETATM 6 C C6 LPP . . . G 4 112.762 118.883 90.787 1 149.17 ? C6 LPP 401 C 1 
HETATM 7 C C7 LPP . . . G 4 112.647 119.576 92.142 1 148.75 ? C7 LPP 401 C 1 
HETATM 8 C C8 LPP . . . G 4 111.537 118.917 92.956 1 148.84 ? C8 LPP 401 C 1 
HETATM 9 O O9 LPP . . . G 4 113.86 119.469 92.831 1 151.78 ? O9 LPP 401 C 1 
HETATM 10 O O27 LPP . . . G 4 110.396 119.722 92.9 1 149.71 ? O27 LPP 401 C 1 
HETATM 11 C C11 LPP . . . G 4 114.442 120.702 93.141 1 151.02 ? C11 LPP 401 C 1 
HETATM 12 O O10 LPP . . . G 4 114.092 121.681 92.572 1 151.2 ? O10 LPP 401 C 1 
HETATM 13 C C12 LPP . . . G 4 115.528 120.789 94.21 1 148.34 ? C12 LPP 401 C 1 
HETATM 14 C C13 LPP . . . G 4 115.375 119.632 95.195 1 146 ? C13 LPP 401 C 1 
HETATM 15 C C14 LPP . . . G 4 114.513 120.078 96.374 1 144.46 ? C14 LPP 401 C 1 
HETATM 16 C C15 LPP . . . G 4 114.581 119.025 97.478 1 146.58 ? C15 LPP 401 C 1 
HETATM 17 C C16 LPP . . . G 4 114.603 119.717 98.838 1 145.75 ? C16 LPP 401 C 1 
HETATM 18 C C17 LPP . . . G 4 114.748 118.673 99.942 1 143.92 ? C17 LPP 401 C 1 
HETATM 19 C C18 LPP . . . G 4 115.65 119.22 101.045 1 145.1 ? C18 LPP 401 C 1 
HETATM 20 C C19 LPP . . . G 4 115.005 120.456 101.667 1 144.93 ? C19 LPP 401 C 1 
HETATM 21 C C20 LPP . . . G 4 115.615 120.713 103.043 1 147.18 ? C20 LPP 401 C 1 
HETATM 22 C C21 LPP . . . G 4 115.038 122.004 103.62 1 147.79 ? C21 LPP 401 C 1 
HETATM 23 C C22 LPP . . . G 4 114.964 121.899 105.141 1 147.34 ? C22 LPP 401 C 1 
HETATM 24 C C23 LPP . . . G 4 116.343 122.148 105.748 1 147.64 ? C23 LPP 401 C 1 
HETATM 25 C C24 LPP . . . G 4 116.216 122.223 107.268 1 147.42 ? C24 LPP 401 C 1 
HETATM 26 C C25 LPP . . . G 4 117.527 122.723 107.872 1 146.62 ? C25 LPP 401 C 1 
HETATM 27 C C26 LPP . . . G 4 118.614 121.666 107.693 1 145.67 ? C26 LPP 401 C 1 
HETATM 28 C C29 LPP . . . G 4 109.655 119.751 94.085 1 151.47 ? C29 LPP 401 C 1 
HETATM 29 O O28 LPP . . . G 4 108.471 119.725 94.042 1 152.39 ? O28 LPP 401 C 1 
HETATM 30 C C30 LPP . . . G 4 110.367 119.81 95.432 1 146.1 ? C30 LPP 401 C 1 
HETATM 31 C C31 LPP . . . G 4 109.414 120.369 96.486 1 144.18 ? C31 LPP 401 C 1 
HETATM 32 C C32 LPP . . . G 4 110.227 120.923 97.652 1 145.66 ? C32 LPP 401 C 1 
HETATM 33 C C33 LPP . . . G 4 109.322 121.128 98.864 1 146.74 ? C33 LPP 401 C 1 
HETATM 34 C C34 LPP . . . G 4 110.136 120.877 100.13 1 146.72 ? C34 LPP 401 C 1 
HETATM 35 C C35 LPP . . . G 4 109.433 121.493 101.336 1 145.35 ? C35 LPP 401 C 1 
HETATM 36 C C36 LPP . . . G 4 109.675 120.613 102.561 1 144.91 ? C36 LPP 401 C 1 
HETATM 37 C C37 LPP . . . G 4 111.173 120.356 102.707 1 144.32 ? C37 LPP 401 C 1 
HETATM 38 C C38 LPP . . . G 4 111.459 119.709 104.06 1 146.31 ? C38 LPP 401 C 1 
HETATM 39 C C39 LPP . . . G 4 110.973 120.625 105.178 1 145.37 ? C39 LPP 401 C 1 
HETATM 40 C C40 LPP . . . G 4 111.51 120.119 106.515 1 144.34 ? C40 LPP 401 C 1 
HETATM 41 C C41 LPP . . . G 4 110.994 121.016 107.636 1 144.5 ? C41 LPP 401 C 1 
HETATM 42 C C42 LPP . . . G 4 111.234 120.338 108.982 1 146.61 ? C42 LPP 401 C 1 
HETATM 43 C C43 LPP . . . G 4 110.528 121.13 110.079 1 147.16 ? C43 LPP 401 C 1 
HETATM 44 C C44 LPP . . . G 4 110.427 120.278 111.341 1 146.58 ? C44 LPP 401 C 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    62 
_model_server_stats.query_time_ms           410 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           44 
#