data_5DYE
#
_model_server_result.job_id            kmD5f2uKtFv39zz9z_ymuw 
_model_server_result.datetime_utc      '2025-08-05 08:32:53' 
_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          5dye 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":301}' 
#
_entry.id    5DYE 
#
_exptl.entry_id    5DYE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              567.65 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            O-[(S)-{[(2S)-2-(hexanoyloxy)-3-(tetradecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-D-serine 
_entity.pdbx_number_of_molecules    1 
_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         120 
_cell.entry_id            5DYE 
_cell.length_a            174.286 
_cell.length_b            174.286 
_cell.length_c            100.858 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5DYE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        149 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 3 1 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C26 H50 N O10 P' 
_chem_comp.formula_weight    567.65 
_chem_comp.id                PS6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              O-[(S)-{[(2S)-2-(hexanoyloxy)-3-(tetradecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-D-serine 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
P O2 PS6 sing 275 n n 
O2 C2 PS6 sing 276 n n 
CB O1 PS6 sing 277 n n 
O1 P PS6 sing 278 n n 
O4 P PS6 doub 279 n n 
O3 P PS6 sing 280 n n 
O3 HO3 PS6 sing 281 n n 
C2 C3 PS6 sing 282 n n 
C2 H2 PS6 sing 283 n n 
C2 H2A PS6 sing 284 n n 
C3 O11 PS6 sing 285 n n 
C3 C4 PS6 sing 286 n n 
C3 H3 PS6 sing 287 n n 
C1 O11 PS6 sing 288 n n 
O12 C1 PS6 doub 289 n n 
C13 C1 PS6 sing 290 n n 
C4 O52 PS6 sing 291 n n 
C4 H4 PS6 sing 292 n n 
C4 H4A PS6 sing 293 n n 
O52 C5 PS6 sing 294 n n 
C5 O51 PS6 doub 295 n n 
C5 C6 PS6 sing 296 n n 
C13 C14 PS6 sing 297 n n 
C13 H13 PS6 sing 298 n n 
C13 H13A PS6 sing 299 n n 
C15 C14 PS6 sing 300 n n 
C14 H14 PS6 sing 301 n n 
C14 H14A PS6 sing 302 n n 
C15 C16 PS6 sing 303 n n 
C15 H15 PS6 sing 304 n n 
C15 H15A PS6 sing 305 n n 
N CA PS6 sing 306 n n 
N HN PS6 sing 307 n n 
N HNA PS6 sing 308 n n 
CB CA PS6 sing 309 n n 
CA C PS6 sing 310 n n 
CA HA PS6 sing 311 n n 
CB HB PS6 sing 312 n n 
CB HBA PS6 sing 313 n n 
OXT C PS6 doub 314 n n 
C O PS6 sing 315 n n 
O HO PS6 sing 316 n n 
C17 C16 PS6 sing 317 n n 
C16 H16 PS6 sing 318 n n 
C16 H16A PS6 sing 319 n n 
C17 H17 PS6 sing 320 n n 
C17 H17A PS6 sing 321 n n 
C17 H17B PS6 sing 322 n n 
C6 C7 PS6 sing 323 n n 
C6 H6 PS6 sing 324 n n 
C6 H6A PS6 sing 325 n n 
C7 C8 PS6 sing 326 n n 
C7 H7 PS6 sing 327 n n 
C7 H7A PS6 sing 328 n n 
C8 C9 PS6 sing 329 n n 
C8 H8 PS6 sing 330 n n 
C8 H8A PS6 sing 331 n n 
C9 C10 PS6 sing 332 n n 
C9 H9 PS6 sing 333 n n 
C9 H9A PS6 sing 334 n n 
C10 C18 PS6 sing 335 n n 
C10 H10 PS6 sing 336 n n 
C10 H10A PS6 sing 337 n n 
C18 C19 PS6 sing 338 n n 
C18 H18 PS6 sing 339 n n 
C18 H18A PS6 sing 340 n n 
C19 C20 PS6 sing 341 n n 
C19 H19 PS6 sing 342 n n 
C19 H19A PS6 sing 343 n n 
C20 C21 PS6 sing 344 n n 
C20 H20 PS6 sing 345 n n 
C20 H20A PS6 sing 346 n n 
C21 C22 PS6 sing 347 n n 
C21 H21 PS6 sing 348 n n 
C21 H21A PS6 sing 349 n n 
C22 C23 PS6 sing 350 n n 
C22 H22 PS6 sing 351 n n 
C22 H22A PS6 sing 352 n n 
C23 C24 PS6 sing 353 n n 
C23 H23 PS6 sing 354 n n 
C23 H23A PS6 sing 355 n n 
C24 C25 PS6 sing 356 n n 
C24 H24 PS6 sing 357 n n 
C24 H24A PS6 sing 358 n n 
C25 H25 PS6 sing 359 n n 
C25 H25A PS6 sing 360 n n 
C25 H25B PS6 sing 361 n n 
#
_atom_sites.entry_id                     5DYE 
_atom_sites.fract_transf_matrix[1][1]    0.005738 
_atom_sites.fract_transf_matrix[1][2]    0.003313 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006625 
_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]    0.009915 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          E 
_pdbx_nonpoly_scheme.entity_id        2 
_pdbx_nonpoly_scheme.mon_id           PS6 
_pdbx_nonpoly_scheme.pdb_strand_id    B 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      301 
_pdbx_nonpoly_scheme.auth_seq_num     266 
_pdbx_nonpoly_scheme.pdb_mon_id       PS6 
_pdbx_nonpoly_scheme.auth_mon_id      PS6 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 O O2 PS6 . . . E 2 145.763 49.897 38.492 1 193.27 ? O2 PS6 301 B 1 
HETATM 2 O O1 PS6 . . . E 2 146.702 48.416 40.3 1 217.37 ? O1 PS6 301 B 1 
HETATM 3 P P PS6 . . . E 2 145.443 49.387 39.989 1 217.31 ? P PS6 301 B 1 
HETATM 4 O O4 PS6 . . . E 2 145.492 50.596 40.894 1 227.92 ? O4 PS6 301 B 1 
HETATM 5 O O3 PS6 . . . E 2 144.199 48.533 39.983 1 214.51 ? O3 PS6 301 B 1 
HETATM 6 C C2 PS6 . . . E 2 144.756 50.144 37.519 1 170.29 ? C2 PS6 301 B 1 
HETATM 7 C C3 PS6 . . . E 2 145.244 49.586 36.186 1 161.93 ? C3 PS6 301 B 1 
HETATM 8 O O11 PS6 . . . E 2 144.746 48.3 35.789 1 165.84 ? O11 PS6 301 B 1 
HETATM 9 O O12 PS6 . . . E 2 145.855 46.648 36.956 1 138.77 ? O12 PS6 301 B 1 
HETATM 10 C C1 PS6 . . . E 2 144.782 47.172 36.699 1 164.23 ? C1 PS6 301 B 1 
HETATM 11 C C4 PS6 . . . E 2 144.744 50.492 35.091 1 150.95 ? C4 PS6 301 B 1 
HETATM 12 C C5 PS6 . . . E 2 144.396 50.229 32.631 1 131.1 ? C5 PS6 301 B 1 
HETATM 13 O O51 PS6 . . . E 2 143.661 51.154 32.751 1 138.85 ? O51 PS6 301 B 1 
HETATM 14 O O52 PS6 . . . E 2 144.949 49.764 33.874 1 142.49 ? O52 PS6 301 B 1 
HETATM 15 C C13 PS6 . . . E 2 143.492 46.624 37.275 1 164.01 ? C13 PS6 301 B 1 
HETATM 16 C C14 PS6 . . . E 2 142.264 47.496 36.957 1 165.7 ? C14 PS6 301 B 1 
HETATM 17 C C15 PS6 . . . E 2 141.397 47.782 38.182 1 167.85 ? C15 PS6 301 B 1 
HETATM 18 N N PS6 . . . E 2 149.131 50.527 41.916 1 214.43 ? N PS6 301 B 1 
HETATM 19 C CA PS6 . . . E 2 148.736 49.658 40.817 1 213.78 ? CA PS6 301 B 1 
HETATM 20 C CB PS6 . . . E 2 147.669 48.677 41.323 1 216.34 ? CB PS6 301 B 1 
HETATM 21 C C PS6 . . . E 2 149.951 48.963 40.241 1 199.85 ? C PS6 301 B 1 
HETATM 22 O O PS6 . . . E 2 151.068 49.535 40.323 1 152.16 ? O PS6 301 B 1 
HETATM 23 O OXT PS6 . . . E 2 149.813 47.846 39.681 1 173.81 ? OXT PS6 301 B 1 
HETATM 24 C C6 PS6 . . . E 2 144.71 49.659 31.27 1 123.62 ? C6 PS6 301 B 1 
HETATM 25 C C7 PS6 . . . E 2 144.384 50.662 30.167 1 119.89 ? C7 PS6 301 B 1 
HETATM 26 C C8 PS6 . . . E 2 144.566 50.015 28.809 1 121.65 ? C8 PS6 301 B 1 
HETATM 27 C C9 PS6 . . . E 2 144.086 50.903 27.677 1 126.89 ? C9 PS6 301 B 1 
HETATM 28 C C10 PS6 . . . E 2 144.943 50.64 26.445 1 129.34 ? C10 PS6 301 B 1 
HETATM 29 C C18 PS6 . . . E 2 144.301 51.281 25.23 1 130.68 ? C18 PS6 301 B 1 
#
_model_server_stats.io_time_ms              54 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           29 
#