data_8QBD
#
_model_server_result.job_id            dcrkgiqYckwCUp0pr-CgOw 
_model_server_result.datetime_utc      '2024-10-10 10:23:33' 
_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          8qbd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"DA","auth_seq_id":402}' 
#
_entry.id    8QBD 
#
_exptl.entry_id    8QBD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              792.075 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine 
_entity.pdbx_number_of_molecules    14 
_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            8QBD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8QBD 
_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    14-meric 
_pdbx_struct_assembly.oligomeric_count      14 
_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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA 
_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
? 3 P N N 
? 3 R N N 
? 3 T N N 
? 3 V N N 
? 3 X N N 
? 3 Z N N 
? 3 BA N N 
? 3 DA N N 
? 3 FA N N 
? 3 HA N N 
? 3 JA N N 
? 3 LA N N 
? 3 NA N N 
? 3 PA N N 
#
_chem_comp.formula           'C42 H82 N O10 P' 
_chem_comp.formula_weight    792.075 
_chem_comp.id                P5S 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'phosphatidyl serine' 
#
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
CA C P5S sing 261 n n 
O C P5S doub 262 n n 
C OXT P5S sing 263 n n 
CA N P5S sing 264 n n 
N HN P5S sing 265 n n 
N HNA P5S sing 266 n n 
O19 C1 P5S sing 267 n n 
C1 C2 P5S sing 268 n n 
C1 H1 P5S sing 269 n n 
C1 H1A P5S sing 270 n n 
C2 O37 P5S sing 271 n n 
C2 C3 P5S sing 272 n n 
C2 H2 P5S sing 273 n n 
O16 C3 P5S sing 274 n n 
C3 H3 P5S sing 275 n n 
C3 H3A P5S sing 276 n n 
CB CA P5S sing 277 n n 
CA HA P5S sing 278 n n 
CB OG P5S sing 279 n n 
CB HB P5S sing 280 n n 
CB HBA P5S sing 281 n n 
P12 OG P5S sing 282 n n 
O16 P12 P5S sing 283 n n 
O13 P12 P5S doub 284 n n 
P12 O15 P5S sing 285 n n 
O15 HO15 P5S sing 286 n n 
C20 C17 P5S sing 287 n n 
O19 C17 P5S sing 288 n n 
C17 O18 P5S doub 289 n n 
C21 C20 P5S sing 290 n n 
C20 H20 P5S sing 291 n n 
C20 H20A P5S sing 292 n n 
C21 C22 P5S sing 293 n n 
C21 H21 P5S sing 294 n n 
C21 H21A P5S sing 295 n n 
C23 C22 P5S sing 296 n n 
C22 H22 P5S sing 297 n n 
C22 H22A P5S sing 298 n n 
C24 C23 P5S sing 299 n n 
C23 H23 P5S sing 300 n n 
C23 H23A P5S sing 301 n n 
C25 C24 P5S sing 302 n n 
C24 H24 P5S sing 303 n n 
C24 H24A P5S sing 304 n n 
C26 C25 P5S sing 305 n n 
C25 H25 P5S sing 306 n n 
C25 H25A P5S sing 307 n n 
C26 C27 P5S sing 308 n n 
C26 H26 P5S sing 309 n n 
C26 H26A P5S sing 310 n n 
C27 C28 P5S sing 311 n n 
C27 H27 P5S sing 312 n n 
C27 H27A P5S sing 313 n n 
C29 C28 P5S sing 314 n n 
C28 H28 P5S sing 315 n n 
C28 H28A P5S sing 316 n n 
C30 C29 P5S sing 317 n n 
C29 H29 P5S sing 318 n n 
C29 H29A P5S sing 319 n n 
C31 C30 P5S sing 320 n n 
C30 H30 P5S sing 321 n n 
C30 H30A P5S sing 322 n n 
C31 C32 P5S sing 323 n n 
C31 H31 P5S sing 324 n n 
C31 H31A P5S sing 325 n n 
C33 C32 P5S sing 326 n n 
C32 H32 P5S sing 327 n n 
C32 H32A P5S sing 328 n n 
C33 C34 P5S sing 329 n n 
C33 H33 P5S sing 330 n n 
C33 H33A P5S sing 331 n n 
C35 C34 P5S sing 332 n n 
C34 H34 P5S sing 333 n n 
C34 H34A P5S sing 334 n n 
C36 C35 P5S sing 335 n n 
C35 H35 P5S sing 336 n n 
C35 H35A P5S sing 337 n n 
C36 H36 P5S sing 338 n n 
C36 H36A P5S sing 339 n n 
C36 H36B P5S sing 340 n n 
C38 O37 P5S sing 341 n n 
O47 C38 P5S doub 342 n n 
C38 C39 P5S sing 343 n n 
C40 C39 P5S sing 344 n n 
C39 H39 P5S sing 345 n n 
C39 H39A P5S sing 346 n n 
C41 C40 P5S sing 347 n n 
C40 H40 P5S sing 348 n n 
C40 H40A P5S sing 349 n n 
C42 C41 P5S sing 350 n n 
C41 H41 P5S sing 351 n n 
C41 H41A P5S sing 352 n n 
C43 C42 P5S sing 353 n n 
C42 H42 P5S sing 354 n n 
C42 H42A P5S sing 355 n n 
C43 C44 P5S sing 356 n n 
C43 H43 P5S sing 357 n n 
C43 H43A P5S sing 358 n n 
C44 C45 P5S sing 359 n n 
C44 H44 P5S sing 360 n n 
C44 H44A P5S sing 361 n n 
C45 C46 P5S sing 362 n n 
C45 H45 P5S sing 363 n n 
C45 H45A P5S sing 364 n n 
C46 C48 P5S sing 365 n n 
C46 H46 P5S sing 366 n n 
C46 H46A P5S sing 367 n n 
C48 C49 P5S sing 368 n n 
C48 H48 P5S sing 369 n n 
C48 H48A P5S sing 370 n n 
C49 C50 P5S sing 371 n n 
C49 H49 P5S sing 372 n n 
C49 H49A P5S sing 373 n n 
C50 C51 P5S sing 374 n n 
C50 H50 P5S sing 375 n n 
C50 H50A P5S sing 376 n n 
C51 C52 P5S sing 377 n n 
C51 H51 P5S sing 378 n n 
C51 H51A P5S sing 379 n n 
C53 C52 P5S sing 380 n n 
C52 H52 P5S sing 381 n n 
C52 H52A P5S sing 382 n n 
C53 C54 P5S sing 383 n n 
C53 H53 P5S sing 384 n n 
C53 H53A P5S sing 385 n n 
C55 C54 P5S sing 386 n n 
C54 H54 P5S sing 387 n n 
C54 H54A P5S sing 388 n n 
C55 C56 P5S sing 389 n n 
C55 H55 P5S sing 390 n n 
C55 H55A P5S sing 391 n n 
C56 H56 P5S sing 392 n n 
C56 H56A P5S sing 393 n n 
C56 H56B P5S sing 394 n n 
OXT HXT P5S sing 395 n n 
#
_atom_sites.entry_id                     8QBD 
_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
O 2 I3P A 1 401 401 I3P I3P . 
P 3 P5S A 1 402 501 P5S P5S . 
Q 2 I3P B 1 401 401 I3P I3P . 
R 3 P5S B 1 402 501 P5S P5S . 
S 2 I3P C 1 401 401 I3P I3P . 
T 3 P5S C 1 402 501 P5S P5S . 
U 2 I3P I 1 401 401 I3P I3P . 
V 3 P5S I 1 402 501 P5S P5S . 
W 2 I3P D 1 401 401 I3P I3P . 
X 3 P5S D 1 402 501 P5S P5S . 
Y 2 I3P J 1 401 401 I3P I3P . 
Z 3 P5S J 1 402 501 P5S P5S . 
AA 2 I3P E 1 401 401 I3P I3P . 
BA 3 P5S E 1 402 501 P5S P5S . 
CA 2 I3P K 1 401 401 I3P I3P . 
DA 3 P5S K 1 402 501 P5S P5S . 
EA 2 I3P F 1 401 401 I3P I3P . 
FA 3 P5S F 1 402 501 P5S P5S . 
GA 2 I3P L 1 401 401 I3P I3P . 
HA 3 P5S L 1 402 501 P5S P5S . 
IA 2 I3P G 1 401 401 I3P I3P . 
JA 3 P5S G 1 402 501 P5S P5S . 
KA 2 I3P M 1 401 401 I3P I3P . 
LA 3 P5S M 1 402 501 P5S P5S . 
MA 2 I3P H 1 401 401 I3P I3P . 
NA 3 P5S H 1 402 501 P5S P5S . 
OA 2 I3P N 1 401 401 I3P I3P . 
PA 3 P5S N 1 402 501 P5S P5S . 
#
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 C P5S . . . DA 3 345.863 183.267 233.126 1 117.01 ? C P5S 402 K 1 
HETATM 2 N N P5S . . . DA 3 346.836 181.193 232.309 1 117.01 ? N P5S 402 K 1 
HETATM 3 O O P5S . . . DA 3 344.889 183.02 232.368 1 117.01 ? O P5S 402 K 1 
HETATM 4 C C1 P5S . . . DA 3 349.511 188.823 229.334 1 117.01 ? C1 P5S 402 K 1 
HETATM 5 C C2 P5S . . . DA 3 350.167 188.544 230.685 1 117.01 ? C2 P5S 402 K 1 
HETATM 6 C C3 P5S . . . DA 3 350.264 187.036 230.905 1 117.01 ? C3 P5S 402 K 1 
HETATM 7 C CA P5S . . . DA 3 347.12 182.403 233.06 1 117.01 ? CA P5S 402 K 1 
HETATM 8 C CB P5S . . . DA 3 348.239 183.178 232.369 1 117.01 ? CB P5S 402 K 1 
HETATM 9 O OG P5S . . . DA 3 347.67 184.24 231.658 1 117.01 ? OG P5S 402 K 1 
HETATM 10 P P12 P5S . . . DA 3 348.608 185.036 230.562 1 117.01 ? P12 P5S 402 K 1 
HETATM 11 O O13 P5S . . . DA 3 347.859 185.166 229.258 1 117.01 ? O13 P5S 402 K 1 
HETATM 12 O O15 P5S . . . DA 3 349.882 184.258 230.334 1 117.01 ? O15 P5S 402 K 1 
HETATM 13 O O16 P5S . . . DA 3 348.978 186.536 231.136 1 117.01 ? O16 P5S 402 K 1 
HETATM 14 C C17 P5S . . . DA 3 349.382 187.993 227.143 1 117.01 ? C17 P5S 402 K 1 
HETATM 15 O O18 P5S . . . DA 3 348.717 188.94 226.886 1 117.01 ? O18 P5S 402 K 1 
HETATM 16 O O19 P5S . . . DA 3 349.919 187.84 228.426 1 117.01 ? O19 P5S 402 K 1 
HETATM 17 C C20 P5S . . . DA 3 349.654 186.939 226.072 1 117.01 ? C20 P5S 402 K 1 
HETATM 18 O O37 P5S . . . DA 3 349.395 189.117 231.701 1 117.01 ? O37 P5S 402 K 1 
HETATM 19 C C38 P5S . . . DA 3 349.561 190.501 231.826 1 117.01 ? C38 P5S 402 K 1 
HETATM 20 C C39 P5S . . . DA 3 350.878 191.073 232.349 1 117.01 ? C39 P5S 402 K 1 
HETATM 21 C C40 P5S . . . DA 3 350.928 191.107 233.875 1 117.01 ? C40 P5S 402 K 1 
HETATM 22 C C41 P5S . . . DA 3 352.352 191.063 234.43 1 117.01 ? C41 P5S 402 K 1 
HETATM 23 C C42 P5S . . . DA 3 353.281 190.189 233.592 1 117.01 ? C42 P5S 402 K 1 
HETATM 24 C C43 P5S . . . DA 3 354.48 190.966 233.053 1 117.01 ? C43 P5S 402 K 1 
HETATM 25 C C44 P5S . . . DA 3 355.133 190.245 231.877 1 117.01 ? C44 P5S 402 K 1 
HETATM 26 C C45 P5S . . . DA 3 354.889 190.973 230.558 1 117.01 ? C45 P5S 402 K 1 
HETATM 27 C C46 P5S . . . DA 3 355.37 190.169 229.354 1 117.01 ? C46 P5S 402 K 1 
HETATM 28 O O47 P5S . . . DA 3 348.676 191.232 231.534 1 117.01 ? O47 P5S 402 K 1 
HETATM 29 C C48 P5S . . . DA 3 354.38 190.234 228.194 1 117.01 ? C48 P5S 402 K 1 
HETATM 30 O OXT P5S . . . DA 3 345.799 184.227 233.938 1 117.01 ? OXT P5S 402 K 1 
#
_model_server_stats.io_time_ms              37 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    36 
_model_server_stats.query_time_ms           258 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           30 
#