data_5VB8
#
_model_server_result.job_id            qW9XJ6NyreNZduSKPaKrjw 
_model_server_result.datetime_utc      '2024-10-27 14:27:11' 
_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          5vb8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1303}' 
#
_entry.id    5VB8 
#
_exptl.entry_id    5VB8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              678.94 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE 
_entity.pdbx_number_of_molecules    4 
_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            5VB8 
_cell.length_a            125.302 
_cell.length_b            125.302 
_cell.length_c            192.424 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VB8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        97 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4 2 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,F,G,H 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_445 -x-1,-y-1,z -1 0 0 0 -1 0 0 0 1 -125.302 -125.302 0 
3 'crystal symmetry operation' 3_455 -y-1,x,z 0 -1 0 1 0 0 0 0 1 -125.302 0 0 
4 'crystal symmetry operation' 4_545 y,-x-1,z 0 1 0 -1 0 0 0 0 1 0 -125.302 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 D N N 
? 3 E N N 
? 3 F N N 
#
_chem_comp.formula           'C36 H73 N O8 P 1' 
_chem_comp.formula_weight    678.94 
_chem_comp.id                PX4 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE 
_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
O1 P1 PX4 sing 277 n n 
O1 H1P PX4 sing 278 n n 
O2 P1 PX4 doub 279 n n 
P1 O3 PX4 sing 280 n n 
P1 O4 PX4 sing 281 n n 
O3 C1 PX4 sing 282 n n 
C1 C2 PX4 sing 283 n n 
C1 H1 PX4 sing 284 n n 
C1 H2 PX4 sing 285 n n 
C2 N1 PX4 sing 286 n n 
C2 H3 PX4 sing 287 n n 
C2 H4 PX4 sing 288 n n 
N1 C3 PX4 sing 289 n n 
N1 C4 PX4 sing 290 n n 
N1 C5 PX4 sing 291 n n 
C3 H5 PX4 sing 292 n n 
C3 H6 PX4 sing 293 n n 
C3 H7 PX4 sing 294 n n 
C4 H8 PX4 sing 295 n n 
C4 H9 PX4 sing 296 n n 
C4 H10 PX4 sing 297 n n 
C5 H11 PX4 sing 298 n n 
C5 H12 PX4 sing 299 n n 
C5 H13 PX4 sing 300 n n 
O4 C6 PX4 sing 301 n n 
C6 C7 PX4 sing 302 n n 
C6 H14 PX4 sing 303 n n 
C6 H15 PX4 sing 304 n n 
C7 C8 PX4 sing 305 n n 
C7 O7 PX4 sing 306 n n 
C7 H16 PX4 sing 307 n n 
C8 O5 PX4 sing 308 n n 
C8 H17 PX4 sing 309 n n 
C8 H18 PX4 sing 310 n n 
O5 C9 PX4 sing 311 n n 
C9 O6 PX4 doub 312 n n 
C9 C10 PX4 sing 313 n n 
C10 C11 PX4 sing 314 n n 
C10 H19 PX4 sing 315 n n 
C10 H20 PX4 sing 316 n n 
C11 C12 PX4 sing 317 n n 
C11 H21 PX4 sing 318 n n 
C11 H22 PX4 sing 319 n n 
C12 C13 PX4 sing 320 n n 
C12 H23 PX4 sing 321 n n 
C12 H24 PX4 sing 322 n n 
C13 C14 PX4 sing 323 n n 
C13 H25 PX4 sing 324 n n 
C13 H26 PX4 sing 325 n n 
C14 C15 PX4 sing 326 n n 
C14 H27 PX4 sing 327 n n 
C14 H28 PX4 sing 328 n n 
C15 C16 PX4 sing 329 n n 
C15 H29 PX4 sing 330 n n 
C15 H30 PX4 sing 331 n n 
C16 C17 PX4 sing 332 n n 
C16 H31 PX4 sing 333 n n 
C16 H32 PX4 sing 334 n n 
C17 C18 PX4 sing 335 n n 
C17 H33 PX4 sing 336 n n 
C17 H34 PX4 sing 337 n n 
C18 C19 PX4 sing 338 n n 
C18 H35 PX4 sing 339 n n 
C18 H36 PX4 sing 340 n n 
C19 C20 PX4 sing 341 n n 
C19 H37 PX4 sing 342 n n 
C19 H38 PX4 sing 343 n n 
C20 C21 PX4 sing 344 n n 
C20 H39 PX4 sing 345 n n 
C20 H40 PX4 sing 346 n n 
C21 C22 PX4 sing 347 n n 
C21 H41 PX4 sing 348 n n 
C21 H42 PX4 sing 349 n n 
C22 H43 PX4 sing 350 n n 
C22 H44 PX4 sing 351 n n 
C22 H45 PX4 sing 352 n n 
O7 C23 PX4 sing 353 n n 
C23 O8 PX4 doub 354 n n 
C23 C24 PX4 sing 355 n n 
C24 C25 PX4 sing 356 n n 
C24 H46 PX4 sing 357 n n 
C24 H47 PX4 sing 358 n n 
C25 C26 PX4 sing 359 n n 
C25 H48 PX4 sing 360 n n 
C25 H49 PX4 sing 361 n n 
C26 C27 PX4 sing 362 n n 
C26 H50 PX4 sing 363 n n 
C26 H51 PX4 sing 364 n n 
C27 C28 PX4 sing 365 n n 
C27 H52 PX4 sing 366 n n 
C27 H53 PX4 sing 367 n n 
C28 C29 PX4 sing 368 n n 
C28 H54 PX4 sing 369 n n 
C28 H55 PX4 sing 370 n n 
C29 C30 PX4 sing 371 n n 
C29 H56 PX4 sing 372 n n 
C29 H57 PX4 sing 373 n n 
C30 C31 PX4 sing 374 n n 
C30 H58 PX4 sing 375 n n 
C30 H59 PX4 sing 376 n n 
C31 C32 PX4 sing 377 n n 
C31 H60 PX4 sing 378 n n 
C31 H61 PX4 sing 379 n n 
C32 C33 PX4 sing 380 n n 
C32 H62 PX4 sing 381 n n 
C32 H63 PX4 sing 382 n n 
C33 C34 PX4 sing 383 n n 
C33 H64 PX4 sing 384 n n 
C33 H65 PX4 sing 385 n n 
C34 C35 PX4 sing 386 n n 
C34 H66 PX4 sing 387 n n 
C34 H67 PX4 sing 388 n n 
C35 C36 PX4 sing 389 n n 
C35 H68 PX4 sing 390 n n 
C35 H69 PX4 sing 391 n n 
C36 H70 PX4 sing 392 n n 
C36 H71 PX4 sing 393 n n 
C36 H72 PX4 sing 394 n n 
#
_atom_sites.entry_id                     5VB8 
_atom_sites.fract_transf_matrix[1][1]    0.007981 
_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]    0.007981 
_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]    0.005197 
_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
B 2 NA A 1 1301 4 NA NA . 
C 3 PX4 A 1 1302 1 PX4 PX4 . 
D 3 PX4 A 1 1303 2 PX4 PX4 . 
E 3 PX4 A 1 1304 3 PX4 PX4 . 
F 3 PX4 A 1 1305 4 PX4 PX4 . 
G 4 SO4 A 1 1306 1 SO4 SO4 . 
H 5 HOH A 1 1401 9 HOH HOH . 
H 5 HOH A 2 1402 13 HOH HOH . 
H 5 HOH A 3 1403 15 HOH HOH . 
H 5 HOH A 4 1404 4 HOH HOH . 
H 5 HOH A 5 1405 7 HOH HOH . 
H 5 HOH A 6 1406 6 HOH HOH . 
H 5 HOH A 7 1407 12 HOH HOH . 
H 5 HOH A 8 1408 2 HOH HOH . 
H 5 HOH A 9 1409 16 HOH HOH . 
H 5 HOH A 10 1410 1 HOH HOH . 
H 5 HOH A 11 1411 5 HOH HOH . 
H 5 HOH A 12 1412 11 HOH HOH . 
#
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 O1 PX4 . . . D 3 -70.145 -84.825 -84.606 1 99.71 -1 O1 PX4 1303 A 1 
HETATM 2 O O2 PX4 . . . D 3 -68.028 -85.907 -84.535 1 97.78 ? O2 PX4 1303 A 1 
HETATM 3 P P1 PX4 . . . D 3 -68.718 -84.609 -84.194 1 100.38 ? P1 PX4 1303 A 1 
HETATM 4 O O3 PX4 . . . D 3 -68.145 -83.343 -85.087 1 102.98 ? O3 PX4 1303 A 1 
HETATM 5 C C1 PX4 . . . D 3 -66.846 -83.548 -85.562 1 106.22 ? C1 PX4 1303 A 1 
HETATM 6 C C2 PX4 . . . D 3 -66.297 -82.422 -86.437 1 108.96 ? C2 PX4 1303 A 1 
HETATM 7 N N1 PX4 . . . D 3 -66.975 -82.288 -87.717 1 111.89 1 N1 PX4 1303 A 1 
HETATM 8 C C3 PX4 . . . D 3 -66.249 -81.336 -88.561 1 113 ? C3 PX4 1303 A 1 
HETATM 9 C C4 PX4 . . . D 3 -68.294 -81.714 -87.484 1 112.94 ? C4 PX4 1303 A 1 
HETATM 10 C C5 PX4 . . . D 3 -67.059 -83.567 -88.411 1 111.72 ? C5 PX4 1303 A 1 
HETATM 11 O O4 PX4 . . . D 3 -68.402 -84.149 -82.595 1 100.01 ? O4 PX4 1303 A 1 
HETATM 12 C C6 PX4 . . . D 3 -69.269 -84.31 -81.49 1 99.81 ? C6 PX4 1303 A 1 
HETATM 13 C C7 PX4 . . . D 3 -68.959 -83.42 -80.273 1 99.74 ? C7 PX4 1303 A 1 
HETATM 14 C C8 PX4 . . . D 3 -68.453 -84.316 -79.115 1 107.06 ? C8 PX4 1303 A 1 
HETATM 15 O O5 PX4 . . . D 3 -69.437 -85.233 -78.713 1 112.97 ? O5 PX4 1303 A 1 
HETATM 16 C C9 PX4 . . . D 3 -70.53 -84.599 -78.115 1 117.85 ? C9 PX4 1303 A 1 
HETATM 17 O O6 PX4 . . . D 3 -71.457 -84.335 -78.829 1 119.88 ? O6 PX4 1303 A 1 
HETATM 18 C C10 PX4 . . . D 3 -70.505 -84.248 -76.618 1 118.8 ? C10 PX4 1303 A 1 
HETATM 19 O O7 PX4 . . . D 3 -68.023 -82.404 -80.537 1 92.55 ? O7 PX4 1303 A 1 
HETATM 20 C C23 PX4 . . . D 3 -67.941 -81.287 -79.643 1 86.83 ? C23 PX4 1303 A 1 
HETATM 21 O O8 PX4 . . . D 3 -67.416 -80.331 -80.049 1 86.03 ? O8 PX4 1303 A 1 
HETATM 22 C C24 PX4 . . . D 3 -68.427 -81.174 -78.168 1 83.15 ? C24 PX4 1303 A 1 
HETATM 23 C C25 PX4 . . . D 3 -68.01 -79.807 -77.57 1 80.08 ? C25 PX4 1303 A 1 
HETATM 24 C C26 PX4 . . . D 3 -67.958 -79.857 -76.01 1 77.88 ? C26 PX4 1303 A 1 
HETATM 25 C C27 PX4 . . . D 3 -69.2 -79.266 -75.328 1 76.81 ? C27 PX4 1303 A 1 
HETATM 26 C C28 PX4 . . . D 3 -68.91 -78.83 -73.882 1 76.86 ? C28 PX4 1303 A 1 
HETATM 27 C C29 PX4 . . . D 3 -70.137 -78.946 -72.926 1 76.74 ? C29 PX4 1303 A 1 
HETATM 28 C C30 PX4 . . . D 3 -69.932 -78.093 -71.657 1 76.76 ? C30 PX4 1303 A 1 
HETATM 29 H H1 PX4 . . . D 3 -66.256 -83.658 -84.8 1 127.46 ? H1 PX4 1303 A 1 
HETATM 30 H H2 PX4 . . . D 3 -66.836 -84.369 -86.079 1 127.46 ? H2 PX4 1303 A 1 
HETATM 31 H H3 PX4 . . . D 3 -65.356 -82.589 -86.602 1 130.75 ? H3 PX4 1303 A 1 
HETATM 32 H H4 PX4 . . . D 3 -66.383 -81.585 -85.953 1 130.75 ? H4 PX4 1303 A 1 
HETATM 33 H H5 PX4 . . . D 3 -66.349 -80.442 -88.2 1 135.59 ? H5 PX4 1303 A 1 
HETATM 34 H H6 PX4 . . . D 3 -66.609 -81.363 -89.462 1 135.59 ? H6 PX4 1303 A 1 
HETATM 35 H H7 PX4 . . . D 3 -65.309 -81.574 -88.582 1 135.59 ? H7 PX4 1303 A 1 
HETATM 36 H H8 PX4 . . . D 3 -68.887 -82.398 -87.135 1 135.52 ? H8 PX4 1303 A 1 
HETATM 37 H H9 PX4 . . . D 3 -68.223 -80.99 -86.842 1 135.52 ? H9 PX4 1303 A 1 
HETATM 38 H H10 PX4 . . . D 3 -68.65 -81.372 -88.319 1 135.52 ? H10 PX4 1303 A 1 
HETATM 39 H H11 PX4 . . . D 3 -66.356 -84.155 -88.091 1 134.06 ? H11 PX4 1303 A 1 
HETATM 40 H H12 PX4 . . . D 3 -66.953 -83.426 -89.364 1 134.06 ? H12 PX4 1303 A 1 
HETATM 41 H H13 PX4 . . . D 3 -67.923 -83.973 -88.238 1 134.06 ? H13 PX4 1303 A 1 
HETATM 42 H H14 PX4 . . . D 3 -69.23 -85.237 -81.206 1 119.77 ? H14 PX4 1303 A 1 
HETATM 43 H H15 PX4 . . . D 3 -70.174 -84.119 -81.783 1 119.77 ? H15 PX4 1303 A 1 
HETATM 44 H H16 PX4 . . . D 3 -69.786 -83 -79.989 1 119.69 ? H16 PX4 1303 A 1 
HETATM 45 H H17 PX4 . . . D 3 -67.66 -84.799 -79.396 1 128.48 ? H17 PX4 1303 A 1 
HETATM 46 H H18 PX4 . . . D 3 -68.225 -83.752 -78.36 1 128.48 ? H18 PX4 1303 A 1 
HETATM 47 H H19 PX4 . . . D 3 -71.327 -83.791 -76.38 1 142.56 ? H19 PX4 1303 A 1 
HETATM 48 H H20 PX4 . . . D 3 -70.426 -85.063 -76.097 1 142.56 ? H20 PX4 1303 A 1 
HETATM 49 H H46 PX4 . . . D 3 -68.031 -81.888 -77.644 1 99.78 ? H46 PX4 1303 A 1 
HETATM 50 H H47 PX4 . . . D 3 -69.394 -81.255 -78.142 1 99.78 ? H47 PX4 1303 A 1 
HETATM 51 H H48 PX4 . . . D 3 -67.133 -79.567 -77.909 1 96.09 ? H48 PX4 1303 A 1 
HETATM 52 H H49 PX4 . . . D 3 -68.651 -79.132 -77.844 1 96.09 ? H49 PX4 1303 A 1 
HETATM 53 H H50 PX4 . . . D 3 -67.177 -79.364 -75.711 1 93.46 ? H50 PX4 1303 A 1 
HETATM 54 H H51 PX4 . . . D 3 -67.864 -80.782 -75.734 1 93.46 ? H51 PX4 1303 A 1 
HETATM 55 H H52 PX4 . . . D 3 -69.501 -78.496 -75.835 1 92.18 ? H52 PX4 1303 A 1 
HETATM 56 H H53 PX4 . . . D 3 -69.903 -79.934 -75.321 1 92.18 ? H53 PX4 1303 A 1 
HETATM 57 H H54 PX4 . . . D 3 -68.193 -79.381 -73.531 1 92.23 ? H54 PX4 1303 A 1 
HETATM 58 H H55 PX4 . . . D 3 -68.613 -77.906 -73.892 1 92.23 ? H55 PX4 1303 A 1 
HETATM 59 H H56 PX4 . . . D 3 -70.932 -78.641 -73.39 1 92.09 ? H56 PX4 1303 A 1 
HETATM 60 H H57 PX4 . . . D 3 -70.254 -79.874 -72.67 1 92.09 ? H57 PX4 1303 A 1 
HETATM 61 H H58 PX4 . . . D 3 -69.441 -78.607 -70.997 1 92.11 ? H58 PX4 1303 A 1 
HETATM 62 H H59 PX4 . . . D 3 -70.795 -77.841 -71.294 1 92.11 ? H59 PX4 1303 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           62 
#