data_5VB8 # _model_server_result.job_id QURK_aBUdTk8pEesIBAuFg _model_server_result.datetime_utc '2024-10-27 14:25:40' _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":"E","auth_seq_id":1304}' # _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 . . . E 3 -74.962 -89.596 -89.288 1 114.2 -1 O1 PX4 1304 A 1 HETATM 2 O O2 PX4 . . . E 3 -77.23 -88.545 -89.591 1 113.49 ? O2 PX4 1304 A 1 HETATM 3 P P1 PX4 . . . E 3 -76.371 -89.473 -88.758 1 114.18 ? P1 PX4 1304 A 1 HETATM 4 O O3 PX4 . . . E 3 -77.056 -90.964 -88.871 1 115.31 ? O3 PX4 1304 A 1 HETATM 5 O O4 PX4 . . . E 3 -76.297 -88.956 -87.183 1 111.7 ? O4 PX4 1304 A 1 HETATM 6 C C6 PX4 . . . E 3 -75.118 -88.371 -86.708 1 109.27 ? C6 PX4 1304 A 1 HETATM 7 C C7 PX4 . . . E 3 -74.895 -88.487 -85.189 1 106.69 ? C7 PX4 1304 A 1 HETATM 8 C C8 PX4 . . . E 3 -73.558 -87.761 -84.899 1 106.22 ? C8 PX4 1304 A 1 HETATM 9 O O5 PX4 . . . E 3 -73.563 -86.979 -83.731 1 105.77 ? O5 PX4 1304 A 1 HETATM 10 C C9 PX4 . . . E 3 -72.93 -87.58 -82.598 1 105.26 ? C9 PX4 1304 A 1 HETATM 11 O O6 PX4 . . . E 3 -72.491 -88.69 -82.648 1 105.5 ? O6 PX4 1304 A 1 HETATM 12 C C10 PX4 . . . E 3 -72.753 -86.82 -81.268 1 104.02 ? C10 PX4 1304 A 1 HETATM 13 C C11 PX4 . . . E 3 -73.593 -87.338 -80.088 1 103.16 ? C11 PX4 1304 A 1 HETATM 14 C C12 PX4 . . . E 3 -73.202 -86.516 -78.845 1 102.29 ? C12 PX4 1304 A 1 HETATM 15 C C13 PX4 . . . E 3 -73.874 -86.991 -77.558 1 101.45 ? C13 PX4 1304 A 1 HETATM 16 C C14 PX4 . . . E 3 -73.584 -86.009 -76.4 1 101.06 ? C14 PX4 1304 A 1 HETATM 17 C C15 PX4 . . . E 3 -74.426 -86.425 -75.176 1 100.65 ? C15 PX4 1304 A 1 HETATM 18 C C16 PX4 . . . E 3 -74.218 -85.552 -73.946 1 99.85 ? C16 PX4 1304 A 1 HETATM 19 C C17 PX4 . . . E 3 -75.406 -85.835 -73.04 1 99.7 ? C17 PX4 1304 A 1 HETATM 20 C C18 PX4 . . . E 3 -75.25 -85.115 -71.7 1 100.03 ? C18 PX4 1304 A 1 HETATM 21 C C19 PX4 . . . E 3 -76.642 -84.995 -71.06 1 100.49 ? C19 PX4 1304 A 1 HETATM 22 C C20 PX4 . . . E 3 -76.625 -84.271 -69.714 1 100.58 ? C20 PX4 1304 A 1 HETATM 23 C C21 PX4 . . . E 3 -76.485 -85.293 -68.6 1 100.74 ? C21 PX4 1304 A 1 HETATM 24 C C22 PX4 . . . E 3 -76.373 -84.544 -67.274 1 100.89 ? C22 PX4 1304 A 1 HETATM 25 O O7 PX4 . . . E 3 -75.962 -87.975 -84.403 1 104.12 ? O7 PX4 1304 A 1 HETATM 26 C C23 PX4 . . . E 3 -76.646 -88.858 -83.481 1 99.93 ? C23 PX4 1304 A 1 HETATM 27 O O8 PX4 . . . E 3 -77.736 -89.268 -83.724 1 99.25 ? O8 PX4 1304 A 1 HETATM 28 C C24 PX4 . . . E 3 -76.076 -89.291 -82.126 1 96.34 ? C24 PX4 1304 A 1 HETATM 29 C C25 PX4 . . . E 3 -77.241 -89.291 -81.114 1 93.51 ? C25 PX4 1304 A 1 HETATM 30 C C26 PX4 . . . E 3 -76.777 -89.733 -79.717 1 91.05 ? C26 PX4 1304 A 1 HETATM 31 C C27 PX4 . . . E 3 -77.704 -89.309 -78.563 1 88.51 ? C27 PX4 1304 A 1 HETATM 32 C C28 PX4 . . . E 3 -76.98 -89.551 -77.201 1 86.55 ? C28 PX4 1304 A 1 HETATM 33 C C29 PX4 . . . E 3 -77.902 -89.291 -75.989 1 85.51 ? C29 PX4 1304 A 1 HETATM 34 C C30 PX4 . . . E 3 -77.124 -89.264 -74.659 1 84.79 ? C30 PX4 1304 A 1 HETATM 35 C C31 PX4 . . . E 3 -77.916 -88.595 -73.524 1 84.03 ? C31 PX4 1304 A 1 HETATM 36 H H14 PX4 . . . E 3 -75.129 -87.43 -86.943 1 131.13 ? H14 PX4 1304 A 1 HETATM 37 H H15 PX4 . . . E 3 -74.368 -88.79 -87.158 1 131.13 ? H15 PX4 1304 A 1 HETATM 38 H H16 PX4 . . . E 3 -74.784 -89.426 -84.971 1 128.03 ? H16 PX4 1304 A 1 HETATM 39 H H17 PX4 . . . E 3 -72.869 -88.437 -84.808 1 127.47 ? H17 PX4 1304 A 1 HETATM 40 H H18 PX4 . . . E 3 -73.341 -87.193 -85.655 1 127.47 ? H18 PX4 1304 A 1 HETATM 41 H H19 PX4 . . . E 3 -71.818 -86.864 -81.016 1 124.83 ? H19 PX4 1304 A 1 HETATM 42 H H20 PX4 . . . E 3 -72.984 -85.89 -81.418 1 124.83 ? H20 PX4 1304 A 1 HETATM 43 H H21 PX4 . . . E 3 -74.537 -87.22 -80.278 1 123.79 ? H21 PX4 1304 A 1 HETATM 44 H H22 PX4 . . . E 3 -73.402 -88.277 -79.935 1 123.79 ? H22 PX4 1304 A 1 HETATM 45 H H23 PX4 . . . E 3 -73.446 -85.59 -78.998 1 122.75 ? H23 PX4 1304 A 1 HETATM 46 H H24 PX4 . . . E 3 -72.24 -86.568 -78.73 1 122.75 ? H24 PX4 1304 A 1 HETATM 47 H H25 PX4 . . . E 3 -74.833 -87.046 -77.698 1 121.75 ? H25 PX4 1304 A 1 HETATM 48 H H26 PX4 . . . E 3 -73.535 -87.869 -77.325 1 121.75 ? H26 PX4 1304 A 1 HETATM 49 H H27 PX4 . . . E 3 -72.641 -86.041 -76.173 1 121.28 ? H27 PX4 1304 A 1 HETATM 50 H H28 PX4 . . . E 3 -73.823 -85.108 -76.669 1 121.28 ? H28 PX4 1304 A 1 HETATM 51 H H29 PX4 . . . E 3 -74.201 -87.34 -74.945 1 120.77 ? H29 PX4 1304 A 1 HETATM 52 H H30 PX4 . . . E 3 -75.363 -86.391 -75.422 1 120.77 ? H30 PX4 1304 A 1 HETATM 53 H H31 PX4 . . . E 3 -74.204 -84.616 -74.197 1 119.82 ? H31 PX4 1304 A 1 HETATM 54 H H32 PX4 . . . E 3 -73.392 -85.793 -73.499 1 119.82 ? H32 PX4 1304 A 1 HETATM 55 H H33 PX4 . . . E 3 -75.468 -86.79 -72.884 1 119.64 ? H33 PX4 1304 A 1 HETATM 56 H H34 PX4 . . . E 3 -76.218 -85.529 -73.474 1 119.64 ? H34 PX4 1304 A 1 HETATM 57 H H35 PX4 . . . E 3 -74.879 -84.23 -71.844 1 120.03 ? H35 PX4 1304 A 1 HETATM 58 H H36 PX4 . . . E 3 -74.665 -85.626 -71.119 1 120.03 ? H36 PX4 1304 A 1 HETATM 59 H H37 PX4 . . . E 3 -77.223 -84.509 -71.666 1 120.59 ? H37 PX4 1304 A 1 HETATM 60 H H38 PX4 . . . E 3 -77.002 -85.886 -70.929 1 120.59 ? H38 PX4 1304 A 1 HETATM 61 H H39 PX4 . . . E 3 -75.875 -83.657 -69.686 1 120.69 ? H39 PX4 1304 A 1 HETATM 62 H H40 PX4 . . . E 3 -77.452 -83.778 -69.6 1 120.69 ? H40 PX4 1304 A 1 HETATM 63 H H41 PX4 . . . E 3 -75.688 -85.826 -68.743 1 120.89 ? H41 PX4 1304 A 1 HETATM 64 H H42 PX4 . . . E 3 -77.266 -85.869 -68.585 1 120.89 ? H42 PX4 1304 A 1 HETATM 65 H H43 PX4 . . . E 3 -77.13 -83.947 -67.174 1 121.07 ? H43 PX4 1304 A 1 HETATM 66 H H44 PX4 . . . E 3 -76.365 -85.181 -66.542 1 121.07 ? H44 PX4 1304 A 1 HETATM 67 H H45 PX4 . . . E 3 -75.551 -84.029 -67.262 1 121.07 ? H45 PX4 1304 A 1 HETATM 68 H H46 PX4 . . . E 3 -75.391 -88.667 -81.841 1 115.6 ? H46 PX4 1304 A 1 HETATM 69 H H47 PX4 . . . E 3 -75.701 -90.183 -82.196 1 115.6 ? H47 PX4 1304 A 1 HETATM 70 H H48 PX4 . . . E 3 -77.61 -88.396 -81.056 1 112.22 ? H48 PX4 1304 A 1 HETATM 71 H H49 PX4 . . . E 3 -77.931 -89.898 -81.425 1 112.22 ? H49 PX4 1304 A 1 HETATM 72 H H50 PX4 . . . E 3 -75.896 -89.359 -79.554 1 109.26 ? H50 PX4 1304 A 1 HETATM 73 H H51 PX4 . . . E 3 -76.705 -90.701 -79.711 1 109.26 ? H51 PX4 1304 A 1 HETATM 74 H H52 PX4 . . . E 3 -77.921 -88.367 -78.651 1 106.21 ? H52 PX4 1304 A 1 HETATM 75 H H53 PX4 . . . E 3 -78.52 -89.833 -78.593 1 106.21 ? H53 PX4 1304 A 1 HETATM 76 H H54 PX4 . . . E 3 -76.671 -90.47 -77.169 1 103.85 ? H54 PX4 1304 A 1 HETATM 77 H H55 PX4 . . . E 3 -76.214 -88.959 -77.144 1 103.85 ? H55 PX4 1304 A 1 HETATM 78 H H56 PX4 . . . E 3 -78.348 -88.438 -76.11 1 102.62 ? H56 PX4 1304 A 1 HETATM 79 H H57 PX4 . . . E 3 -78.571 -89.992 -75.947 1 102.62 ? H57 PX4 1304 A 1 HETATM 80 H H58 PX4 . . . E 3 -76.295 -88.778 -74.791 1 101.74 ? H58 PX4 1304 A 1 HETATM 81 H H59 PX4 . . . E 3 -76.915 -90.175 -74.4 1 101.74 ? H59 PX4 1304 A 1 HETATM 82 H H60 PX4 . . . E 3 -77.304 -88.119 -72.941 1 100.84 ? H60 PX4 1304 A 1 HETATM 83 H H61 PX4 . . . E 3 -78.386 -89.273 -73.015 1 100.84 ? H61 PX4 1304 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 83 #