data_5VB8 # _model_server_result.job_id x-YBsFIXgrBqdXeYtWLA4w _model_server_result.datetime_utc '2024-10-27 14:25:41' _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":"C","auth_seq_id":1302}' # _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 . . . C 3 -57.691 -88.911 -89.314 1 121.29 -1 O1 PX4 1302 A 1 HETATM 2 O O2 PX4 . . . C 3 -56.183 -90.495 -90.472 1 124.22 ? O2 PX4 1302 A 1 HETATM 3 P P1 PX4 . . . C 3 -56.352 -89.062 -90.011 1 122.08 ? P1 PX4 1302 A 1 HETATM 4 O O3 PX4 . . . C 3 -56.251 -88.068 -91.341 1 123.22 ? O3 PX4 1302 A 1 HETATM 5 O O4 PX4 . . . C 3 -55.049 -88.818 -89.01 1 116.94 ? O4 PX4 1302 A 1 HETATM 6 C C6 PX4 . . . C 3 -54.706 -87.67 -88.259 1 110.01 ? C6 PX4 1302 A 1 HETATM 7 C C7 PX4 . . . C 3 -55.685 -87.503 -87.113 1 102.29 ? C7 PX4 1302 A 1 HETATM 8 C C8 PX4 . . . C 3 -56.037 -88.92 -86.637 1 100.03 ? C8 PX4 1302 A 1 HETATM 9 O O5 PX4 . . . C 3 -56.09 -89.045 -85.258 1 98.15 ? O5 PX4 1302 A 1 HETATM 10 C C9 PX4 . . . C 3 -57.236 -89.71 -84.793 1 97.6 ? C9 PX4 1302 A 1 HETATM 11 O O6 PX4 . . . C 3 -57.956 -90.235 -85.552 1 98.01 ? O6 PX4 1302 A 1 HETATM 12 C C10 PX4 . . . C 3 -57.612 -89.774 -83.319 1 97.34 ? C10 PX4 1302 A 1 HETATM 13 C C11 PX4 . . . C 3 -58.883 -90.577 -83.075 1 97.19 ? C11 PX4 1302 A 1 HETATM 14 C C12 PX4 . . . C 3 -59.058 -90.672 -81.549 1 97.63 ? C12 PX4 1302 A 1 HETATM 15 O O7 PX4 . . . C 3 -55.123 -86.651 -86.138 1 96.81 ? O7 PX4 1302 A 1 HETATM 16 C C23 PX4 . . . C 3 -55.999 -85.778 -85.436 1 91.57 ? C23 PX4 1302 A 1 HETATM 17 O O8 PX4 . . . C 3 -56.945 -85.286 -85.939 1 90.9 ? O8 PX4 1302 A 1 HETATM 18 C C24 PX4 . . . C 3 -55.754 -85.422 -83.972 1 87.67 ? C24 PX4 1302 A 1 HETATM 19 C C25 PX4 . . . C 3 -56.455 -86.391 -83.007 1 83.7 ? C25 PX4 1302 A 1 HETATM 20 C C26 PX4 . . . C 3 -56.501 -85.753 -81.635 1 81.51 ? C26 PX4 1302 A 1 HETATM 21 C C27 PX4 . . . C 3 -55.456 -86.296 -80.634 1 80.34 ? C27 PX4 1302 A 1 HETATM 22 C C28 PX4 . . . C 3 -55.887 -85.862 -79.214 1 79.25 ? C28 PX4 1302 A 1 HETATM 23 C C29 PX4 . . . C 3 -54.78 -85.962 -78.182 1 78.35 ? C29 PX4 1302 A 1 HETATM 24 C C30 PX4 . . . C 3 -55.372 -85.535 -76.83 1 78.28 ? C30 PX4 1302 A 1 HETATM 25 C C31 PX4 . . . C 3 -54.349 -85.738 -75.705 1 78.31 ? C31 PX4 1302 A 1 HETATM 26 H H14 PX4 . . . C 3 -54.741 -86.887 -88.83 1 132.01 ? H14 PX4 1302 A 1 HETATM 27 H H15 PX4 . . . C 3 -53.809 -87.772 -87.905 1 132.01 ? H15 PX4 1302 A 1 HETATM 28 H H16 PX4 . . . C 3 -56.491 -87.086 -87.456 1 122.75 ? H16 PX4 1302 A 1 HETATM 29 H H17 PX4 . . . C 3 -56.907 -89.15 -86.999 1 120.04 ? H17 PX4 1302 A 1 HETATM 30 H H18 PX4 . . . C 3 -55.378 -89.541 -86.984 1 120.04 ? H18 PX4 1302 A 1 HETATM 31 H H19 PX4 . . . C 3 -56.883 -90.184 -82.827 1 116.81 ? H19 PX4 1302 A 1 HETATM 32 H H20 PX4 . . . C 3 -57.744 -88.871 -82.99 1 116.81 ? H20 PX4 1302 A 1 HETATM 33 H H21 PX4 . . . C 3 -59.644 -90.122 -83.468 1 116.63 ? H21 PX4 1302 A 1 HETATM 34 H H22 PX4 . . . C 3 -58.794 -91.465 -83.455 1 116.63 ? H22 PX4 1302 A 1 HETATM 35 H H23 PX4 . . . C 3 -58.712 -89.868 -81.133 1 117.16 ? H23 PX4 1302 A 1 HETATM 36 H H24 PX4 . . . C 3 -58.574 -91.443 -81.216 1 117.16 ? H24 PX4 1302 A 1 HETATM 37 H H46 PX4 . . . C 3 -56.082 -84.524 -83.808 1 105.21 ? H46 PX4 1302 A 1 HETATM 38 H H47 PX4 . . . C 3 -54.8 -85.444 -83.8 1 105.21 ? H47 PX4 1302 A 1 HETATM 39 H H48 PX4 . . . C 3 -57.357 -86.564 -83.317 1 100.45 ? H48 PX4 1302 A 1 HETATM 40 H H49 PX4 . . . C 3 -55.959 -87.223 -82.964 1 100.45 ? H49 PX4 1302 A 1 HETATM 41 H H50 PX4 . . . C 3 -57.385 -85.896 -81.261 1 97.81 ? H50 PX4 1302 A 1 HETATM 42 H H51 PX4 . . . C 3 -56.361 -84.799 -81.736 1 97.81 ? H51 PX4 1302 A 1 HETATM 43 H H52 PX4 . . . C 3 -55.424 -87.264 -80.686 1 96.41 ? H52 PX4 1302 A 1 HETATM 44 H H53 PX4 . . . C 3 -54.583 -85.927 -80.839 1 96.41 ? H53 PX4 1302 A 1 HETATM 45 H H54 PX4 . . . C 3 -56.192 -84.942 -79.252 1 95.11 ? H54 PX4 1302 A 1 HETATM 46 H H55 PX4 . . . C 3 -56.626 -86.422 -78.93 1 95.11 ? H55 PX4 1302 A 1 HETATM 47 H H56 PX4 . . . C 3 -54.461 -86.877 -78.129 1 94.02 ? H56 PX4 1302 A 1 HETATM 48 H H57 PX4 . . . C 3 -54.049 -85.372 -78.424 1 94.02 ? H57 PX4 1302 A 1 HETATM 49 H H58 PX4 . . . C 3 -56.161 -86.067 -76.644 1 93.94 ? H58 PX4 1302 A 1 HETATM 50 H H59 PX4 . . . C 3 -55.62 -84.598 -76.872 1 93.94 ? H59 PX4 1302 A 1 HETATM 51 H H60 PX4 . . . C 3 -54.376 -86.66 -75.406 1 93.97 ? H60 PX4 1302 A 1 HETATM 52 H H61 PX4 . . . C 3 -53.46 -85.531 -76.035 1 93.97 ? H61 PX4 1302 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 52 #