data_8YK0 # _model_server_result.job_id zncza78ryX30ABVItnHKDw _model_server_result.datetime_utc '2025-03-13 00:57:46' _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 8yk0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":402}' # _entry.id 8YK0 # _exptl.entry_id 8YK0 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 777.06 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate' _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 8YK0 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YK0 _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_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 _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 ? _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 ? 6 F N N ? 6 G N N ? 6 P N N ? 6 Q N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 170 B CYS 191 1_555 A SG CYS 195 B CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 E SG CYS 170 A CYS 191 1_555 E SG CYS 195 A CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? # _chem_comp.formula 'C42 H81 O10 P' _chem_comp.formula_weight 777.06 _chem_comp.id MW9 _chem_comp.mon_nstd_flag . _chem_comp.name '(21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "1-stearoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol)" # 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 C33 C32 MW9 doub 312 z n C33 C34 MW9 sing 313 n n C32 C31 MW9 sing 314 n n C34 C35 MW9 sing 315 n n C35 C36 MW9 sing 316 n n C31 C30 MW9 sing 317 n n C30 C29 MW9 sing 318 n n C36 C37 MW9 sing 319 n n C28 C29 MW9 sing 320 n n C28 C27 MW9 sing 321 n n O4 P MW9 doub 322 n n C37 C38 MW9 sing 323 n n C27 C26 MW9 sing 324 n n C26 C25 MW9 sing 325 n n O9 C24 MW9 doub 326 n n C38 C39 MW9 sing 327 n n P O2 MW9 sing 328 n n P O3 MW9 sing 329 n n P O5 MW9 sing 330 n n C24 C25 MW9 sing 331 n n C24 O8 MW9 sing 332 n n O2 C20 MW9 sing 333 n n O8 C19 MW9 sing 334 n n O5 C21 MW9 sing 335 n n C21 C22 MW9 sing 336 n n C39 C40 MW9 sing 337 n n C20 C19 MW9 sing 338 n n C19 C18 MW9 sing 339 n n O7 C22 MW9 sing 340 n n C40 C41 MW9 sing 341 n n C22 C23 MW9 sing 342 n n C16 C15 MW9 sing 343 n n C16 C17 MW9 sing 344 n n O6 C23 MW9 sing 345 n n C18 O1 MW9 sing 346 n n C15 C14 MW9 sing 347 n n C17 O1 MW9 sing 348 n n C17 O MW9 doub 349 n n C14 C13 MW9 sing 350 n n C2 C3 MW9 sing 351 n n C2 C1 MW9 sing 352 n n C4 C3 MW9 sing 353 n n C4 C5 MW9 sing 354 n n C13 C12 MW9 sing 355 n n C C1 MW9 sing 356 n n C5 C6 MW9 sing 357 n n C12 C11 MW9 sing 358 n n C6 C7 MW9 sing 359 n n C9 C10 MW9 sing 360 n n C9 C8 MW9 sing 361 n n C10 C11 MW9 sing 362 n n C7 C8 MW9 sing 363 n n C H1 MW9 sing 364 n n C H2 MW9 sing 365 n n C H3 MW9 sing 366 n n C1 H4 MW9 sing 367 n n C1 H5 MW9 sing 368 n n C10 H6 MW9 sing 369 n n C10 H7 MW9 sing 370 n n C11 H8 MW9 sing 371 n n C11 H9 MW9 sing 372 n n C12 H10 MW9 sing 373 n n C12 H11 MW9 sing 374 n n C13 H12 MW9 sing 375 n n C13 H13 MW9 sing 376 n n C14 H14 MW9 sing 377 n n C14 H15 MW9 sing 378 n n C15 H16 MW9 sing 379 n n C15 H17 MW9 sing 380 n n C16 H18 MW9 sing 381 n n C16 H19 MW9 sing 382 n n C18 H20 MW9 sing 383 n n C18 H21 MW9 sing 384 n n C19 H22 MW9 sing 385 n n C2 H23 MW9 sing 386 n n C2 H24 MW9 sing 387 n n C20 H25 MW9 sing 388 n n C20 H26 MW9 sing 389 n n C21 H27 MW9 sing 390 n n C21 H28 MW9 sing 391 n n C22 H29 MW9 sing 392 n n C23 H30 MW9 sing 393 n n C23 H31 MW9 sing 394 n n C25 H32 MW9 sing 395 n n C25 H33 MW9 sing 396 n n C26 H34 MW9 sing 397 n n C26 H35 MW9 sing 398 n n C27 H36 MW9 sing 399 n n C27 H37 MW9 sing 400 n n C28 H38 MW9 sing 401 n n C28 H39 MW9 sing 402 n n C29 H40 MW9 sing 403 n n C29 H41 MW9 sing 404 n n C3 H42 MW9 sing 405 n n C3 H43 MW9 sing 406 n n C30 H44 MW9 sing 407 n n C30 H45 MW9 sing 408 n n C31 H46 MW9 sing 409 n n C31 H47 MW9 sing 410 n n C32 H48 MW9 sing 411 n n C33 H49 MW9 sing 412 n n C34 H50 MW9 sing 413 n n C34 H51 MW9 sing 414 n n C35 H52 MW9 sing 415 n n C35 H53 MW9 sing 416 n n C36 H54 MW9 sing 417 n n C36 H55 MW9 sing 418 n n C37 H56 MW9 sing 419 n n C37 H57 MW9 sing 420 n n C38 H58 MW9 sing 421 n n C38 H59 MW9 sing 422 n n C39 H60 MW9 sing 423 n n C39 H61 MW9 sing 424 n n C4 H62 MW9 sing 425 n n C4 H63 MW9 sing 426 n n C40 H64 MW9 sing 427 n n C40 H65 MW9 sing 428 n n C41 H66 MW9 sing 429 n n C41 H67 MW9 sing 430 n n C41 H68 MW9 sing 431 n n C5 H69 MW9 sing 432 n n C5 H70 MW9 sing 433 n n C6 H71 MW9 sing 434 n n C6 H72 MW9 sing 435 n n C7 H73 MW9 sing 436 n n C7 H74 MW9 sing 437 n n C8 H75 MW9 sing 438 n n C8 H76 MW9 sing 439 n n C9 H77 MW9 sing 440 n n C9 H78 MW9 sing 441 n n O3 H79 MW9 sing 442 n n O6 H80 MW9 sing 443 n n O7 H81 MW9 sing 444 n n # _atom_sites.entry_id 8YK0 _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 F 6 MW9 B 1 401 402 MW9 LIG . G 6 MW9 B 1 402 403 MW9 LIG . H 7 CLR B 1 403 411 CLR CLR . I 7 CLR B 1 404 412 CLR CLR . J 7 CLR B 1 405 415 CLR CLR . K 7 CLR B 1 406 417 CLR CLR . L 7 CLR B 1 407 424 CLR CLR . M 7 CLR B 1 408 425 CLR CLR . N 7 CLR A 1 401 409 CLR CLR . O 7 CLR A 1 402 413 CLR CLR . P 6 MW9 A 1 403 403 MW9 LIG . Q 6 MW9 A 1 404 420 MW9 LIG . R 7 CLR A 1 405 423 CLR CLR . S 7 CLR A 1 406 431 CLR CLR . T 7 CLR A 1 407 433 CLR CLR . # 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 MW9 . . . G 6 118.08 121.701 142.229 1 100.27 ? C MW9 402 B 1 HETATM 2 O O MW9 . . . G 6 120.887 124.044 157.194 1 100.27 ? O MW9 402 B 1 HETATM 3 C C1 MW9 . . . G 6 117.323 123.02 142.487 1 100.27 ? C1 MW9 402 B 1 HETATM 4 C C10 MW9 . . . G 6 115.648 125.736 151.283 1 100.27 ? C10 MW9 402 B 1 HETATM 5 C C11 MW9 . . . G 6 117.149 125.769 151.634 1 100.27 ? C11 MW9 402 B 1 HETATM 6 C C12 MW9 . . . G 6 117.526 124.436 152.327 1 100.27 ? C12 MW9 402 B 1 HETATM 7 C C13 MW9 . . . G 6 117.382 124.615 153.858 1 100.27 ? C13 MW9 402 B 1 HETATM 8 C C14 MW9 . . . G 6 118.463 123.768 154.569 1 100.27 ? C14 MW9 402 B 1 HETATM 9 C C15 MW9 . . . G 6 119.851 124.378 154.266 1 100.27 ? C15 MW9 402 B 1 HETATM 10 C C16 MW9 . . . G 6 120.215 125.395 155.369 1 100.27 ? C16 MW9 402 B 1 HETATM 11 C C17 MW9 . . . G 6 121.249 124.752 156.317 1 100.27 ? C17 MW9 402 B 1 HETATM 12 C C18 MW9 . . . G 6 123.011 126.328 156.438 1 100.27 ? C18 MW9 402 B 1 HETATM 13 C C19 MW9 . . . G 6 123.473 126.995 155.141 1 100.27 ? C19 MW9 402 B 1 HETATM 14 C C2 MW9 . . . G 6 117.083 123.184 144.001 1 100.27 ? C2 MW9 402 B 1 HETATM 15 C C20 MW9 . . . G 6 124.849 126.443 154.752 1 100.27 ? C20 MW9 402 B 1 HETATM 16 C C21 MW9 . . . G 6 128.181 125.165 156.864 1 100.27 ? C21 MW9 402 B 1 HETATM 17 C C22 MW9 . . . G 6 129.525 124.582 157.31 1 100.27 ? C22 MW9 402 B 1 HETATM 18 C C23 MW9 . . . G 6 129.476 124.299 158.816 1 100.27 ? C23 MW9 402 B 1 HETATM 19 C C24 MW9 . . . G 6 122.816 129.127 154.405 1 100.27 ? C24 MW9 402 B 1 HETATM 20 C C25 MW9 . . . G 6 123.032 128.923 152.888 1 100.27 ? C25 MW9 402 B 1 HETATM 21 C C26 MW9 . . . G 6 121.756 128.313 152.262 1 100.27 ? C26 MW9 402 B 1 HETATM 22 C C27 MW9 . . . G 6 121.906 128.347 150.721 1 100.27 ? C27 MW9 402 B 1 HETATM 23 C C28 MW9 . . . G 6 121.817 129.82 150.25 1 100.27 ? C28 MW9 402 B 1 HETATM 24 C C29 MW9 . . . G 6 120.451 130.043 149.558 1 100.27 ? C29 MW9 402 B 1 HETATM 25 C C3 MW9 . . . G 6 117.094 124.688 144.351 1 100.27 ? C3 MW9 402 B 1 HETATM 26 C C30 MW9 . . . G 6 120.704 130.232 148.042 1 100.27 ? C30 MW9 402 B 1 HETATM 27 C C31 MW9 . . . G 6 119.812 129.242 147.252 1 100.27 ? C31 MW9 402 B 1 HETATM 28 C C32 MW9 . . . G 6 118.967 130.045 146.235 1 100.27 ? C32 MW9 402 B 1 HETATM 29 C C33 MW9 . . . G 6 118.26 129.26 145.43 1 100.27 ? C33 MW9 402 B 1 HETATM 30 C C34 MW9 . . . G 6 117.271 129.042 144.27 1 100.27 ? C34 MW9 402 B 1 HETATM 31 C C35 MW9 . . . G 6 117.572 130.087 143.18 1 100.27 ? C35 MW9 402 B 1 HETATM 32 C C36 MW9 . . . G 6 116.269 130.773 142.716 1 100.27 ? C36 MW9 402 B 1 HETATM 33 C C37 MW9 . . . G 6 115.279 130.876 143.897 1 100.27 ? C37 MW9 402 B 1 HETATM 34 C C38 MW9 . . . G 6 113.944 131.468 143.395 1 100.27 ? C38 MW9 402 B 1 HETATM 35 C C39 MW9 . . . G 6 113.477 130.708 142.132 1 100.27 ? C39 MW9 402 B 1 HETATM 36 C C4 MW9 . . . G 6 116.603 124.88 145.805 1 100.27 ? C4 MW9 402 B 1 HETATM 37 C C40 MW9 . . . G 6 112.03 131.136 141.817 1 100.27 ? C40 MW9 402 B 1 HETATM 38 C C41 MW9 . . . G 6 111.414 130.146 140.811 1 100.27 ? C41 MW9 402 B 1 HETATM 39 C C5 MW9 . . . G 6 115.234 125.602 145.768 1 100.27 ? C5 MW9 402 B 1 HETATM 40 C C6 MW9 . . . G 6 114.973 126.322 147.111 1 100.27 ? C6 MW9 402 B 1 HETATM 41 C C7 MW9 . . . G 6 116.274 126.98 147.624 1 100.27 ? C7 MW9 402 B 1 HETATM 42 C C8 MW9 . . . G 6 116.491 126.565 149.092 1 100.27 ? C8 MW9 402 B 1 HETATM 43 C C9 MW9 . . . G 6 115.449 126.156 149.814 1 100.27 ? C9 MW9 402 B 1 HETATM 44 O O1 MW9 . . . G 6 122.627 125.002 156.141 1 100.27 ? O1 MW9 402 B 1 HETATM 45 O O2 MW9 . . . G 6 125.803 126.897 155.687 1 100.27 ? O2 MW9 402 B 1 HETATM 46 O O3 MW9 . . . G 6 127.688 128.455 154.847 1 100.27 ? O3 MW9 402 B 1 HETATM 47 O O4 MW9 . . . G 6 127.534 126.172 153.924 1 100.27 ? O4 MW9 402 B 1 HETATM 48 O O5 MW9 . . . G 6 128.39 126.466 156.352 1 100.27 ? O5 MW9 402 B 1 HETATM 49 O O6 MW9 . . . G 6 128.378 123.465 159.091 1 100.27 ? O6 MW9 402 B 1 HETATM 50 O O7 MW9 . . . G 6 130.542 125.498 157.039 1 100.27 ? O7 MW9 402 B 1 HETATM 51 O O8 MW9 . . . G 6 123.562 128.37 155.337 1 100.27 ? O8 MW9 402 B 1 HETATM 52 O O9 MW9 . . . G 6 122.021 129.919 154.789 1 100.27 ? O9 MW9 402 B 1 HETATM 53 P P MW9 . . . G 6 127.373 127.015 155.166 1 100.27 ? P MW9 402 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 53 #