data_5EGI # _model_server_result.job_id q8mLw_xWFaGHMOErd2UvOA _model_server_result.datetime_utc '2024-11-16 16:41:09' _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 5egi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 5EGI # _exptl.entry_id 5EGI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 1047.088 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate' _entity.pdbx_number_of_molecules 3 _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 5EGI _cell.length_a 102.05 _cell.length_b 102.05 _cell.length_c 279.99 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EGI _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? 2 D N N ? 2 E N N ? 2 G 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 metalc ? metalc1 F CA CA . B CA 302 1_555 J O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc2 F CA CA . B CA 302 1_555 J O HOH . B HOH 401 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc3 F CA CA . B CA 302 1_555 J O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc4 F CA CA . B CA 302 1_555 J O HOH . B HOH 402 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc5 F CA CA . B CA 302 1_555 K O HOH . C HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc6 F CA CA . B CA 302 1_555 K O HOH . C HOH 404 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? # _chem_comp.formula 'C47 H85 O19 P3' _chem_comp.formula_weight 1047.088 _chem_comp.id PT5 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Phosphatidylinositol 4,5-bisphosphate;PtdIns(4,5)P2' # 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 C23 C24 PT5 sing 353 n n C23 C22 PT5 sing 354 n n C22 C21 PT5 doub 355 e n C21 C20 PT5 sing 356 n n C20 C19 PT5 sing 357 n n C19 C18 PT5 doub 358 z n C16 C17 PT5 sing 359 n n C16 C15 PT5 doub 360 z n C18 C17 PT5 sing 361 n n C15 C14 PT5 sing 362 n n C14 C13 PT5 sing 363 n n C13 C12 PT5 sing 364 n n O17 C10 PT5 doub 365 n n O52 P5 PT5 doub 366 n n O6 C6 PT5 sing 367 n n C12 C10 PT5 sing 368 n n O53 P5 PT5 sing 369 n n C10 O16 PT5 sing 370 n n P5 O5 PT5 sing 371 n n P5 O51 PT5 sing 372 n n O5 C5 PT5 sing 373 n n C5 C6 PT5 sing 374 n n C5 C4 PT5 sing 375 n n C6 C1 PT5 sing 376 n n C1 C2 PT5 sing 377 n n C1 O1 PT5 sing 378 n n O16 C8 PT5 sing 379 n n C7 O13 PT5 sing 380 n n C7 C8 PT5 sing 381 n n C2 O2 PT5 sing 382 n n C2 C3 PT5 sing 383 n n O13 P1 PT5 sing 384 n n C8 C9 PT5 sing 385 n n O4 C4 PT5 sing 386 n n O4 P4 PT5 sing 387 n n C4 C3 PT5 sing 388 n n C3 O3 PT5 sing 389 n n O1 P1 PT5 sing 390 n n O42 P4 PT5 doub 391 n n P1 O11 PT5 doub 392 n n P1 O12 PT5 sing 393 n n P4 O41 PT5 sing 394 n n P4 O43 PT5 sing 395 n n C9 O18 PT5 sing 396 n n C31 C11 PT5 sing 397 n n C31 C32 PT5 sing 398 n n O18 C11 PT5 sing 399 n n C11 O19 PT5 doub 400 n n C32 C33 PT5 sing 401 n n C33 C34 PT5 sing 402 n n C34 C35 PT5 sing 403 n n C35 C36 PT5 sing 404 n n C36 C37 PT5 sing 405 n n C37 C38 PT5 sing 406 n n C40 C39 PT5 sing 407 n n C39 C38 PT5 sing 408 n n O12 H1 PT5 sing 409 n n O6 H2 PT5 sing 410 n n C1 H3 PT5 sing 411 n n C6 H4 PT5 sing 412 n n C2 H5 PT5 sing 413 n n O2 H6 PT5 sing 414 n n C3 H7 PT5 sing 415 n n O3 H8 PT5 sing 416 n n C4 H9 PT5 sing 417 n n O41 H10 PT5 sing 418 n n O43 H11 PT5 sing 419 n n C5 H12 PT5 sing 420 n n O51 H13 PT5 sing 421 n n O53 H14 PT5 sing 422 n n C7 H15 PT5 sing 423 n n C7 H16 PT5 sing 424 n n C8 H17 PT5 sing 425 n n C9 H18 PT5 sing 426 n n C9 H19 PT5 sing 427 n n C12 H20 PT5 sing 428 n n C12 H21 PT5 sing 429 n n C13 H22 PT5 sing 430 n n C13 H23 PT5 sing 431 n n C14 H24 PT5 sing 432 n n C14 H25 PT5 sing 433 n n C15 H26 PT5 sing 434 n n C16 H28 PT5 sing 435 n n C17 H30 PT5 sing 436 n n C17 H31 PT5 sing 437 n n C18 H32 PT5 sing 438 n n C19 H33 PT5 sing 439 n n C20 H34 PT5 sing 440 n n C20 H35 PT5 sing 441 n n C21 H36 PT5 sing 442 n n C22 H38 PT5 sing 443 n n C23 H40 PT5 sing 444 n n C23 H41 PT5 sing 445 n n C24 H42 PT5 sing 446 n n C31 H45 PT5 sing 447 n n C31 H46 PT5 sing 448 n n C32 H47 PT5 sing 449 n n C32 H48 PT5 sing 450 n n C33 H49 PT5 sing 451 n n C33 H50 PT5 sing 452 n n C34 H51 PT5 sing 453 n n C34 H52 PT5 sing 454 n n C35 H53 PT5 sing 455 n n C35 H54 PT5 sing 456 n n C36 H55 PT5 sing 457 n n C36 H56 PT5 sing 458 n n C37 H57 PT5 sing 459 n n C37 H58 PT5 sing 460 n n C38 H59 PT5 sing 461 n n C38 H60 PT5 sing 462 n n C39 H61 PT5 sing 463 n n C39 H62 PT5 sing 464 n n C40 H63 PT5 sing 465 n n C40 H64 PT5 sing 466 n n C24 C25 PT5 doub 467 n n C25 C26 PT5 sing 468 n n C26 C27 PT5 sing 469 n n C27 C28 PT5 sing 470 n n C28 C29 PT5 sing 471 n n C29 C30 PT5 sing 472 n n C40 C41 PT5 sing 473 n n C41 C42 PT5 sing 474 n n C42 C43 PT5 sing 475 n n C43 C44 PT5 sing 476 n n C44 C45 PT5 sing 477 n n C45 C46 PT5 sing 478 n n C46 C47 PT5 sing 479 n n C25 H27 PT5 sing 480 n n C26 H29 PT5 sing 481 n n C26 H37 PT5 sing 482 n n C27 H39 PT5 sing 483 n n C27 H43 PT5 sing 484 n n C28 H44 PT5 sing 485 n n C28 H65 PT5 sing 486 n n C29 H66 PT5 sing 487 n n C29 H67 PT5 sing 488 n n C30 H68 PT5 sing 489 n n C30 H69 PT5 sing 490 n n C30 H70 PT5 sing 491 n n C41 H71 PT5 sing 492 n n C41 H72 PT5 sing 493 n n C42 H73 PT5 sing 494 n n C42 H74 PT5 sing 495 n n C43 H75 PT5 sing 496 n n C43 H76 PT5 sing 497 n n C44 H77 PT5 sing 498 n n C44 H78 PT5 sing 499 n n C45 H79 PT5 sing 500 n n C45 H80 PT5 sing 501 n n C46 H81 PT5 sing 502 n n C46 H82 PT5 sing 503 n n C47 H83 PT5 sing 504 n n C47 H84 PT5 sing 505 n n C47 H85 PT5 sing 506 n n # _atom_sites.entry_id 5EGI _atom_sites.fract_transf_matrix[1][1] 0.009799 _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] 0.009799 _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] 0.003572 _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 D 2 PT5 A 1 301 185 PT5 PIO . E 2 PT5 B 1 301 187 PT5 PIO . F 3 CA B 1 302 7 CA CA2 . G 2 PT5 C 1 301 188 PT5 PIO . H 4 DMU C 1 302 1 DMU DMU . I 5 HOH A 1 401 6 HOH HOH . J 5 HOH B 1 401 8 HOH HOH . J 5 HOH B 2 402 9 HOH HOH . K 5 HOH C 1 401 4 HOH HOH . K 5 HOH C 2 402 3 HOH HOH . K 5 HOH C 3 403 2 HOH HOH . K 5 HOH C 4 404 1 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 O12 PT5 . . . E 2 22.647 17.534 10.329 1 131.72 ? O12 PT5 301 B 1 HETATM 2 P P1 PT5 . . . E 2 21.514 16.547 10.604 1 132.13 ? P1 PT5 301 B 1 HETATM 3 O O13 PT5 . . . E 2 21.855 15.313 11.779 1 127.47 ? O13 PT5 301 B 1 HETATM 4 O O11 PT5 . . . E 2 21.016 15.698 9.291 1 134.2 ? O11 PT5 301 B 1 HETATM 5 O O6 PT5 . . . E 2 18.427 19.53 10.705 1 143.76 ? O6 PT5 301 B 1 HETATM 6 O O1 PT5 . . . E 2 20.174 17.189 11.178 1 136.02 ? O1 PT5 301 B 1 HETATM 7 C C1 PT5 . . . E 2 20.172 18.421 11.916 1 141.32 ? C1 PT5 301 B 1 HETATM 8 C C6 PT5 . . . E 2 18.709 18.848 11.945 1 144.09 ? C6 PT5 301 B 1 HETATM 9 C C2 PT5 . . . E 2 20.758 18.261 13.353 1 141.99 ? C2 PT5 301 B 1 HETATM 10 O O2 PT5 . . . E 2 20.043 17.216 14.044 1 141.53 ? O2 PT5 301 B 1 HETATM 11 C C3 PT5 . . . E 2 20.582 19.586 14.136 1 143.16 ? C3 PT5 301 B 1 HETATM 12 O O3 PT5 . . . E 2 21.236 19.442 15.399 1 143.18 ? O3 PT5 301 B 1 HETATM 13 C C4 PT5 . . . E 2 19.134 19.91 14.367 1 144.85 ? C4 PT5 301 B 1 HETATM 14 O O4 PT5 . . . E 2 18.997 21.233 14.834 1 144.13 ? O4 PT5 301 B 1 HETATM 15 P P4 PT5 . . . E 2 18.591 21.478 16.4 1 144.34 ? P4 PT5 301 B 1 HETATM 16 O O41 PT5 . . . E 2 19.503 20.615 17.423 1 144.52 ? O41 PT5 301 B 1 HETATM 17 O O42 PT5 . . . E 2 17.029 21.095 16.681 1 143.81 ? O42 PT5 301 B 1 HETATM 18 O O43 PT5 . . . E 2 18.801 22.939 16.705 1 145.19 ? O43 PT5 301 B 1 HETATM 19 C C5 PT5 . . . E 2 18.19 19.75 13.127 1 146.59 ? C5 PT5 301 B 1 HETATM 20 O O5 PT5 . . . E 2 16.957 19.188 13.651 1 151.67 ? O5 PT5 301 B 1 HETATM 21 P P5 PT5 . . . E 2 15.526 19.542 12.901 1 154.24 ? P5 PT5 301 B 1 HETATM 22 O O52 PT5 . . . E 2 15.58 20.891 12.064 1 153.37 ? O52 PT5 301 B 1 HETATM 23 O O51 PT5 . . . E 2 15.11 18.211 11.951 1 153.73 ? O51 PT5 301 B 1 HETATM 24 O O53 PT5 . . . E 2 14.499 19.571 14.22 1 152.35 ? O53 PT5 301 B 1 HETATM 25 C C7 PT5 . . . E 2 21.356 13.958 11.586 1 121.78 ? C7 PT5 301 B 1 HETATM 26 C C8 PT5 . . . E 2 22.57 12.99 11.665 1 118.05 ? C8 PT5 301 B 1 HETATM 27 C C9 PT5 . . . E 2 22.733 11.951 10.498 1 121.38 ? C9 PT5 301 B 1 HETATM 28 O O16 PT5 . . . E 2 22.5 12.229 12.933 1 111 ? O16 PT5 301 B 1 HETATM 29 C C10 PT5 . . . E 2 23.204 12.738 13.981 1 103.81 ? C10 PT5 301 B 1 HETATM 30 O O17 PT5 . . . E 2 22.982 13.82 14.478 1 105.32 ? O17 PT5 301 B 1 HETATM 31 O O18 PT5 . . . E 2 21.396 11.424 10.04 1 126.75 ? O18 PT5 301 B 1 HETATM 32 C C11 PT5 . . . E 2 20.992 11.417 8.632 1 129.03 ? C11 PT5 301 B 1 HETATM 33 O O19 PT5 . . . E 2 20.512 12.412 7.975 1 128.33 ? O19 PT5 301 B 1 HETATM 34 C C12 PT5 . . . E 2 24.311 11.822 14.491 1 97.53 ? C12 PT5 301 B 1 HETATM 35 C C13 PT5 . . . E 2 23.96 10.781 15.573 1 91.27 ? C13 PT5 301 B 1 HETATM 36 C C14 PT5 . . . E 2 24.928 9.572 15.487 1 89.27 ? C14 PT5 301 B 1 HETATM 37 C C15 PT5 . . . E 2 24.423 8.295 16.203 1 87.24 ? C15 PT5 301 B 1 HETATM 38 C C16 PT5 . . . E 2 24.623 6.983 15.381 1 83.05 ? C16 PT5 301 B 1 HETATM 39 C C17 PT5 . . . E 2 24.869 5.719 16.263 1 81.1 ? C17 PT5 301 B 1 HETATM 40 C C18 PT5 . . . E 2 24.754 4.404 15.483 1 81.16 ? C18 PT5 301 B 1 HETATM 41 C C19 PT5 . . . E 2 24.041 3.418 15.803 1 80.68 ? C19 PT5 301 B 1 HETATM 42 C C20 PT5 . . . E 2 23.445 2.14 15.172 1 78.01 ? C20 PT5 301 B 1 HETATM 43 C C21 PT5 . . . E 2 21.926 1.885 15.387 1 75.14 ? C21 PT5 301 B 1 HETATM 44 C C22 PT5 . . . E 2 21.358 0.807 14.436 1 71.83 ? C22 PT5 301 B 1 HETATM 45 C C23 PT5 . . . E 2 20.391 -0.178 15.155 1 69.89 ? C23 PT5 301 B 1 HETATM 46 C C24 PT5 . . . E 2 19.591 -1.101 14.182 1 64.6 ? C24 PT5 301 B 1 HETATM 47 C C31 PT5 . . . E 2 21.188 10.037 7.969 1 129.61 ? C31 PT5 301 B 1 HETATM 48 C C32 PT5 . . . E 2 22.682 9.718 7.608 1 129.49 ? C32 PT5 301 B 1 HETATM 49 C C33 PT5 . . . E 2 23.092 8.238 7.901 1 127.72 ? C33 PT5 301 B 1 HETATM 50 C C34 PT5 . . . E 2 23.763 8.004 9.291 1 126.52 ? C34 PT5 301 B 1 HETATM 51 C C35 PT5 . . . E 2 22.936 8.257 10.663 1 123.12 ? C35 PT5 301 B 1 HETATM 52 C C36 PT5 . . . E 2 21.75 7.617 10.972 1 121.89 ? C36 PT5 301 B 1 HETATM 53 C C37 PT5 . . . E 2 21.793 6.219 11.63 1 120.86 ? C37 PT5 301 B 1 HETATM 54 C C38 PT5 . . . E 2 21.075 6.34 12.879 1 121.32 ? C38 PT5 301 B 1 HETATM 55 C C39 PT5 . . . E 2 20.469 5.291 13.691 1 121.96 ? C39 PT5 301 B 1 HETATM 56 C C40 PT5 . . . E 2 19.009 5.315 13.994 1 123.39 ? C40 PT5 301 B 1 HETATM 57 C C25 PT5 . . . E 2 18.145 -1.384 14.686 1 62.43 ? C25 PT5 301 B 1 HETATM 58 C C26 PT5 . . . E 2 17.422 -2.46 13.866 1 58.65 ? C26 PT5 301 B 1 HETATM 59 C C41 PT5 . . . E 2 18.195 4.052 13.668 1 123.79 ? C41 PT5 301 B 1 HETATM 60 C C42 PT5 . . . E 2 16.675 4.269 13.793 1 123.98 ? C42 PT5 301 B 1 HETATM 61 C C43 PT5 . . . E 2 16.086 3.776 15.126 1 123.79 ? C43 PT5 301 B 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 249 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 61 #