data_5HYM # _model_server_result.job_id oHO-gaVhV0JFJXIbN7dGMQ _model_server_result.datetime_utc '2025-08-02 22:38:34' _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 5hym # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 5HYM # _exptl.entry_id 5HYM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 887.128 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Phosphatidylinositol _entity.pdbx_number_of_molecules 1 _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 5HYM _cell.length_a 106.98 _cell.length_b 106.98 _cell.length_c 143.39 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HYM _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C47 H83 O13 P' _chem_comp.formula_weight 887.128 _chem_comp.id T7X _chem_comp.mon_nstd_flag . _chem_comp.name Phosphatidylinositol _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 O2 C2 T7X sing 381 n n O3 C3 T7X sing 382 n n C2 C3 T7X sing 383 n n C2 C1 T7X sing 384 n n O1 C1 T7X sing 385 n n O1 P1 T7X sing 386 n n O11 P1 T7X doub 387 n n O6 C6 T7X sing 388 n n C3 C4 T7X sing 389 n n C1 C6 T7X sing 390 n n C7 C8 T7X sing 391 n n C7 O13 T7X sing 392 n n P1 O13 T7X sing 393 n n P1 O12 T7X sing 394 n n O17 C10 T7X doub 395 n n C6 C5 T7X sing 396 n n C4 O4 T7X sing 397 n n C4 C5 T7X sing 398 n n C8 O16 T7X sing 399 n n C8 C9 T7X sing 400 n n O16 C10 T7X sing 401 n n C10 C12 T7X sing 402 n n C5 O5 T7X sing 403 n n C9 O18 T7X sing 404 n n C14 C13 T7X sing 405 n n C14 C15 T7X sing 406 n n C13 C12 T7X sing 407 n n O18 C11 T7X sing 408 n n C17 C16 T7X sing 409 n n C17 C18 T7X sing 410 n n C15 C16 T7X doub 411 z n C11 O19 T7X doub 412 n n C11 C31 T7X sing 413 n n C20 C21 T7X sing 414 n n C20 C19 T7X sing 415 n n C22 C21 T7X doub 416 e n C22 C23 T7X sing 417 n n C31 C32 T7X sing 418 n n C23 C24 T7X sing 419 n n C24 C25 T7X doub 420 e n C18 C19 T7X doub 421 z n C25 C26 T7X sing 422 n n C32 C33 T7X sing 423 n n C33 C34 T7X sing 424 n n C26 C27 T7X sing 425 n n C35 C34 T7X sing 426 n n C35 C36 T7X sing 427 n n C37 C36 T7X sing 428 n n C37 C38 T7X sing 429 n n C41 C40 T7X sing 430 n n C39 C38 T7X sing 431 n n C39 C40 T7X sing 432 n n C1 H1 T7X sing 433 n n C2 H2 T7X sing 434 n n O2 H3 T7X sing 435 n n C3 H4 T7X sing 436 n n O3 H5 T7X sing 437 n n C4 H6 T7X sing 438 n n O4 H7 T7X sing 439 n n C5 H8 T7X sing 440 n n O5 H9 T7X sing 441 n n C6 H10 T7X sing 442 n n O6 H11 T7X sing 443 n n C7 H12 T7X sing 444 n n C7 H13 T7X sing 445 n n C8 H14 T7X sing 446 n n C9 H15 T7X sing 447 n n C9 H16 T7X sing 448 n n C12 H17 T7X sing 449 n n C12 H18 T7X sing 450 n n O12 H19 T7X sing 451 n n C13 H20 T7X sing 452 n n C13 H21 T7X sing 453 n n C14 H22 T7X sing 454 n n C14 H23 T7X sing 455 n n C15 H24 T7X sing 456 n n C16 H25 T7X sing 457 n n C17 H26 T7X sing 458 n n C17 H27 T7X sing 459 n n C18 H28 T7X sing 460 n n C19 H29 T7X sing 461 n n C20 H30 T7X sing 462 n n C21 H32 T7X sing 463 n n C22 H34 T7X sing 464 n n C23 H36 T7X sing 465 n n C24 H38 T7X sing 466 n n C25 H40 T7X sing 467 n n C26 H42 T7X sing 468 n n C26 H43 T7X sing 469 n n C27 H44 T7X sing 470 n n C27 H45 T7X sing 471 n n C31 H47 T7X sing 472 n n C31 H48 T7X sing 473 n n C32 H49 T7X sing 474 n n C32 H50 T7X sing 475 n n C33 H51 T7X sing 476 n n C33 H52 T7X sing 477 n n C34 H53 T7X sing 478 n n C34 H54 T7X sing 479 n n C35 H55 T7X sing 480 n n C35 H56 T7X sing 481 n n C36 H57 T7X sing 482 n n C36 H58 T7X sing 483 n n C37 H59 T7X sing 484 n n C37 H60 T7X sing 485 n n C38 H61 T7X sing 486 n n C38 H62 T7X sing 487 n n C39 H63 T7X sing 488 n n C39 H64 T7X sing 489 n n C40 H65 T7X sing 490 n n C40 H66 T7X sing 491 n n C41 H67 T7X sing 492 n n C41 H68 T7X sing 493 n n C27 C28 T7X sing 494 n n C28 C29 T7X sing 495 n n C29 C30 T7X sing 496 n n C41 C42 T7X sing 497 n n C42 C43 T7X sing 498 n n C43 C44 T7X sing 499 n n C44 C45 T7X sing 500 n n C45 C46 T7X sing 501 n n C20 H31 T7X sing 502 n n C23 H33 T7X sing 503 n n C28 H35 T7X sing 504 n n C28 H37 T7X sing 505 n n C29 H39 T7X sing 506 n n C29 H41 T7X sing 507 n n C30 H46 T7X sing 508 n n C30 H69 T7X sing 509 n n C30 H70 T7X sing 510 n n C42 H71 T7X sing 511 n n C42 H72 T7X sing 512 n n C43 H73 T7X sing 513 n n C43 H74 T7X sing 514 n n C44 H75 T7X sing 515 n n C44 H76 T7X sing 516 n n C45 H77 T7X sing 517 n n C45 H78 T7X sing 518 n n C46 H79 T7X sing 519 n n C46 H80 T7X sing 520 n n C46 C47 T7X sing 521 n n C47 H81 T7X sing 522 n n C47 H82 T7X sing 523 n n C47 H83 T7X sing 524 n n # _atom_sites.entry_id 5HYM _atom_sites.fract_transf_matrix[1][1] 0.009348 _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] 0.009348 _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] 0.006974 _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 FAD A 1 501 500 FAD FAD . C 3 T7X A 1 502 501 T7X T7X . D 4 CL A 1 503 1 CL CL . E 5 HOH A 1 601 9 HOH HOH . E 5 HOH A 2 602 14 HOH HOH . E 5 HOH A 3 603 6 HOH HOH . E 5 HOH A 4 604 15 HOH HOH . E 5 HOH A 5 605 4 HOH HOH . E 5 HOH A 6 606 7 HOH HOH . E 5 HOH A 7 607 3 HOH HOH . E 5 HOH A 8 608 12 HOH HOH . E 5 HOH A 9 609 11 HOH HOH . E 5 HOH A 10 610 13 HOH HOH . E 5 HOH A 11 611 10 HOH HOH . E 5 HOH A 12 612 5 HOH HOH . E 5 HOH A 13 613 2 HOH HOH . E 5 HOH A 14 614 8 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 C C1 T7X . . . C 3 -6.043 1.94 -14.758 1 42.87 ? C1 T7X 502 A 1 HETATM 2 O O1 T7X . . . C 3 -4.864 1.996 -15.421 1 36.67 ? O1 T7X 502 A 1 HETATM 3 P P1 T7X . . . C 3 -3.581 2.373 -14.438 1 38.2 ? P1 T7X 502 A 1 HETATM 4 C C2 T7X . . . C 3 -7.248 2.429 -15.658 1 43.45 ? C2 T7X 502 A 1 HETATM 5 O O2 T7X . . . C 3 -6.963 3.724 -16.065 1 41.87 ? O2 T7X 502 A 1 HETATM 6 C C3 T7X . . . C 3 -8.581 2.351 -14.857 1 42.08 ? C3 T7X 502 A 1 HETATM 7 O O3 T7X . . . C 3 -9.676 2.725 -15.696 1 44.14 ? O3 T7X 502 A 1 HETATM 8 C C4 T7X . . . C 3 -8.808 0.966 -14.242 1 40.75 ? C4 T7X 502 A 1 HETATM 9 O O4 T7X . . . C 3 -10.015 1.021 -13.452 1 44.92 ? O4 T7X 502 A 1 HETATM 10 C C5 T7X . . . C 3 -7.634 0.496 -13.386 1 42.03 ? C5 T7X 502 A 1 HETATM 11 O O5 T7X . . . C 3 -7.795 -0.788 -12.753 1 42.78 ? O5 T7X 502 A 1 HETATM 12 C C6 T7X . . . C 3 -6.347 0.467 -14.243 1 43.26 ? C6 T7X 502 A 1 HETATM 13 O O6 T7X . . . C 3 -6.459 -0.362 -15.367 1 39.33 ? O6 T7X 502 A 1 HETATM 14 C C7 T7X . . . C 3 -4.102 5.185 -14.609 1 32.28 ? C7 T7X 502 A 1 HETATM 15 C C8 T7X . . . C 3 -5.026 6.244 -13.879 1 33.34 ? C8 T7X 502 A 1 HETATM 16 C C9 T7X . . . C 3 -5.816 5.553 -12.757 1 30.39 ? C9 T7X 502 A 1 HETATM 17 C C10 T7X . . . C 3 -4.975 8.723 -13.404 1 33.38 ? C10 T7X 502 A 1 HETATM 18 C C11 T7X . . . C 3 -6.94 5.944 -10.825 1 38.34 ? C11 T7X 502 A 1 HETATM 19 O O11 T7X . . . C 3 -2.419 2.294 -15.39 1 39.01 ? O11 T7X 502 A 1 HETATM 20 C C12 T7X . . . C 3 -5.024 9.357 -12.036 1 36.89 ? C12 T7X 502 A 1 HETATM 21 O O12 T7X . . . C 3 -3.444 1.341 -13.295 1 33.67 ? O12 T7X 502 A 1 HETATM 22 C C13 T7X . . . C 3 -5.994 10.528 -12.093 1 38.31 ? C13 T7X 502 A 1 HETATM 23 O O13 T7X . . . C 3 -3.822 3.979 -13.841 1 35.66 ? O13 T7X 502 A 1 HETATM 24 C C14 T7X . . . C 3 -5.183 11.806 -12.244 1 38.67 ? C14 T7X 502 A 1 HETATM 25 C C15 T7X . . . C 3 -5.276 12.577 -10.912 1 35.29 ? C15 T7X 502 A 1 HETATM 26 C C16 T7X . . . C 3 -4.266 13.301 -10.4 1 34.12 ? C16 T7X 502 A 1 HETATM 27 O O16 T7X . . . C 3 -4.342 7.424 -13.499 1 33.46 ? O16 T7X 502 A 1 HETATM 28 C C17 T7X . . . C 3 -2.895 13.463 -11.052 1 35.41 ? C17 T7X 502 A 1 HETATM 29 O O17 T7X . . . C 3 -5.42 9.436 -14.258 1 30.53 ? O17 T7X 502 A 1 HETATM 30 C C18 T7X . . . C 3 -1.881 13.364 -9.897 1 35.61 ? C18 T7X 502 A 1 HETATM 31 O O18 T7X . . . C 3 -5.559 5.803 -11.378 1 31.36 ? O18 T7X 502 A 1 HETATM 32 C C19 T7X . . . C 3 -0.824 14.123 -9.776 1 35.65 ? C19 T7X 502 A 1 HETATM 33 O O19 T7X . . . C 3 -7.626 5.006 -10.711 1 39.04 ? O19 T7X 502 A 1 HETATM 34 C C20 T7X . . . C 3 -0.526 15.168 -10.814 1 37.04 ? C20 T7X 502 A 1 HETATM 35 C C21 T7X . . . C 3 0.8 15.826 -10.432 1 37.6 ? C21 T7X 502 A 1 HETATM 36 C C22 T7X . . . C 3 0.803 17.159 -10.514 1 37.93 ? C22 T7X 502 A 1 HETATM 37 C C23 T7X . . . C 3 2.054 17.963 -10.204 1 37.11 ? C23 T7X 502 A 1 HETATM 38 C C24 T7X . . . C 3 1.741 19.472 -10.148 1 35.54 ? C24 T7X 502 A 1 HETATM 39 C C25 T7X . . . C 3 2.139 20.048 -9.016 1 37.6 ? C25 T7X 502 A 1 HETATM 40 C C26 T7X . . . C 3 1.958 21.517 -8.658 1 37.2 ? C26 T7X 502 A 1 HETATM 41 C C27 T7X . . . C 3 2.399 21.681 -7.171 1 37.65 ? C27 T7X 502 A 1 HETATM 42 C C31 T7X . . . C 3 -7.724 7.248 -10.46 1 34.09 ? C31 T7X 502 A 1 HETATM 43 C C32 T7X . . . C 3 -8.012 7.447 -8.943 1 33.45 ? C32 T7X 502 A 1 HETATM 44 C C33 T7X . . . C 3 -8.331 8.953 -8.67 1 33.29 ? C33 T7X 502 A 1 HETATM 45 C C34 T7X . . . C 3 -7.771 9.49 -7.286 1 34.71 ? C34 T7X 502 A 1 HETATM 46 C C35 T7X . . . C 3 -6.575 10.476 -7.486 1 32.62 ? C35 T7X 502 A 1 HETATM 47 C C36 T7X . . . C 3 -5.499 10.339 -6.378 1 29.57 ? C36 T7X 502 A 1 HETATM 48 C C37 T7X . . . C 3 -4.189 11.055 -6.833 1 27.93 ? C37 T7X 502 A 1 HETATM 49 C C38 T7X . . . C 3 -3.11 11.13 -5.704 1 27.36 ? C38 T7X 502 A 1 HETATM 50 C C39 T7X . . . C 3 -1.84 11.881 -6.266 1 26.7 ? C39 T7X 502 A 1 HETATM 51 C C40 T7X . . . C 3 -0.515 11.866 -5.434 1 23.6 ? C40 T7X 502 A 1 HETATM 52 C C41 T7X . . . C 3 0.648 12.188 -6.454 1 23.42 ? C41 T7X 502 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 52 #