data_8CRQ # _model_server_result.job_id Hl0-J3S9dcEwVfs3Q_N7eg _model_server_result.datetime_utc '2025-03-13 18:04:49' _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 8crq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1002}' # _entry.id 8CRQ # _exptl.entry_id 8CRQ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 746.566 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' _entity.pdbx_number_of_molecules 2 _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 8CRQ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CRQ _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 5 H N N ? 5 J N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n E NAG 1 A 1 NAG C 895 NAG 3 n E NAG 2 A 2 NAG C 896 NAG 3 n F NAG 1 F 1 NAG E 895 NAG 3 n F NAG 2 F 2 NAG E 896 NAG # 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 covale ? covale1 C ND2 ASN 642 C ASN 642 1_555 E C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 D ND2 ASN 642 E ASN 642 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 E O4 NAG . A NAG 1 1_555 E C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _chem_comp.formula 'C25 H49 O19 P3' _chem_comp.formula_weight 746.566 _chem_comp.id PIO _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate' # 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 C1 O1 PIO sing 365 n n C1 C2 PIO sing 366 n n C1 C6 PIO sing 367 n n C1 H1 PIO sing 368 n n O1 P1 PIO sing 369 n n P1 O11 PIO sing 370 n n O11 H11 PIO sing 371 n n P1 O12 PIO doub 372 n n P1 O13 PIO sing 373 n n C2 O2 PIO sing 374 n n C2 C3 PIO sing 375 n n C2 H2 PIO sing 376 n n O2 HO2 PIO sing 377 n n C3 O3 PIO sing 378 n n C3 C4 PIO sing 379 n n C3 H3 PIO sing 380 n n O3 HO3 PIO sing 381 n n C4 O4 PIO sing 382 n n C4 C5 PIO sing 383 n n C4 H4 PIO sing 384 n n O4 P4 PIO sing 385 n n P4 O41 PIO sing 386 n n O41 H41 PIO sing 387 n n P4 O42 PIO doub 388 n n P4 O43 PIO sing 389 n n O43 H43 PIO sing 390 n n C5 O5 PIO sing 391 n n C5 C6 PIO sing 392 n n C5 H5 PIO sing 393 n n O5 P5 PIO sing 394 n n P5 O51 PIO sing 395 n n O51 H51 PIO sing 396 n n P5 O52 PIO sing 397 n n O52 H52 PIO sing 398 n n P5 O53 PIO doub 399 n n C6 O6 PIO sing 400 n n C6 H6 PIO sing 401 n n O6 HO6 PIO sing 402 n n O13 C1C PIO sing 403 n n C1A O1A PIO doub 404 n n C1A C2A PIO sing 405 n n C1A O2C PIO sing 406 n n C1B O1B PIO doub 407 n n C1B C2B PIO sing 408 n n C1B O3C PIO sing 409 n n C1C C2C PIO sing 410 n n C1C H1C PIO sing 411 n n C1C H1CA PIO sing 412 n n C2A C3A PIO sing 413 n n C2A H2A PIO sing 414 n n C2A H2AA PIO sing 415 n n C2B C3B PIO sing 416 n n C2B H2B PIO sing 417 n n C2B H2BA PIO sing 418 n n C2C O2C PIO sing 419 n n C2C C3C PIO sing 420 n n C2C H2C PIO sing 421 n n C3A C4A PIO sing 422 n n C3A H3A PIO sing 423 n n C3A H3AA PIO sing 424 n n C3B C4B PIO sing 425 n n C3B H3B PIO sing 426 n n C3B H3BA PIO sing 427 n n C3C O3C PIO sing 428 n n C3C H3C PIO sing 429 n n C3C H3CA PIO sing 430 n n C4A C5A PIO sing 431 n n C4A H4A PIO sing 432 n n C4A H4AA PIO sing 433 n n C4B C5B PIO sing 434 n n C4B H4B PIO sing 435 n n C4B H4BA PIO sing 436 n n C5A C6A PIO sing 437 n n C5A H5A PIO sing 438 n n C5A H5AA PIO sing 439 n n C5B C6B PIO sing 440 n n C5B H5B PIO sing 441 n n C5B H5BA PIO sing 442 n n C6A C7A PIO sing 443 n n C6A H6A PIO sing 444 n n C6A H6AA PIO sing 445 n n C6B C7B PIO sing 446 n n C6B H6B PIO sing 447 n n C6B H6BA PIO sing 448 n n C7A C8A PIO sing 449 n n C7A H7A PIO sing 450 n n C7A H7AA PIO sing 451 n n C7B C8B PIO sing 452 n n C7B H7B PIO sing 453 n n C7B H7BA PIO sing 454 n n C8A H8A PIO sing 455 n n C8A H8AA PIO sing 456 n n C8A H8AB PIO sing 457 n n C8B H8B PIO sing 458 n n C8B H8BA PIO sing 459 n n C8B H8BB PIO sing 460 n n # _atom_sites.entry_id 8CRQ _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 G 4 CLR C 1 1001 201 CLR CLR . H 5 PIO C 1 1002 901 PIO PIO . I 4 CLR E 1 1001 201 CLR CLR . J 5 PIO E 1 1002 901 PIO PIO . # 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 PIO . . . H 5 85.761 107.763 88.315 1 65.67 ? C1 PIO 1002 C 1 HETATM 2 O O1 PIO . . . H 5 85.589 108.658 87.246 1 65.94 ? O1 PIO 1002 C 1 HETATM 3 P P1 PIO . . . H 5 86.885 109.568 86.787 1 77.42 ? P1 PIO 1002 C 1 HETATM 4 C C2 PIO . . . H 5 85.279 106.379 87.88 1 62.79 ? C2 PIO 1002 C 1 HETATM 5 O O2 PIO . . . H 5 83.934 106.485 87.494 1 64.84 ? O2 PIO 1002 C 1 HETATM 6 C C3 PIO . . . H 5 85.384 105.372 89.027 1 63.52 ? C3 PIO 1002 C 1 HETATM 7 O O3 PIO . . . H 5 84.896 104.127 88.594 1 67.9 ? O3 PIO 1002 C 1 HETATM 8 C C4 PIO . . . H 5 84.582 105.824 90.251 1 60.78 ? C4 PIO 1002 C 1 HETATM 9 O O4 PIO . . . H 5 84.897 104.975 91.325 1 65.83 ? O4 PIO 1002 C 1 HETATM 10 P P4 PIO . . . H 5 83.965 103.652 91.633 1 77.88 ? P4 PIO 1002 C 1 HETATM 11 C C5 PIO . . . H 5 84.931 107.256 90.682 1 64.8 ? C5 PIO 1002 C 1 HETATM 12 O O5 PIO . . . H 5 83.972 107.688 91.615 1 70.25 ? O5 PIO 1002 C 1 HETATM 13 P P5 PIO . . . H 5 84.501 108.091 93.12 1 76.7 ? P5 PIO 1002 C 1 HETATM 14 C C6 PIO . . . H 5 84.99 108.278 89.537 1 68.15 ? C6 PIO 1002 C 1 HETATM 15 O O6 PIO . . . H 5 85.638 109.434 90.01 1 69.76 ? O6 PIO 1002 C 1 HETATM 16 O O11 PIO . . . H 5 88.089 108.677 86.625 1 68.94 ? O11 PIO 1002 C 1 HETATM 17 O O12 PIO . . . H 5 87.172 110.605 87.846 1 68.2 ? O12 PIO 1002 C 1 HETATM 18 O O13 PIO . . . H 5 86.572 110.313 85.352 1 70.41 ? O13 PIO 1002 C 1 HETATM 19 C C1A PIO . . . H 5 87.102 107.043 83.818 1 67.99 ? C1A PIO 1002 C 1 HETATM 20 O O1A PIO . . . H 5 86.786 106.738 84.919 1 70.14 ? O1A PIO 1002 C 1 HETATM 21 C C1B PIO . . . H 5 85.589 108.731 80.041 1 66.77 ? C1B PIO 1002 C 1 HETATM 22 O O1B PIO . . . H 5 84.565 108.191 80.297 1 63.84 ? O1B PIO 1002 C 1 HETATM 23 C C1C PIO . . . H 5 87.11 109.763 84.186 1 62.78 ? C1C PIO 1002 C 1 HETATM 24 C C2A PIO . . . H 5 88.444 106.582 83.258 1 65.28 ? C2A PIO 1002 C 1 HETATM 25 C C2B PIO . . . H 5 85.995 108.999 78.593 1 69.56 ? C2B PIO 1002 C 1 HETATM 26 C C2C PIO . . . H 5 85.984 109.127 83.372 1 68.01 ? C2C PIO 1002 C 1 HETATM 27 O O2C PIO . . . H 5 86.239 107.795 83.016 1 69.08 ? O2C PIO 1002 C 1 HETATM 28 C C3A PIO . . . H 5 88.259 105.246 82.544 1 60.31 ? C3A PIO 1002 C 1 HETATM 29 C C3B PIO . . . H 5 86.019 107.692 77.802 1 66.71 ? C3B PIO 1002 C 1 HETATM 30 C C3C PIO . . . H 5 85.81 109.891 82.065 1 69.46 ? C3C PIO 1002 C 1 HETATM 31 O O3C PIO . . . H 5 86.436 109.134 81.075 1 68.71 ? O3C PIO 1002 C 1 HETATM 32 O O41 PIO . . . H 5 82.545 104.079 91.913 1 68.75 ? O41 PIO 1002 C 1 HETATM 33 O O42 PIO . . . H 5 83.991 102.728 90.444 1 67.19 ? O42 PIO 1002 C 1 HETATM 34 O O43 PIO . . . H 5 84.517 102.919 92.832 1 73.56 ? O43 PIO 1002 C 1 HETATM 35 C C4A PIO . . . H 5 87.746 105.501 81.13 1 62.1 ? C4A PIO 1002 C 1 HETATM 36 C C4B PIO . . . H 5 84.787 107.611 76.906 1 63.51 ? C4B PIO 1002 C 1 HETATM 37 O O51 PIO . . . H 5 84.467 106.87 94.008 1 66.93 ? O51 PIO 1002 C 1 HETATM 38 O O52 PIO . . . H 5 85.916 108.603 93.026 1 70.76 ? O52 PIO 1002 C 1 HETATM 39 O O53 PIO . . . H 5 83.615 109.168 93.696 1 65.7 ? O53 PIO 1002 C 1 HETATM 40 C C5A PIO . . . H 5 87.969 104.259 80.273 1 61.16 ? C5A PIO 1002 C 1 HETATM 41 C C5B PIO . . . H 5 84.132 106.245 77.089 1 67.5 ? C5B PIO 1002 C 1 HETATM 42 C C6A PIO . . . H 5 86.981 104.266 79.111 1 65.98 ? C6A PIO 1002 C 1 HETATM 43 C C6B PIO . . . H 5 82.899 106.376 77.984 1 68.96 ? C6B PIO 1002 C 1 HETATM 44 C C7A PIO . . . H 5 87.445 103.283 78.04 1 64.69 ? C7A PIO 1002 C 1 HETATM 45 C C7B PIO . . . H 5 82.342 104.996 78.333 1 68.74 ? C7B PIO 1002 C 1 HETATM 46 C C8A PIO . . . H 5 86.307 103.014 77.058 1 64.59 ? C8A PIO 1002 C 1 HETATM 47 C C8B PIO . . . H 5 82.353 104.077 77.11 1 64.58 ? C8B PIO 1002 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 47 #