data_8CT3
#
_model_server_result.job_id            sUAHel7Szsv1E-1Ge8mdWw 
_model_server_result.datetime_utc      '2025-03-28 13:39:10' 
_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          8ct3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":1004}' 
#
_entry.id    8CT3 
#
_exptl.entry_id    8CT3 
_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            8CT3 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8CT3 
_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,K,L 
_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 L 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
covale ? covale1 C ND2 ASN 642 C ASN 642 1_555 F C1 NAG . C NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale2 D ND2 ASN 642 E ASN 642 1_555 J C1 NAG . E NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
#
_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                     8CT3 
_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
E 3 CLR C 1 1001 201 CLR CLR . 
F 4 NAG C 1 1002 895 NAG NAG . 
G 3 CLR C 1 1003 901 CLR CLR . 
H 5 PIO C 1 1004 901 PIO PIO . 
I 3 CLR E 1 1001 201 CLR CLR . 
J 4 NAG E 1 1002 895 NAG NAG . 
K 3 CLR E 1 1003 901 CLR CLR . 
L 5 PIO E 1 1004 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 . . . L 5 87.826 104.923 82.786 1 27.37 ? C1 PIO 1004 E 1 
HETATM 2 O O1 PIO . . . L 5 87.659 105.526 81.526 1 27.37 ? O1 PIO 1004 E 1 
HETATM 3 P P1 PIO . . . L 5 88.914 106.389 80.897 1 27.37 ? P1 PIO 1004 E 1 
HETATM 4 C C2 PIO . . . L 5 87.318 103.477 82.714 1 27.37 ? C2 PIO 1004 E 1 
HETATM 5 O O2 PIO . . . L 5 85.994 103.485 82.236 1 27.37 ? O2 PIO 1004 E 1 
HETATM 6 C C3 PIO . . . L 5 87.341 102.788 84.084 1 27.37 ? C3 PIO 1004 E 1 
HETATM 7 O O3 PIO . . . L 5 86.734 101.525 83.959 1 27.37 ? O3 PIO 1004 E 1 
HETATM 8 C C4 PIO . . . L 5 86.595 103.597 85.155 1 27.37 ? C4 PIO 1004 E 1 
HETATM 9 O O4 PIO . . . L 5 86.824 103.015 86.415 1 27.37 ? O4 PIO 1004 E 1 
HETATM 10 P P4 PIO . . . L 5 85.755 101.91 87.008 1 27.37 ? P4 PIO 1004 E 1 
HETATM 11 C C5 PIO . . . L 5 87.07 105.055 85.214 1 27.37 ? C5 PIO 1004 E 1 
HETATM 12 O O5 PIO . . . L 5 86.236 105.779 86.087 1 27.37 ? O5 PIO 1004 E 1 
HETATM 13 P P5 PIO . . . L 5 86.822 106.175 87.575 1 27.37 ? P5 PIO 1004 E 1 
HETATM 14 C C6 PIO . . . L 5 87.061 105.737 83.84 1 27.37 ? C6 PIO 1004 E 1 
HETATM 15 O O6 PIO . . . L 5 87.66 107.005 83.962 1 27.37 ? O6 PIO 1004 E 1 
HETATM 16 O O11 PIO . . . L 5 90.17 105.554 80.945 1 27.37 ? O11 PIO 1004 E 1 
HETATM 17 O O12 PIO . . . L 5 89.111 107.642 81.716 1 27.37 ? O12 PIO 1004 E 1 
HETATM 18 O O13 PIO . . . L 5 88.586 106.796 79.333 1 27.37 ? O13 PIO 1004 E 1 
HETATM 19 C C1A PIO . . . L 5 88.795 103.296 78.584 1 27.37 ? C1A PIO 1004 E 1 
HETATM 20 O O1A PIO . . . L 5 88.019 103.261 79.479 1 27.37 ? O1A PIO 1004 E 1 
HETATM 21 C C1B PIO . . . L 5 88.4 104.409 74.324 1 27.37 ? C1B PIO 1004 E 1 
HETATM 22 O O1B PIO . . . L 5 87.614 103.585 74.652 1 27.37 ? O1B PIO 1004 E 1 
HETATM 23 C C1C PIO . . . L 5 89.191 106.068 78.302 1 27.37 ? C1C PIO 1004 E 1 
HETATM 24 C C2A PIO . . . L 5 90.152 102.608 78.722 1 27.37 ? C2A PIO 1004 E 1 
HETATM 25 C C2B PIO . . . L 5 88.807 104.532 72.856 1 27.37 ? C2B PIO 1004 E 1 
HETATM 26 C C2C PIO . . . L 5 88.125 105.306 77.515 1 27.37 ? C2C PIO 1004 E 1 
HETATM 27 O O2C PIO . . . L 5 88.468 103.954 77.395 1 27.37 ? O2C PIO 1004 E 1 
HETATM 28 C C3A PIO . . . L 5 90.02 101.132 78.351 1 27.37 ? C3A PIO 1004 E 1 
HETATM 29 C C3B PIO . . . L 5 88.769 103.151 72.202 1 27.37 ? C3B PIO 1004 E 1 
HETATM 30 C C3C PIO . . . L 5 88.004 105.889 76.108 1 27.37 ? C3C PIO 1004 E 1 
HETATM 31 O O3C PIO . . . L 5 88.948 105.267 75.284 1 27.37 ? O3C PIO 1004 E 1 
HETATM 32 O O41 PIO . . . L 5 84.399 102.556 87.153 1 27.37 ? O41 PIO 1004 E 1 
HETATM 33 O O42 PIO . . . L 5 85.654 100.742 86.058 1 27.37 ? O42 PIO 1004 E 1 
HETATM 34 O O43 PIO . . . L 5 86.235 101.423 88.354 1 27.37 ? O43 PIO 1004 E 1 
HETATM 35 C C4A PIO . . . L 5 89.951 100.982 76.833 1 27.37 ? C4A PIO 1004 E 1 
HETATM 36 C C4B PIO . . . L 5 87.455 102.957 71.448 1 27.37 ? C4B PIO 1004 E 1 
HETATM 37 O O51 PIO . . . L 5 86.393 105.129 88.576 1 27.37 ? O51 PIO 1004 E 1 
HETATM 38 O O52 PIO . . . L 5 88.329 106.237 87.52 1 27.37 ? O52 PIO 1004 E 1 
HETATM 39 O O53 PIO . . . L 5 86.278 107.521 87.991 1 27.37 ? O53 PIO 1004 E 1 
HETATM 40 C C5A PIO . . . L 5 90.175 99.518 76.459 1 27.37 ? C5A PIO 1004 E 1 
HETATM 41 C C5B PIO . . . L 5 86.856 101.599 71.813 1 27.37 ? C5B PIO 1004 E 1 
HETATM 42 C C6A PIO . . . L 5 89.9 99.323 74.969 1 27.37 ? C6A PIO 1004 E 1 
HETATM 43 C C6B PIO . . . L 5 85.606 101.8 72.669 1 27.37 ? C6B PIO 1004 E 1 
HETATM 44 C C7A PIO . . . L 5 88.395 99.221 74.733 1 27.37 ? C7A PIO 1004 E 1 
HETATM 45 C C7B PIO . . . L 5 85.222 100.488 73.352 1 27.37 ? C7B PIO 1004 E 1 
HETATM 46 C C8A PIO . . . L 5 88.031 97.78 74.384 1 27.37 ? C8A PIO 1004 E 1 
HETATM 47 C C8B PIO . . . L 5 85.084 99.375 72.315 1 27.37 ? C8B PIO 1004 E 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           40 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           397 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           47 
#