data_8DDV
#
_model_server_result.job_id            IwdBoybXkm_lakDH0bT-YQ 
_model_server_result.datetime_utc      '2024-12-26 15:49:10' 
_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          8ddv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":1402}' 
#
_entry.id    8DDV 
#
_exptl.entry_id    8DDV 
_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    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            8DDV 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DDV 
_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    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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,U,V 
_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 K N N 
? 5 O N N 
? 5 S N N 
? 5 V N N 
#
_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 482 n n 
C1 C2 PIO sing 483 n n 
C1 C6 PIO sing 484 n n 
C1 H1 PIO sing 485 n n 
O1 P1 PIO sing 486 n n 
P1 O11 PIO sing 487 n n 
O11 H11 PIO sing 488 n n 
P1 O12 PIO doub 489 n n 
P1 O13 PIO sing 490 n n 
C2 O2 PIO sing 491 n n 
C2 C3 PIO sing 492 n n 
C2 H2 PIO sing 493 n n 
O2 HO2 PIO sing 494 n n 
C3 O3 PIO sing 495 n n 
C3 C4 PIO sing 496 n n 
C3 H3 PIO sing 497 n n 
O3 HO3 PIO sing 498 n n 
C4 O4 PIO sing 499 n n 
C4 C5 PIO sing 500 n n 
C4 H4 PIO sing 501 n n 
O4 P4 PIO sing 502 n n 
P4 O41 PIO sing 503 n n 
O41 H41 PIO sing 504 n n 
P4 O42 PIO doub 505 n n 
P4 O43 PIO sing 506 n n 
O43 H43 PIO sing 507 n n 
C5 O5 PIO sing 508 n n 
C5 C6 PIO sing 509 n n 
C5 H5 PIO sing 510 n n 
O5 P5 PIO sing 511 n n 
P5 O51 PIO sing 512 n n 
O51 H51 PIO sing 513 n n 
P5 O52 PIO sing 514 n n 
O52 H52 PIO sing 515 n n 
P5 O53 PIO doub 516 n n 
C6 O6 PIO sing 517 n n 
C6 H6 PIO sing 518 n n 
O6 HO6 PIO sing 519 n n 
O13 C1C PIO sing 520 n n 
C1A O1A PIO doub 521 n n 
C1A C2A PIO sing 522 n n 
C1A O2C PIO sing 523 n n 
C1B O1B PIO doub 524 n n 
C1B C2B PIO sing 525 n n 
C1B O3C PIO sing 526 n n 
C1C C2C PIO sing 527 n n 
C1C H1C PIO sing 528 n n 
C1C H1CA PIO sing 529 n n 
C2A C3A PIO sing 530 n n 
C2A H2A PIO sing 531 n n 
C2A H2AA PIO sing 532 n n 
C2B C3B PIO sing 533 n n 
C2B H2B PIO sing 534 n n 
C2B H2BA PIO sing 535 n n 
C2C O2C PIO sing 536 n n 
C2C C3C PIO sing 537 n n 
C2C H2C PIO sing 538 n n 
C3A C4A PIO sing 539 n n 
C3A H3A PIO sing 540 n n 
C3A H3AA PIO sing 541 n n 
C3B C4B PIO sing 542 n n 
C3B H3B PIO sing 543 n n 
C3B H3BA PIO sing 544 n n 
C3C O3C PIO sing 545 n n 
C3C H3C PIO sing 546 n n 
C3C H3CA PIO sing 547 n n 
C4A C5A PIO sing 548 n n 
C4A H4A PIO sing 549 n n 
C4A H4AA PIO sing 550 n n 
C4B C5B PIO sing 551 n n 
C4B H4B PIO sing 552 n n 
C4B H4BA PIO sing 553 n n 
C5A C6A PIO sing 554 n n 
C5A H5A PIO sing 555 n n 
C5A H5AA PIO sing 556 n n 
C5B C6B PIO sing 557 n n 
C5B H5B PIO sing 558 n n 
C5B H5BA PIO sing 559 n n 
C6A C7A PIO sing 560 n n 
C6A H6A PIO sing 561 n n 
C6A H6AA PIO sing 562 n n 
C6B C7B PIO sing 563 n n 
C6B H6B PIO sing 564 n n 
C6B H6BA PIO sing 565 n n 
C7A C8A PIO sing 566 n n 
C7A H7A PIO sing 567 n n 
C7A H7AA PIO sing 568 n n 
C7B C8B PIO sing 569 n n 
C7B H7B PIO sing 570 n n 
C7B H7BA PIO sing 571 n n 
C8A H8A PIO sing 572 n n 
C8A H8AA PIO sing 573 n n 
C8A H8AB PIO sing 574 n n 
C8B H8B PIO sing 575 n n 
C8B H8BA PIO sing 576 n n 
C8B H8BB PIO sing 577 n n 
#
_atom_sites.entry_id                     8DDV 
_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
I 3 3PH A 1 1401 1401 3PH 3PH . 
J 4 9Z9 A 1 1402 1402 9Z9 9Z9 . 
K 5 PIO A 1 1403 1403 PIO PIO . 
L 4 9Z9 A 1 1404 1402 9Z9 9Z9 . 
M 6 NA A 1 1405 2 NA NA . 
N 3 3PH B 1 1401 1401 3PH 3PH . 
O 5 PIO B 1 1402 1403 PIO PIO . 
P 4 9Z9 C 1 1401 1402 9Z9 9Z9 . 
Q 3 3PH C 1 1402 1401 3PH 3PH . 
R 4 9Z9 C 1 1403 1402 9Z9 9Z9 . 
S 5 PIO C 1 1404 1403 PIO PIO . 
T 6 NA C 1 1405 1 NA NA . 
U 3 3PH D 1 1401 1401 3PH 3PH . 
V 5 PIO D 1 1402 1403 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 . . . V 5 183.163 189.736 218.591 1 59.75 ? C1 PIO 1402 D 1 
HETATM 2 O O1 PIO . . . V 5 182.302 189.067 219.479 1 59.75 ? O1 PIO 1402 D 1 
HETATM 3 P P1 PIO . . . V 5 182.744 187.614 220.119 1 59.75 ? P1 PIO 1402 D 1 
HETATM 4 C C2 PIO . . . V 5 182.974 191.243 218.826 1 59.75 ? C2 PIO 1402 D 1 
HETATM 5 O O2 PIO . . . V 5 181.604 191.495 219.03 1 59.75 ? O2 PIO 1402 D 1 
HETATM 6 C C3 PIO . . . V 5 183.463 192.119 217.667 1 59.75 ? C3 PIO 1402 D 1 
HETATM 7 O O3 PIO . . . V 5 183.064 193.447 217.9 1 59.75 ? O3 PIO 1402 D 1 
HETATM 8 C C4 PIO . . . V 5 182.873 191.645 216.332 1 59.75 ? C4 PIO 1402 D 1 
HETATM 9 O O4 PIO . . . V 5 183.23 192.48 215.247 1 59.75 ? O4 PIO 1402 D 1 
HETATM 10 P P4 PIO . . . V 5 184.692 193.24 215.111 1 59.75 ? P4 PIO 1402 D 1 
HETATM 11 C C5 PIO . . . V 5 183.275 190.195 216.042 1 59.75 ? C5 PIO 1402 D 1 
HETATM 12 O O5 PIO . . . V 5 182.645 189.794 214.849 1 59.75 ? O5 PIO 1402 D 1 
HETATM 13 P P5 PIO . . . V 5 183.405 188.734 213.838 1 59.75 ? P5 PIO 1402 D 1 
HETATM 14 C C6 PIO . . . V 5 182.822 189.255 217.167 1 59.75 ? C6 PIO 1402 D 1 
HETATM 15 O O6 PIO . . . V 5 183.429 188 216.97 1 59.75 ? O6 PIO 1402 D 1 
HETATM 16 O O11 PIO . . . V 5 182.614 186.54 219.066 1 59.75 ? O11 PIO 1402 D 1 
HETATM 17 O O12 PIO . . . V 5 181.823 187.292 221.271 1 59.75 ? O12 PIO 1402 D 1 
HETATM 18 O O13 PIO . . . V 5 184.304 187.678 220.652 1 59.75 ? O13 PIO 1402 D 1 
HETATM 19 C C1A PIO . . . V 5 183.486 187.894 224.58 1 59.75 ? C1A PIO 1402 D 1 
HETATM 20 O O1A PIO . . . V 5 184.353 188.553 225.054 1 59.75 ? O1A PIO 1402 D 1 
HETATM 21 C C1B PIO . . . V 5 186.954 186.367 225.54 1 59.75 ? C1B PIO 1402 D 1 
HETATM 22 O O1B PIO . . . V 5 186.782 187.426 226.041 1 59.75 ? O1B PIO 1402 D 1 
HETATM 23 C C1C PIO . . . V 5 184.549 187.991 221.994 1 59.75 ? C1C PIO 1402 D 1 
HETATM 24 C C2A PIO . . . V 5 182.04 188.353 224.751 1 59.75 ? C2A PIO 1402 D 1 
HETATM 25 C C2B PIO . . . V 5 188.172 185.54 225.938 1 59.75 ? C2B PIO 1402 D 1 
HETATM 26 C C2C PIO . . . V 5 184.666 186.711 222.827 1 59.75 ? C2C PIO 1402 D 1 
HETATM 27 O O2C PIO . . . V 5 183.754 186.694 223.899 1 59.75 ? O2C PIO 1402 D 1 
HETATM 28 C C3A PIO . . . V 5 181.696 188.346 226.239 1 59.75 ? C3A PIO 1402 D 1 
HETATM 29 C C3B PIO . . . V 5 187.767 184.521 226.999 1 59.75 ? C3B PIO 1402 D 1 
HETATM 30 C C3C PIO . . . V 5 186.091 186.547 223.36 1 59.75 ? C3C PIO 1402 D 1 
HETATM 31 O O3C PIO . . . V 5 186.045 185.882 224.591 1 59.75 ? O3C PIO 1402 D 1 
HETATM 32 O O41 PIO . . . V 5 184.714 194.495 215.953 1 59.75 ? O41 PIO 1402 D 1 
HETATM 33 O O42 PIO . . . V 5 184.894 193.629 213.666 1 59.75 ? O42 PIO 1402 D 1 
HETATM 34 O O43 PIO . . . V 5 185.82 192.324 215.523 1 59.75 ? O43 PIO 1402 D 1 
HETATM 35 C C4A PIO . . . V 5 182.098 187.004 226.849 1 59.75 ? C4A PIO 1402 D 1 
HETATM 36 C C4B PIO . . . V 5 187.674 185.211 228.358 1 59.75 ? C4B PIO 1402 D 1 
HETATM 37 O O51 PIO . . . V 5 183.807 187.493 214.598 1 59.75 ? O51 PIO 1402 D 1 
HETATM 38 O O52 PIO . . . V 5 182.461 188.349 212.725 1 59.75 ? O52 PIO 1402 D 1 
HETATM 39 O O53 PIO . . . V 5 184.632 189.389 213.252 1 59.75 ? O53 PIO 1402 D 1 
HETATM 40 C C5A PIO . . . V 5 182.957 187.244 228.088 1 59.75 ? C5A PIO 1402 D 1 
HETATM 41 C C5B PIO . . . V 5 187.826 184.171 229.465 1 59.75 ? C5B PIO 1402 D 1 
HETATM 42 C C6A PIO . . . V 5 182.122 187.936 229.162 1 59.75 ? C6A PIO 1402 D 1 
HETATM 43 C C6B PIO . . . V 5 187.594 184.828 230.823 1 59.75 ? C6B PIO 1402 D 1 
HETATM 44 C C7A PIO . . . V 5 181.45 186.887 230.047 1 59.75 ? C7A PIO 1402 D 1 
HETATM 45 C C7B PIO . . . V 5 186.118 185.193 230.955 1 59.75 ? C7B PIO 1402 D 1 
HETATM 46 C C8A PIO . . . V 5 182.423 186.43 231.132 1 59.75 ? C8A PIO 1402 D 1 
HETATM 47 C C8B PIO . . . V 5 185.658 184.938 232.388 1 59.75 ? C8B PIO 1402 D 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    66 
_model_server_stats.query_time_ms           346 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           47 
#