data_8YR2
#
_model_server_result.job_id            set2ddh9AYYmVtPA1pie5w 
_model_server_result.datetime_utc      '2025-03-03 20:01:20' 
_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          8yr2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":702}' 
#
_entry.id    8YR2 
#
_exptl.entry_id    8YR2 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              746.566 
_entity.id                          3 
_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            8YR2 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YR2 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA 
_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
? 3 D N N 
? 3 V 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 A O GLY 71 B GLY 71 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? 
metalc ? metalc2 A O ALA 73 B ALA 73 1_555 E NA NA . B NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? 
metalc ? metalc3 A O VAL 74 B VAL 74 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc4 A OD1 ASN 78 B ASN 78 1_555 E NA NA . B NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? 
metalc ? metalc5 A O SER 318 B SER 318 1_555 E NA NA . B NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? 
metalc ? metalc6 A OD1 ASP 418 B ASP 418 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc7 A OD2 ASP 418 B ASP 418 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.177 ? 
metalc ? metalc8 A OG SER 419 B SER 419 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.895 ? 
metalc ? metalc9 B O GLY 71 A GLY 71 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc10 B O VAL 74 A VAL 74 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc11 B OD1 ASN 78 A ASN 78 1_555 W NA NA . A NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? 
metalc ? metalc12 B O SER 318 A SER 318 1_555 W NA NA . A NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc13 B O LEU 415 A LEU 415 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.026 ? 
metalc ? metalc14 B OD2 ASP 418 A ASP 418 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.077 ? 
metalc ? metalc15 B OG SER 419 A SER 419 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? 
#
_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 465 n n 
C1 C2 PIO sing 466 n n 
C1 C6 PIO sing 467 n n 
C1 H1 PIO sing 468 n n 
O1 P1 PIO sing 469 n n 
P1 O11 PIO sing 470 n n 
O11 H11 PIO sing 471 n n 
P1 O12 PIO doub 472 n n 
P1 O13 PIO sing 473 n n 
C2 O2 PIO sing 474 n n 
C2 C3 PIO sing 475 n n 
C2 H2 PIO sing 476 n n 
O2 HO2 PIO sing 477 n n 
C3 O3 PIO sing 478 n n 
C3 C4 PIO sing 479 n n 
C3 H3 PIO sing 480 n n 
O3 HO3 PIO sing 481 n n 
C4 O4 PIO sing 482 n n 
C4 C5 PIO sing 483 n n 
C4 H4 PIO sing 484 n n 
O4 P4 PIO sing 485 n n 
P4 O41 PIO sing 486 n n 
O41 H41 PIO sing 487 n n 
P4 O42 PIO doub 488 n n 
P4 O43 PIO sing 489 n n 
O43 H43 PIO sing 490 n n 
C5 O5 PIO sing 491 n n 
C5 C6 PIO sing 492 n n 
C5 H5 PIO sing 493 n n 
O5 P5 PIO sing 494 n n 
P5 O51 PIO sing 495 n n 
O51 H51 PIO sing 496 n n 
P5 O52 PIO sing 497 n n 
O52 H52 PIO sing 498 n n 
P5 O53 PIO doub 499 n n 
C6 O6 PIO sing 500 n n 
C6 H6 PIO sing 501 n n 
O6 HO6 PIO sing 502 n n 
O13 C1C PIO sing 503 n n 
C1A O1A PIO doub 504 n n 
C1A C2A PIO sing 505 n n 
C1A O2C PIO sing 506 n n 
C1B O1B PIO doub 507 n n 
C1B C2B PIO sing 508 n n 
C1B O3C PIO sing 509 n n 
C1C C2C PIO sing 510 n n 
C1C H1C PIO sing 511 n n 
C1C H1CA PIO sing 512 n n 
C2A C3A PIO sing 513 n n 
C2A H2A PIO sing 514 n n 
C2A H2AA PIO sing 515 n n 
C2B C3B PIO sing 516 n n 
C2B H2B PIO sing 517 n n 
C2B H2BA PIO sing 518 n n 
C2C O2C PIO sing 519 n n 
C2C C3C PIO sing 520 n n 
C2C H2C PIO sing 521 n n 
C3A C4A PIO sing 522 n n 
C3A H3A PIO sing 523 n n 
C3A H3AA PIO sing 524 n n 
C3B C4B PIO sing 525 n n 
C3B H3B PIO sing 526 n n 
C3B H3BA PIO sing 527 n n 
C3C O3C PIO sing 528 n n 
C3C H3C PIO sing 529 n n 
C3C H3CA PIO sing 530 n n 
C4A C5A PIO sing 531 n n 
C4A H4A PIO sing 532 n n 
C4A H4AA PIO sing 533 n n 
C4B C5B PIO sing 534 n n 
C4B H4B PIO sing 535 n n 
C4B H4BA PIO sing 536 n n 
C5A C6A PIO sing 537 n n 
C5A H5A PIO sing 538 n n 
C5A H5AA PIO sing 539 n n 
C5B C6B PIO sing 540 n n 
C5B H5B PIO sing 541 n n 
C5B H5BA PIO sing 542 n n 
C6A C7A PIO sing 543 n n 
C6A H6A PIO sing 544 n n 
C6A H6AA PIO sing 545 n n 
C6B C7B PIO sing 546 n n 
C6B H6B PIO sing 547 n n 
C6B H6BA PIO sing 548 n n 
C7A C8A PIO sing 549 n n 
C7A H7A PIO sing 550 n n 
C7A H7AA PIO sing 551 n n 
C7B C8B PIO sing 552 n n 
C7B H7B PIO sing 553 n n 
C7B H7BA PIO sing 554 n n 
C8A H8A PIO sing 555 n n 
C8A H8AA PIO sing 556 n n 
C8A H8AB PIO sing 557 n n 
C8B H8B PIO sing 558 n n 
C8B H8BA PIO sing 559 n n 
C8B H8BB PIO sing 560 n n 
#
_atom_sites.entry_id                     8YR2 
_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
C 2 41U B 1 701 701 41U 41U . 
D 3 PIO B 1 702 702 PIO PIO . 
E 4 NA B 1 703 12 NA NA . 
F 4 NA B 1 704 13 NA NA . 
G 5 CL B 1 705 6 CL CL . 
H 6 CLR B 1 706 704 CLR CLR . 
I 6 CLR B 1 707 706 CLR CLR . 
J 6 CLR B 1 708 709 CLR CLR . 
K 6 CLR B 1 709 710 CLR CLR . 
L 6 CLR B 1 710 712 CLR CLR . 
M 6 CLR B 1 711 713 CLR CLR . 
N 6 CLR B 1 712 714 CLR CLR . 
O 7 A1LX7 B 1 713 705 A1LX7 PI0 . 
P 7 A1LX7 B 1 714 716 A1LX7 PI0 . 
Q 6 CLR B 1 715 701 CLR CLR . 
R 6 CLR B 1 716 702 CLR CLR . 
S 6 CLR B 1 717 703 CLR CLR . 
T 6 CLR B 1 718 704 CLR CLR . 
U 2 41U A 1 701 701 41U 41U . 
V 3 PIO A 1 702 702 PIO PIO . 
W 4 NA A 1 703 10 NA NA . 
X 4 NA A 1 704 11 NA NA . 
Y 5 CL A 1 705 5 CL CL . 
Z 6 CLR A 1 706 707 CLR CLR . 
AA 6 CLR A 1 707 708 CLR CLR . 
BA 6 CLR A 1 708 711 CLR CLR . 
CA 6 CLR A 1 709 715 CLR CLR . 
DA 6 CLR A 1 710 718 CLR CLR . 
EA 7 A1LX7 A 1 711 712 A1LX7 PI0 . 
FA 7 A1LX7 A 1 712 713 A1LX7 PI0 . 
GA 6 CLR A 1 713 707 CLR CLR . 
HA 6 CLR A 1 714 708 CLR CLR . 
IA 6 CLR A 1 715 709 CLR CLR . 
JA 6 CLR A 1 716 713 CLR CLR . 
KA 8 HOH B 1 801 7 HOH HOH . 
KA 8 HOH B 2 802 6 HOH HOH . 
KA 8 HOH B 3 803 5 HOH HOH . 
LA 8 HOH A 1 801 4 HOH HOH . 
LA 8 HOH A 2 802 3 HOH HOH . 
LA 8 HOH A 3 803 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 C C1 PIO . . . D 3 114.06 91.508 105.616 1 30 ? C1 PIO 702 B 1 
HETATM 2 O O1 PIO . . . D 3 113.116 92.431 105.127 1 30 ? O1 PIO 702 B 1 
HETATM 3 P P1 PIO . . . D 3 112.692 92.417 103.54 1 30 ? P1 PIO 702 B 1 
HETATM 4 C C2 PIO . . . D 3 113.903 91.349 107.136 1 30 ? C2 PIO 702 B 1 
HETATM 5 O O2 PIO . . . D 3 112.602 90.896 107.398 1 30 ? O2 PIO 702 B 1 
HETATM 6 C C3 PIO . . . D 3 114.138 92.656 107.903 1 30 ? C3 PIO 702 B 1 
HETATM 7 O O3 PIO . . . D 3 112.899 93.296 108.048 1 30 ? O3 PIO 702 B 1 
HETATM 8 C C4 PIO . . . D 3 115.074 93.626 107.165 1 30 ? C4 PIO 702 B 1 
HETATM 9 O O4 PIO . . . D 3 115.648 94.554 108.062 1 30 ? O4 PIO 702 B 1 
HETATM 10 P P4 PIO . . . D 3 116.977 94.29 108.999 1 30 ? P4 PIO 702 B 1 
HETATM 11 C C5 PIO . . . D 3 116.111 92.93 106.265 1 30 ? C5 PIO 702 B 1 
HETATM 12 O O5 PIO . . . D 3 116.727 93.937 105.517 1 30 ? O5 PIO 702 B 1 
HETATM 13 P P5 PIO . . . D 3 118.23 93.694 104.9 1 30 ? P5 PIO 702 B 1 
HETATM 14 C C6 PIO . . . D 3 115.481 91.955 105.259 1 30 ? C6 PIO 702 B 1 
HETATM 15 O O6 PIO . . . D 3 116.283 90.807 105.193 1 30 ? O6 PIO 702 B 1 
HETATM 16 O O11 PIO . . . D 3 113.794 92.974 102.673 1 30 ? O11 PIO 702 B 1 
HETATM 17 O O12 PIO . . . D 3 112.401 90.992 103.138 1 30 ? O12 PIO 702 B 1 
HETATM 18 O O13 PIO . . . D 3 111.328 93.318 103.362 1 30 ? O13 PIO 702 B 1 
HETATM 19 C C1A PIO . . . D 3 109.682 92.414 106.265 1 30 ? C1A PIO 702 B 1 
HETATM 20 O O1A PIO . . . D 3 110.346 93.374 106.436 1 30 ? O1A PIO 702 B 1 
HETATM 21 C C1B PIO . . . D 3 107.801 89.879 102.118 1 30 ? C1B PIO 702 B 1 
HETATM 22 O O1B PIO . . . D 3 106.86 89.595 102.775 1 30 ? O1B PIO 702 B 1 
HETATM 23 C C1C PIO . . . D 3 110.183 92.695 102.864 1 30 ? C1C PIO 702 B 1 
HETATM 24 C C2A PIO . . . D 3 108.89 91.826 107.423 1 30 ? C2A PIO 702 B 1 
HETATM 25 C C2B PIO . . . D 3 108.356 88.888 101.097 1 30 ? C2B PIO 702 B 1 
HETATM 26 C C2C PIO . . . D 3 109.138 92.581 103.97 1 30 ? C2C PIO 702 B 1 
HETATM 27 O O2C PIO . . . D 3 109.638 91.804 105.013 1 30 ? O2C PIO 702 B 1 
HETATM 28 C C3A PIO . . . D 3 109.09 92.63 108.702 1 30 ? C3A PIO 702 B 1 
HETATM 29 C C3B PIO . . . D 3 108.034 89.274 99.657 1 30 ? C3B PIO 702 B 1 
HETATM 30 C C3C PIO . . . D 3 107.941 91.852 103.378 1 30 ? C3C PIO 702 B 1 
HETATM 31 O O3C PIO . . . D 3 108.409 91.125 102.281 1 30 ? O3C PIO 702 B 1 
HETATM 32 O O41 PIO . . . D 3 116.868 95.174 110.217 1 30 ? O41 PIO 702 B 1 
HETATM 33 O O42 PIO . . . D 3 117.068 92.849 109.441 1 30 ? O42 PIO 702 B 1 
HETATM 34 O O43 PIO . . . D 3 118.228 94.681 108.253 1 30 ? O43 PIO 702 B 1 
HETATM 35 C C4A PIO . . . D 3 109.996 91.916 109.697 1 30 ? C4A PIO 702 B 1 
HETATM 36 C C4B PIO . . . D 3 106.891 88.448 99.073 1 30 ? C4B PIO 702 B 1 
HETATM 37 O O51 PIO . . . D 3 119.051 94.946 105.089 1 30 ? O51 PIO 702 B 1 
HETATM 38 O O52 PIO . . . D 3 118.125 93.36 103.429 1 30 ? O52 PIO 702 B 1 
HETATM 39 O O53 PIO . . . D 3 118.878 92.549 105.637 1 30 ? O53 PIO 702 B 1 
HETATM 40 C C5A PIO . . . D 3 110.475 92.86 110.792 1 30 ? C5A PIO 702 B 1 
HETATM 41 C C5B PIO . . . D 3 106.688 88.711 97.581 1 30 ? C5B PIO 702 B 1 
HETATM 42 C C6A PIO . . . D 3 111.879 92.524 111.279 1 30 ? C6A PIO 702 B 1 
HETATM 43 C C6B PIO . . . D 3 105.325 88.253 97.062 1 30 ? C6B PIO 702 B 1 
HETATM 44 C C7A PIO . . . D 3 112.654 93.78 111.661 1 30 ? C7A PIO 702 B 1 
HETATM 45 C C7B PIO . . . D 3 104.251 88.21 98.147 1 30 ? C7B PIO 702 B 1 
HETATM 46 C C8A PIO . . . D 3 111.742 94.847 112.259 1 30 ? C8A PIO 702 B 1 
HETATM 47 C C8B PIO . . . D 3 102.835 88.194 97.573 1 30 ? C8B PIO 702 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           47 
#