data_5L0C
#
_model_server_result.job_id            bjmRsc6ZLRVh9abSAnuVhw 
_model_server_result.datetime_utc      '2025-03-12 04:41:34' 
_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          5l0c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":1202}' 
#
_entry.id    5L0C 
#
_exptl.entry_id    5L0C 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              746.566 
_entity.id                          2 
_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    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          122.49 
_cell.angle_gamma         90 
_cell.entry_id            5L0C 
_cell.length_a            114.52 
_cell.length_b            100.676 
_cell.length_c            105.615 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5L0C 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,M 1 1 
C,K,O 1 2 
B,G,H,I,J,N 2 1 
D,L,P 2 3 
#
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' 3_545 x+1/2,y-1/2,z 1 0 0 0 1 0 0 0 1 57.26 -50.338 0 
3 'crystal symmetry operation' 4_656 -x+3/2,y+1/2,-z+1 -1 0 0 0 1 0 0 0 -1 115.048649 50.338 89.08469 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 G N N 
? 2 H N N 
? 2 K N N 
? 2 L 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 260 n n 
C1 C2 PIO sing 261 n n 
C1 C6 PIO sing 262 n n 
C1 H1 PIO sing 263 n n 
O1 P1 PIO sing 264 n n 
P1 O11 PIO sing 265 n n 
O11 H11 PIO sing 266 n n 
P1 O12 PIO doub 267 n n 
P1 O13 PIO sing 268 n n 
C2 O2 PIO sing 269 n n 
C2 C3 PIO sing 270 n n 
C2 H2 PIO sing 271 n n 
O2 HO2 PIO sing 272 n n 
C3 O3 PIO sing 273 n n 
C3 C4 PIO sing 274 n n 
C3 H3 PIO sing 275 n n 
O3 HO3 PIO sing 276 n n 
C4 O4 PIO sing 277 n n 
C4 C5 PIO sing 278 n n 
C4 H4 PIO sing 279 n n 
O4 P4 PIO sing 280 n n 
P4 O41 PIO sing 281 n n 
O41 H41 PIO sing 282 n n 
P4 O42 PIO doub 283 n n 
P4 O43 PIO sing 284 n n 
O43 H43 PIO sing 285 n n 
C5 O5 PIO sing 286 n n 
C5 C6 PIO sing 287 n n 
C5 H5 PIO sing 288 n n 
O5 P5 PIO sing 289 n n 
P5 O51 PIO sing 290 n n 
O51 H51 PIO sing 291 n n 
P5 O52 PIO sing 292 n n 
O52 H52 PIO sing 293 n n 
P5 O53 PIO doub 294 n n 
C6 O6 PIO sing 295 n n 
C6 H6 PIO sing 296 n n 
O6 HO6 PIO sing 297 n n 
O13 C1C PIO sing 298 n n 
C1A O1A PIO doub 299 n n 
C1A C2A PIO sing 300 n n 
C1A O2C PIO sing 301 n n 
C1B O1B PIO doub 302 n n 
C1B C2B PIO sing 303 n n 
C1B O3C PIO sing 304 n n 
C1C C2C PIO sing 305 n n 
C1C H1C PIO sing 306 n n 
C1C H1CA PIO sing 307 n n 
C2A C3A PIO sing 308 n n 
C2A H2A PIO sing 309 n n 
C2A H2AA PIO sing 310 n n 
C2B C3B PIO sing 311 n n 
C2B H2B PIO sing 312 n n 
C2B H2BA PIO sing 313 n n 
C2C O2C PIO sing 314 n n 
C2C C3C PIO sing 315 n n 
C2C H2C PIO sing 316 n n 
C3A C4A PIO sing 317 n n 
C3A H3A PIO sing 318 n n 
C3A H3AA PIO sing 319 n n 
C3B C4B PIO sing 320 n n 
C3B H3B PIO sing 321 n n 
C3B H3BA PIO sing 322 n n 
C3C O3C PIO sing 323 n n 
C3C H3C PIO sing 324 n n 
C3C H3CA PIO sing 325 n n 
C4A C5A PIO sing 326 n n 
C4A H4A PIO sing 327 n n 
C4A H4AA PIO sing 328 n n 
C4B C5B PIO sing 329 n n 
C4B H4B PIO sing 330 n n 
C4B H4BA PIO sing 331 n n 
C5A C6A PIO sing 332 n n 
C5A H5A PIO sing 333 n n 
C5A H5AA PIO sing 334 n n 
C5B C6B PIO sing 335 n n 
C5B H5B PIO sing 336 n n 
C5B H5BA PIO sing 337 n n 
C6A C7A PIO sing 338 n n 
C6A H6A PIO sing 339 n n 
C6A H6AA PIO sing 340 n n 
C6B C7B PIO sing 341 n n 
C6B H6B PIO sing 342 n n 
C6B H6BA PIO sing 343 n n 
C7A C8A PIO sing 344 n n 
C7A H7A PIO sing 345 n n 
C7A H7AA PIO sing 346 n n 
C7B C8B PIO sing 347 n n 
C7B H7B PIO sing 348 n n 
C7B H7BA PIO sing 349 n n 
C8A H8A PIO sing 350 n n 
C8A H8AA PIO sing 351 n n 
C8A H8AB PIO sing 352 n n 
C8B H8B PIO sing 353 n n 
C8B H8BA PIO sing 354 n n 
C8B H8BB PIO sing 355 n n 
#
_atom_sites.entry_id                     5L0C 
_atom_sites.fract_transf_matrix[1][1]    0.008732 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005561 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009933 
_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]    0.011225 
_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 2 PIO A 1 1201 3 PIO PIO . 
F 3 PO4 A 1 1202 1 PO4 PO4 . 
G 2 PIO B 1 1201 1 PIO PIO . 
H 2 PIO B 1 1202 2 PIO PIO . 
I 3 PO4 B 1 1203 2 PO4 PO4 . 
J 3 PO4 B 1 1204 3 PO4 PO4 . 
K 2 PIO C 1 1201 5 PIO PIO . 
L 2 PIO D 1 1201 4 PIO PIO . 
M 4 HOH A 1 1301 3 HOH HOH . 
M 4 HOH A 2 1302 17 HOH HOH . 
M 4 HOH A 3 1303 48 HOH HOH . 
M 4 HOH A 4 1304 2 HOH HOH . 
M 4 HOH A 5 1305 45 HOH HOH . 
M 4 HOH A 6 1306 51 HOH HOH . 
M 4 HOH A 7 1307 49 HOH HOH . 
M 4 HOH A 8 1308 19 HOH HOH . 
M 4 HOH A 9 1309 54 HOH HOH . 
M 4 HOH A 10 1310 31 HOH HOH . 
M 4 HOH A 11 1311 9 HOH HOH . 
N 4 HOH B 1 1301 14 HOH HOH . 
N 4 HOH B 2 1302 47 HOH HOH . 
N 4 HOH B 3 1303 53 HOH HOH . 
N 4 HOH B 4 1304 61 HOH HOH . 
N 4 HOH B 5 1305 42 HOH HOH . 
N 4 HOH B 6 1306 55 HOH HOH . 
N 4 HOH B 7 1307 50 HOH HOH . 
N 4 HOH B 8 1308 26 HOH HOH . 
N 4 HOH B 9 1309 7 HOH HOH . 
N 4 HOH B 10 1310 25 HOH HOH . 
N 4 HOH B 11 1311 60 HOH HOH . 
N 4 HOH B 12 1312 1 HOH HOH . 
N 4 HOH B 13 1313 24 HOH HOH . 
N 4 HOH B 14 1314 12 HOH HOH . 
N 4 HOH B 15 1315 39 HOH HOH . 
N 4 HOH B 16 1316 52 HOH HOH . 
N 4 HOH B 17 1317 44 HOH HOH . 
N 4 HOH B 18 1318 20 HOH HOH . 
N 4 HOH B 19 1319 5 HOH HOH . 
O 4 HOH C 1 1301 8 HOH HOH . 
O 4 HOH C 2 1302 46 HOH HOH . 
O 4 HOH C 3 1303 59 HOH HOH . 
O 4 HOH C 4 1304 43 HOH HOH . 
O 4 HOH C 5 1305 4 HOH HOH . 
O 4 HOH C 6 1306 28 HOH HOH . 
O 4 HOH C 7 1307 22 HOH HOH . 
O 4 HOH C 8 1308 33 HOH HOH . 
O 4 HOH C 9 1309 16 HOH HOH . 
O 4 HOH C 10 1310 21 HOH HOH . 
O 4 HOH C 11 1311 37 HOH HOH . 
O 4 HOH C 12 1312 40 HOH HOH . 
O 4 HOH C 13 1313 18 HOH HOH . 
O 4 HOH C 14 1314 36 HOH HOH . 
O 4 HOH C 15 1315 13 HOH HOH . 
O 4 HOH C 16 1316 23 HOH HOH . 
O 4 HOH C 17 1317 38 HOH HOH . 
O 4 HOH C 18 1318 35 HOH HOH . 
P 4 HOH D 1 1301 32 HOH HOH . 
P 4 HOH D 2 1302 10 HOH HOH . 
P 4 HOH D 3 1303 11 HOH HOH . 
P 4 HOH D 4 1304 15 HOH HOH . 
P 4 HOH D 5 1305 34 HOH HOH . 
P 4 HOH D 6 1306 58 HOH HOH . 
P 4 HOH D 7 1307 30 HOH HOH . 
P 4 HOH D 8 1308 57 HOH HOH . 
P 4 HOH D 9 1309 56 HOH HOH . 
P 4 HOH D 10 1310 6 HOH HOH . 
P 4 HOH D 11 1311 27 HOH HOH . 
P 4 HOH D 12 1312 41 HOH HOH . 
P 4 HOH D 13 1313 29 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 . . . H 2 72.546 41.08 -2.873 0.5 121.88 ? C1 PIO 1202 B 1 
HETATM 2 O O1 PIO . . . H 2 73.927 41.095 -2.456 0.5 125.33 ? O1 PIO 1202 B 1 
HETATM 3 P P1 PIO . . . H 2 74.83 42.437 -2.432 0.5 128.01 ? P1 PIO 1202 B 1 
HETATM 4 C C2 PIO . . . H 2 72.437 41.32 -4.372 0.5 119.98 ? C2 PIO 1202 B 1 
HETATM 5 O O2 PIO . . . H 2 73.022 42.57 -4.716 0.5 120.12 ? O2 PIO 1202 B 1 
HETATM 6 C C3 PIO . . . H 2 70.974 41.294 -4.797 0.5 118.7 ? C3 PIO 1202 B 1 
HETATM 7 O O3 PIO . . . H 2 70.869 41.55 -6.193 0.5 117.92 ? O3 PIO 1202 B 1 
HETATM 8 C C4 PIO . . . H 2 70.188 42.331 -4.009 0.5 118.85 ? C4 PIO 1202 B 1 
HETATM 9 O O4 PIO . . . H 2 68.805 42.108 -4.357 0.5 118.38 ? O4 PIO 1202 B 1 
HETATM 10 P P4 PIO . . . H 2 68.076 40.825 -4.991 0.5 117.64 ? P4 PIO 1202 B 1 
HETATM 11 C C5 PIO . . . H 2 70.34 42.122 -2.514 0.5 120.33 ? C5 PIO 1202 B 1 
HETATM 12 O O5 PIO . . . H 2 69.673 43.207 -1.837 0.5 120.97 ? O5 PIO 1202 B 1 
HETATM 13 P P5 PIO . . . H 2 69.093 44.586 -2.444 0.5 120.62 ? P5 PIO 1202 B 1 
HETATM 14 C C6 PIO . . . H 2 71.802 42.154 -2.094 0.5 120.69 ? C6 PIO 1202 B 1 
HETATM 15 O O6 PIO . . . H 2 71.919 41.919 -0.695 0.5 119.77 ? O6 PIO 1202 B 1 
HETATM 16 O O11 PIO . . . H 2 74.875 42.648 -0.916 0.5 128.4 ? O11 PIO 1202 B 1 
HETATM 17 O O12 PIO . . . H 2 74.301 43.537 -3.269 0.5 128.03 ? O12 PIO 1202 B 1 
HETATM 18 O O13 PIO . . . H 2 76.365 42.052 -2.711 0.5 127.2 ? O13 PIO 1202 B 1 
HETATM 19 O O41 PIO . . . H 2 66.587 40.758 -4.908 0.5 115.57 ? O41 PIO 1202 B 1 
HETATM 20 O O42 PIO . . . H 2 68.604 40.819 -6.428 0.5 117.6 ? O42 PIO 1202 B 1 
HETATM 21 O O43 PIO . . . H 2 68.779 39.716 -4.204 0.5 117.76 ? O43 PIO 1202 B 1 
HETATM 22 O O51 PIO . . . H 2 70.222 45.188 -3.284 0.5 120.85 ? O51 PIO 1202 B 1 
HETATM 23 O O52 PIO . . . H 2 68.502 45.55 -1.469 0.5 119.73 ? O52 PIO 1202 B 1 
HETATM 24 O O53 PIO . . . H 2 68.057 43.966 -3.386 0.5 120.39 ? O53 PIO 1202 B 1 
#
_model_server_stats.io_time_ms              63 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           24 
#