data_4PR9
#
_model_server_result.job_id            G-KxZjMVNBDqueXFVymSqw 
_model_server_result.datetime_utc      '2025-02-05 07:44:06' 
_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          4pr9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":1101}' 
#
_entry.id    4PR9 
#
_exptl.entry_id    4PR9 
_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    3 
_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         120 
_cell.entry_id            4PR9 
_cell.length_a            102.579 
_cell.length_b            102.579 
_cell.length_c            190.772 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PR9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        153 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 32 1 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
? dimeric 2 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,G,H,I,M,N 1 1 
C,D,J,O,P 2 1 
E,F,K,L,Q 3 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
? 2 G N N 
? 2 H N N 
? 2 K 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 273 n n 
C1 C2 PIO sing 274 n n 
C1 C6 PIO sing 275 n n 
C1 H1 PIO sing 276 n n 
O1 P1 PIO sing 277 n n 
P1 O11 PIO sing 278 n n 
O11 H11 PIO sing 279 n n 
P1 O12 PIO doub 280 n n 
P1 O13 PIO sing 281 n n 
C2 O2 PIO sing 282 n n 
C2 C3 PIO sing 283 n n 
C2 H2 PIO sing 284 n n 
O2 HO2 PIO sing 285 n n 
C3 O3 PIO sing 286 n n 
C3 C4 PIO sing 287 n n 
C3 H3 PIO sing 288 n n 
O3 HO3 PIO sing 289 n n 
C4 O4 PIO sing 290 n n 
C4 C5 PIO sing 291 n n 
C4 H4 PIO sing 292 n n 
O4 P4 PIO sing 293 n n 
P4 O41 PIO sing 294 n n 
O41 H41 PIO sing 295 n n 
P4 O42 PIO doub 296 n n 
P4 O43 PIO sing 297 n n 
O43 H43 PIO sing 298 n n 
C5 O5 PIO sing 299 n n 
C5 C6 PIO sing 300 n n 
C5 H5 PIO sing 301 n n 
O5 P5 PIO sing 302 n n 
P5 O51 PIO sing 303 n n 
O51 H51 PIO sing 304 n n 
P5 O52 PIO sing 305 n n 
O52 H52 PIO sing 306 n n 
P5 O53 PIO doub 307 n n 
C6 O6 PIO sing 308 n n 
C6 H6 PIO sing 309 n n 
O6 HO6 PIO sing 310 n n 
O13 C1C PIO sing 311 n n 
C1A O1A PIO doub 312 n n 
C1A C2A PIO sing 313 n n 
C1A O2C PIO sing 314 n n 
C1B O1B PIO doub 315 n n 
C1B C2B PIO sing 316 n n 
C1B O3C PIO sing 317 n n 
C1C C2C PIO sing 318 n n 
C1C H1C PIO sing 319 n n 
C1C H1CA PIO sing 320 n n 
C2A C3A PIO sing 321 n n 
C2A H2A PIO sing 322 n n 
C2A H2AA PIO sing 323 n n 
C2B C3B PIO sing 324 n n 
C2B H2B PIO sing 325 n n 
C2B H2BA PIO sing 326 n n 
C2C O2C PIO sing 327 n n 
C2C C3C PIO sing 328 n n 
C2C H2C PIO sing 329 n n 
C3A C4A PIO sing 330 n n 
C3A H3A PIO sing 331 n n 
C3A H3AA PIO sing 332 n n 
C3B C4B PIO sing 333 n n 
C3B H3B PIO sing 334 n n 
C3B H3BA PIO sing 335 n n 
C3C O3C PIO sing 336 n n 
C3C H3C PIO sing 337 n n 
C3C H3CA PIO sing 338 n n 
C4A C5A PIO sing 339 n n 
C4A H4A PIO sing 340 n n 
C4A H4AA PIO sing 341 n n 
C4B C5B PIO sing 342 n n 
C4B H4B PIO sing 343 n n 
C4B H4BA PIO sing 344 n n 
C5A C6A PIO sing 345 n n 
C5A H5A PIO sing 346 n n 
C5A H5AA PIO sing 347 n n 
C5B C6B PIO sing 348 n n 
C5B H5B PIO sing 349 n n 
C5B H5BA PIO sing 350 n n 
C6A C7A PIO sing 351 n n 
C6A H6A PIO sing 352 n n 
C6A H6AA PIO sing 353 n n 
C6B C7B PIO sing 354 n n 
C6B H6B PIO sing 355 n n 
C6B H6BA PIO sing 356 n n 
C7A C8A PIO sing 357 n n 
C7A H7A PIO sing 358 n n 
C7A H7AA PIO sing 359 n n 
C7B C8B PIO sing 360 n n 
C7B H7B PIO sing 361 n n 
C7B H7BA PIO sing 362 n n 
C8A H8A PIO sing 363 n n 
C8A H8AA PIO sing 364 n n 
C8A H8AB PIO sing 365 n n 
C8B H8B PIO sing 366 n n 
C8B H8BA PIO sing 367 n n 
C8B H8BB PIO sing 368 n n 
#
_atom_sites.entry_id                     4PR9 
_atom_sites.fract_transf_matrix[1][1]    0.009749 
_atom_sites.fract_transf_matrix[1][2]    0.005628 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011257 
_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]    0.005242 
_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 2 PIO A 1 1101 1 PIO PIO . 
H 2 PIO B 1 1101 1 PIO PIO . 
I 3 GOL B 1 1102 1 GOL GOL . 
J 3 GOL C 1 1101 3 GOL GOL . 
K 2 PIO E 1 1101 1 PIO PIO . 
L 3 GOL F 1 1101 2 GOL GOL . 
M 4 HOH A 1 1201 1 HOH HOH . 
M 4 HOH A 2 1202 2 HOH HOH . 
M 4 HOH A 3 1203 7 HOH HOH . 
M 4 HOH A 4 1204 8 HOH HOH . 
M 4 HOH A 5 1205 22 HOH HOH . 
M 4 HOH A 6 1206 23 HOH HOH . 
M 4 HOH A 7 1207 29 HOH HOH . 
N 4 HOH B 1 1201 4 HOH HOH . 
N 4 HOH B 2 1202 5 HOH HOH . 
N 4 HOH B 3 1203 6 HOH HOH . 
N 4 HOH B 4 1204 9 HOH HOH . 
N 4 HOH B 5 1205 10 HOH HOH . 
N 4 HOH B 6 1206 11 HOH HOH . 
N 4 HOH B 7 1207 16 HOH HOH . 
N 4 HOH B 8 1208 17 HOH HOH . 
N 4 HOH B 9 1209 19 HOH HOH . 
N 4 HOH B 10 1210 20 HOH HOH . 
N 4 HOH B 11 1211 21 HOH HOH . 
N 4 HOH B 12 1212 24 HOH HOH . 
N 4 HOH B 13 1213 26 HOH HOH . 
N 4 HOH B 14 1214 28 HOH HOH . 
N 4 HOH B 15 1215 33 HOH HOH . 
N 4 HOH B 16 1216 36 HOH HOH . 
N 4 HOH B 17 1217 37 HOH HOH . 
N 4 HOH B 18 1218 39 HOH HOH . 
O 4 HOH C 1 1201 13 HOH HOH . 
O 4 HOH C 2 1202 14 HOH HOH . 
O 4 HOH C 3 1203 34 HOH HOH . 
O 4 HOH C 4 1204 38 HOH HOH . 
O 4 HOH C 5 1205 40 HOH HOH . 
P 4 HOH D 1 1101 3 HOH HOH . 
P 4 HOH D 2 1102 15 HOH HOH . 
P 4 HOH D 3 1103 18 HOH HOH . 
P 4 HOH D 4 1104 25 HOH HOH . 
P 4 HOH D 5 1105 27 HOH HOH . 
P 4 HOH D 6 1106 30 HOH HOH . 
P 4 HOH D 7 1107 31 HOH HOH . 
P 4 HOH D 8 1108 32 HOH HOH . 
P 4 HOH D 9 1109 35 HOH HOH . 
Q 4 HOH F 1 1201 12 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 . . . K 2 34.02 77.188 48.415 0.91 225.55 ? C1 PIO 1101 E 1 
HETATM 2 O O1 PIO . . . K 2 35.238 76.49 48.751 0.91 222.21 ? O1 PIO 1101 E 1 
HETATM 3 P P1 PIO . . . K 2 35.302 74.896 49.013 0.91 218.7 ? P1 PIO 1101 E 1 
HETATM 4 C C2 PIO . . . K 2 34.325 78.438 47.603 0.91 225.71 ? C2 PIO 1101 E 1 
HETATM 5 O O2 PIO . . . K 2 35.182 79.306 48.337 0.91 224.38 ? O2 PIO 1101 E 1 
HETATM 6 C C3 PIO . . . K 2 33.03 79.158 47.252 0.91 227.46 ? C3 PIO 1101 E 1 
HETATM 7 O O3 PIO . . . K 2 33.316 80.344 46.52 0.91 226.69 ? O3 PIO 1101 E 1 
HETATM 8 C C4 PIO . . . K 2 32.263 79.494 48.522 0.91 230.03 ? C4 PIO 1101 E 1 
HETATM 9 O O4 PIO . . . K 2 30.992 80.011 48.077 0.91 231.82 ? O4 PIO 1101 E 1 
HETATM 10 P P4 PIO . . . K 2 30.638 81.278 47.157 0.91 232.86 ? P4 PIO 1101 E 1 
HETATM 11 C C5 PIO . . . K 2 32.005 78.252 49.356 0.91 229.98 ? C5 PIO 1101 E 1 
HETATM 12 O O5 PIO . . . K 2 31.387 78.662 50.594 0.91 230.61 ? O5 PIO 1101 E 1 
HETATM 13 P P5 PIO . . . K 2 32.067 78.938 52.032 0.91 230.13 ? P5 PIO 1101 E 1 
HETATM 14 C C6 PIO . . . K 2 33.302 77.539 49.709 0.91 228.56 ? C6 PIO 1101 E 1 
HETATM 15 O O6 PIO . . . K 2 33.029 76.361 50.458 0.91 229.48 ? O6 PIO 1101 E 1 
HETATM 16 O O11 PIO . . . K 2 34.656 74.872 50.401 0.91 218.92 ? O11 PIO 1101 E 1 
HETATM 17 O O12 PIO . . . K 2 36.655 74.313 48.868 0.91 218.53 ? O12 PIO 1101 E 1 
HETATM 18 O O13 PIO . . . K 2 34.156 74.168 48.153 0.91 213.98 ? O13 PIO 1101 E 1 
HETATM 19 C C1A PIO . . . K 2 31.533 73.599 47.816 0.91 196.1 ? C1A PIO 1101 E 1 
HETATM 20 O O1A PIO . . . K 2 31.609 74.703 47.351 0.91 195.88 ? O1A PIO 1101 E 1 
HETATM 21 C C1B PIO . . . K 2 35.382 70.338 46.629 0.91 188.7 ? C1B PIO 1101 E 1 
HETATM 22 O O1B PIO . . . K 2 36.16 70.875 45.887 0.91 188.25 ? O1B PIO 1101 E 1 
HETATM 23 C C1C PIO . . . K 2 34.531 73.359 47.02 0.91 208.23 ? C1C PIO 1101 E 1 
HETATM 24 C C2A PIO . . . K 2 30.58 73.185 48.896 0.91 192.54 ? C2A PIO 1101 E 1 
HETATM 25 C C2B PIO . . . K 2 35.753 69.333 47.677 0.91 185.44 ? C2B PIO 1101 E 1 
HETATM 26 C C2C PIO . . . K 2 33.284 72.819 46.372 0.91 201.65 ? C2C PIO 1101 E 1 
HETATM 27 O O2C PIO . . . K 2 32.301 72.57 47.426 0.91 199.31 ? O2C PIO 1101 E 1 
HETATM 28 C C3A PIO . . . K 2 29.183 73.762 48.707 0.91 188.97 ? C3A PIO 1101 E 1 
HETATM 29 C C3B PIO . . . K 2 35.694 69.9 49.089 0.91 182.51 ? C3B PIO 1101 E 1 
HETATM 30 C C3C PIO . . . K 2 33.544 71.515 45.666 0.91 197.03 ? C3C PIO 1101 E 1 
HETATM 31 O O3C PIO . . . K 2 34.064 70.564 46.624 0.91 192.61 ? O3C PIO 1101 E 1 
HETATM 32 O O41 PIO . . . K 2 31.959 81.538 46.427 0.91 233.26 ? O41 PIO 1101 E 1 
HETATM 33 O O42 PIO . . . K 2 29.466 81.168 46.238 0.91 232.62 ? O42 PIO 1101 E 1 
HETATM 34 O O43 PIO . . . K 2 30.46 82.342 48.243 0.91 232.57 ? O43 PIO 1101 E 1 
HETATM 35 C C4A PIO . . . K 2 28.538 73.339 47.4 0.91 185.74 ? C4A PIO 1101 E 1 
HETATM 36 C C4B PIO . . . K 2 36.074 68.885 50.153 0.91 180.26 ? C4B PIO 1101 E 1 
HETATM 37 O O51 PIO . . . K 2 33.448 79.532 51.741 0.91 229.48 ? O51 PIO 1101 E 1 
HETATM 38 O O52 PIO . . . K 2 31.132 80.064 52.48 0.91 230 ? O52 PIO 1101 E 1 
HETATM 39 O O53 PIO . . . K 2 32.107 77.789 52.984 0.91 230.18 ? O53 PIO 1101 E 1 
HETATM 40 C C5A PIO . . . K 2 27.145 73.903 47.187 0.91 182.47 ? C5A PIO 1101 E 1 
HETATM 41 C C5B PIO . . . K 2 37.481 68.333 50.007 0.91 178.05 ? C5B PIO 1101 E 1 
HETATM 42 C C6A PIO . . . K 2 26.501 73.48 45.879 0.91 179.64 ? C6A PIO 1101 E 1 
HETATM 43 C C6B PIO . . . K 2 38.572 69.384 50.102 0.91 175.67 ? C6B PIO 1101 E 1 
HETATM 44 C C7A PIO . . . K 2 25.11 74.044 45.664 0.91 177.38 ? C7A PIO 1101 E 1 
HETATM 45 C C7B PIO . . . K 2 38.494 70.458 49.035 0.91 173.62 ? C7B PIO 1101 E 1 
HETATM 46 C C8A PIO . . . K 2 24.487 73.613 44.359 0.91 176.11 ? C8A PIO 1101 E 1 
HETATM 47 C C8B PIO . . . K 2 39.587 71.493 49.148 0.91 172.77 ? C8B PIO 1101 E 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           270 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           47 
#