data_5L0G
#
_model_server_result.job_id            Xa5rFb8VZC7g-am9SaCRDw 
_model_server_result.datetime_utc      '2024-11-04 20:34:10' 
_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          5l0g 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1201}' 
#
_entry.id    5L0G 
#
_exptl.entry_id    5L0G 
_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    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         120 
_cell.entry_id            5L0G 
_cell.length_a            56.858 
_cell.length_b            56.858 
_cell.length_c            193.132 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5L0G 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32' 
#
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
B,E,H 1 1 
A,G 1 2 
C,F,I 2 1 
D,J 2 2 
#
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_675 -x+y+1,-x+2,z+1/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 98.480945 64.377333 
#
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 F 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 B CB ALA 31 B ALA 989 1_555 D NH1 ARG 55 D ARG 1013 3_775 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? 
covale ? covale2 C ND2 ASN 27 C ASN 985 1_555 C CG1 ILE 30 C ILE 988 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? 
#
_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                     5L0G 
_atom_sites.fract_transf_matrix[1][1]    0.017588 
_atom_sites.fract_transf_matrix[1][2]    0.010154 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020308 
_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]    0.005178 
_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 B 1 1201 2 PIO PIO . 
F 2 PIO C 1 1201 1 PIO PIO . 
G 3 HOH A 1 1201 33 HOH HOH . 
G 3 HOH A 2 1202 23 HOH HOH . 
G 3 HOH A 3 1203 41 HOH HOH . 
G 3 HOH A 4 1204 7 HOH HOH . 
G 3 HOH A 5 1205 1 HOH HOH . 
G 3 HOH A 6 1206 13 HOH HOH . 
G 3 HOH A 7 1207 3 HOH HOH . 
G 3 HOH A 8 1208 1 HOH HOH . 
G 3 HOH A 9 1209 38 HOH HOH . 
G 3 HOH A 10 1210 34 HOH HOH . 
G 3 HOH A 11 1211 32 HOH HOH . 
G 3 HOH A 12 1212 47 HOH HOH . 
H 3 HOH B 1 1301 36 HOH HOH . 
H 3 HOH B 2 1302 21 HOH HOH . 
H 3 HOH B 3 1303 7 HOH HOH . 
H 3 HOH B 4 1304 11 HOH HOH . 
H 3 HOH B 5 1305 6 HOH HOH . 
H 3 HOH B 6 1306 43 HOH HOH . 
H 3 HOH B 7 1307 22 HOH HOH . 
H 3 HOH B 8 1308 48 HOH HOH . 
H 3 HOH B 9 1309 24 HOH HOH . 
H 3 HOH B 10 1310 2 HOH HOH . 
H 3 HOH B 11 1311 50 HOH HOH . 
H 3 HOH B 12 1312 17 HOH HOH . 
H 3 HOH B 13 1313 27 HOH HOH . 
I 3 HOH C 1 1301 46 HOH HOH . 
I 3 HOH C 2 1302 29 HOH HOH . 
I 3 HOH C 3 1303 5 HOH HOH . 
I 3 HOH C 4 1304 37 HOH HOH . 
I 3 HOH C 5 1305 42 HOH HOH . 
I 3 HOH C 6 1306 2 HOH HOH . 
I 3 HOH C 7 1307 12 HOH HOH . 
I 3 HOH C 8 1308 30 HOH HOH . 
I 3 HOH C 9 1309 4 HOH HOH . 
J 3 HOH D 1 1201 5 HOH HOH . 
J 3 HOH D 2 1202 3 HOH HOH . 
J 3 HOH D 3 1203 49 HOH HOH . 
J 3 HOH D 4 1204 39 HOH HOH . 
J 3 HOH D 5 1205 51 HOH HOH . 
J 3 HOH D 6 1206 31 HOH HOH . 
J 3 HOH D 7 1207 10 HOH HOH . 
J 3 HOH D 8 1208 4 HOH HOH . 
J 3 HOH D 9 1209 40 HOH HOH . 
J 3 HOH D 10 1210 15 HOH HOH . 
J 3 HOH D 11 1211 9 HOH HOH . 
J 3 HOH D 12 1212 20 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 . . . F 2 23.705 27.701 -20.509 1 226.03 ? C1 PIO 1201 C 1 
HETATM 2 O O1 PIO . . . F 2 23.103 27.69 -21.821 1 225 ? O1 PIO 1201 C 1 
HETATM 3 P P1 PIO . . . F 2 21.735 28.477 -22.174 1 224.02 ? P1 PIO 1201 C 1 
HETATM 4 C C2 PIO . . . F 2 22.743 27.136 -19.474 1 226.28 ? C2 PIO 1201 C 1 
HETATM 5 O O2 PIO . . . F 2 21.541 27.898 -19.45 1 226.37 ? O2 PIO 1201 C 1 
HETATM 6 C C3 PIO . . . F 2 23.395 27.148 -18.098 1 226.12 ? C3 PIO 1201 C 1 
HETATM 7 O O3 PIO . . . F 2 22.485 26.65 -17.124 1 225.56 ? O3 PIO 1201 C 1 
HETATM 8 C C4 PIO . . . F 2 23.827 28.562 -17.742 1 226.43 ? C4 PIO 1201 C 1 
HETATM 9 O O4 PIO . . . F 2 24.577 28.436 -16.515 1 225.39 ? O4 PIO 1201 C 1 
HETATM 10 P P4 PIO . . . F 2 25.907 27.6 -16.179 1 224.05 ? P4 PIO 1201 C 1 
HETATM 11 C C5 PIO . . . F 2 24.745 29.143 -18.802 1 227.17 ? C5 PIO 1201 C 1 
HETATM 12 O O5 PIO . . . F 2 25.013 30.519 -18.461 1 227.47 ? O5 PIO 1201 C 1 
HETATM 13 P P5 PIO . . . F 2 25.028 31.226 -17.01 1 226.66 ? P5 PIO 1201 C 1 
HETATM 14 C C6 PIO . . . F 2 24.088 29.134 -20.173 1 226.71 ? C6 PIO 1201 C 1 
HETATM 15 O O6 PIO . . . F 2 24.982 29.649 -21.153 1 226.41 ? O6 PIO 1201 C 1 
HETATM 16 O O11 PIO . . . F 2 20.748 27.336 -21.914 1 223.46 ? O11 PIO 1201 C 1 
HETATM 17 O O12 PIO . . . F 2 21.597 28.616 -23.769 1 224 ? O12 PIO 1201 C 1 
HETATM 18 O O13 PIO . . . F 2 21.551 29.738 -21.42 1 223.63 ? O13 PIO 1201 C 1 
HETATM 19 O O41 PIO . . . F 2 26.89 28.204 -15.232 1 224.03 ? O41 PIO 1201 C 1 
HETATM 20 O O42 PIO . . . F 2 26.49 27.33 -17.569 1 223.81 ? O42 PIO 1201 C 1 
HETATM 21 O O43 PIO . . . F 2 25.271 26.31 -15.653 1 223.57 ? O43 PIO 1201 C 1 
HETATM 22 O O51 PIO . . . F 2 25.862 30.574 -15.957 1 225.67 ? O51 PIO 1201 C 1 
HETATM 23 O O52 PIO . . . F 2 23.525 31.14 -16.732 1 226.97 ? O52 PIO 1201 C 1 
HETATM 24 O O53 PIO . . . F 2 25.399 32.691 -17.255 1 226.73 ? O53 PIO 1201 C 1 
#
_model_server_stats.io_time_ms              54 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           24 
#