data_6UP7
#
_model_server_result.job_id            f8HB1aqBWS_5byVTYh2kag 
_model_server_result.datetime_utc      '2024-11-22 23:23:23' 
_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          6up7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":400}' 
#
_entry.id    6UP7 
#
_exptl.entry_id    6UP7 
_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    1 
_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            6UP7 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6UP7 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_struct_conn.conn_type_id                   disulf 
_struct_conn.details                        ? 
_struct_conn.id                             disulf1 
_struct_conn.ptnr1_label_asym_id            C 
_struct_conn.ptnr1_label_atom_id            SG 
_struct_conn.ptnr1_label_comp_id            CYS 
_struct_conn.ptnr1_label_seq_id             92 
_struct_conn.ptnr1_auth_asym_id             R 
_struct_conn.ptnr1_auth_comp_id             CYS 
_struct_conn.ptnr1_auth_seq_id              141 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            C 
_struct_conn.ptnr2_label_atom_id            SG 
_struct_conn.ptnr2_label_comp_id            CYS 
_struct_conn.ptnr2_label_seq_id             175 
_struct_conn.ptnr2_auth_asym_id             R 
_struct_conn.ptnr2_auth_comp_id             CYS 
_struct_conn.ptnr2_auth_seq_id              224 
_struct_conn.ptnr2_symmetry                 1_555 
_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                2.023 
_struct_conn.pdbx_value_order               ? 
#
_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 258 n n 
C1 C2 PIO sing 259 n n 
C1 C6 PIO sing 260 n n 
C1 H1 PIO sing 261 n n 
O1 P1 PIO sing 262 n n 
P1 O11 PIO sing 263 n n 
O11 H11 PIO sing 264 n n 
P1 O12 PIO doub 265 n n 
P1 O13 PIO sing 266 n n 
C2 O2 PIO sing 267 n n 
C2 C3 PIO sing 268 n n 
C2 H2 PIO sing 269 n n 
O2 HO2 PIO sing 270 n n 
C3 O3 PIO sing 271 n n 
C3 C4 PIO sing 272 n n 
C3 H3 PIO sing 273 n n 
O3 HO3 PIO sing 274 n n 
C4 O4 PIO sing 275 n n 
C4 C5 PIO sing 276 n n 
C4 H4 PIO sing 277 n n 
O4 P4 PIO sing 278 n n 
P4 O41 PIO sing 279 n n 
O41 H41 PIO sing 280 n n 
P4 O42 PIO doub 281 n n 
P4 O43 PIO sing 282 n n 
O43 H43 PIO sing 283 n n 
C5 O5 PIO sing 284 n n 
C5 C6 PIO sing 285 n n 
C5 H5 PIO sing 286 n n 
O5 P5 PIO sing 287 n n 
P5 O51 PIO sing 288 n n 
O51 H51 PIO sing 289 n n 
P5 O52 PIO sing 290 n n 
O52 H52 PIO sing 291 n n 
P5 O53 PIO doub 292 n n 
C6 O6 PIO sing 293 n n 
C6 H6 PIO sing 294 n n 
O6 HO6 PIO sing 295 n n 
O13 C1C PIO sing 296 n n 
C1A O1A PIO doub 297 n n 
C1A C2A PIO sing 298 n n 
C1A O2C PIO sing 299 n n 
C1B O1B PIO doub 300 n n 
C1B C2B PIO sing 301 n n 
C1B O3C PIO sing 302 n n 
C1C C2C PIO sing 303 n n 
C1C H1C PIO sing 304 n n 
C1C H1CA PIO sing 305 n n 
C2A C3A PIO sing 306 n n 
C2A H2A PIO sing 307 n n 
C2A H2AA PIO sing 308 n n 
C2B C3B PIO sing 309 n n 
C2B H2B PIO sing 310 n n 
C2B H2BA PIO sing 311 n n 
C2C O2C PIO sing 312 n n 
C2C C3C PIO sing 313 n n 
C2C H2C PIO sing 314 n n 
C3A C4A PIO sing 315 n n 
C3A H3A PIO sing 316 n n 
C3A H3AA PIO sing 317 n n 
C3B C4B PIO sing 318 n n 
C3B H3B PIO sing 319 n n 
C3B H3BA PIO sing 320 n n 
C3C O3C PIO sing 321 n n 
C3C H3C PIO sing 322 n n 
C3C H3CA PIO sing 323 n n 
C4A C5A PIO sing 324 n n 
C4A H4A PIO sing 325 n n 
C4A H4AA PIO sing 326 n n 
C4B C5B PIO sing 327 n n 
C4B H4B PIO sing 328 n n 
C4B H4BA PIO sing 329 n n 
C5A C6A PIO sing 330 n n 
C5A H5A PIO sing 331 n n 
C5A H5AA PIO sing 332 n n 
C5B C6B PIO sing 333 n n 
C5B H5B PIO sing 334 n n 
C5B H5BA PIO sing 335 n n 
C6A C7A PIO sing 336 n n 
C6A H6A PIO sing 337 n n 
C6A H6AA PIO sing 338 n n 
C6B C7B PIO sing 339 n n 
C6B H6B PIO sing 340 n n 
C6B H6BA PIO sing 341 n n 
C7A C8A PIO sing 342 n n 
C7A H7A PIO sing 343 n n 
C7A H7AA PIO sing 344 n n 
C7B C8B PIO sing 345 n n 
C7B H7B PIO sing 346 n n 
C7B H7BA PIO sing 347 n n 
C8A H8A PIO sing 348 n n 
C8A H8AA PIO sing 349 n n 
C8A H8AB PIO sing 350 n n 
C8B H8B PIO sing 351 n n 
C8B H8BA PIO sing 352 n n 
C8B H8BB PIO sing 353 n n 
#
_atom_sites.entry_id                     6UP7 
_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 
#
_pdbx_nonpoly_scheme.asym_id          E 
_pdbx_nonpoly_scheme.entity_id        5 
_pdbx_nonpoly_scheme.mon_id           PIO 
_pdbx_nonpoly_scheme.pdb_strand_id    R 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      400 
_pdbx_nonpoly_scheme.auth_seq_num     400 
_pdbx_nonpoly_scheme.pdb_mon_id       PIO 
_pdbx_nonpoly_scheme.auth_mon_id      PIP 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 . . . E 5 124.743 105.912 114.53 1 146.47 ? C1 PIO 400 R 1 
HETATM 2 O O1 PIO . . . E 5 123.579 106.569 115.038 1 146.23 ? O1 PIO 400 R 1 
HETATM 3 P P1 PIO . . . E 5 123.649 107.997 115.792 1 118.15 ? P1 PIO 400 R 1 
HETATM 4 C C2 PIO . . . E 5 125.449 106.74 113.473 1 146.47 ? C2 PIO 400 R 1 
HETATM 5 O O2 PIO . . . E 5 124.664 106.778 112.278 1 146.26 ? O2 PIO 400 R 1 
HETATM 6 C C3 PIO . . . E 5 126.78 106.066 113.191 1 146.81 ? C3 PIO 400 R 1 
HETATM 7 O O3 PIO . . . E 5 127.557 106.882 112.307 1 146.76 ? O3 PIO 400 R 1 
HETATM 8 C C4 PIO . . . E 5 126.555 104.693 112.567 1 147.24 ? C4 PIO 400 R 1 
HETATM 9 O O4 PIO . . . E 5 127.815 104.033 112.455 1 147.51 ? O4 PIO 400 R 1 
HETATM 10 P P4 PIO . . . E 5 128.321 103.428 111.049 1 141.95 ? P4 PIO 400 R 1 
HETATM 11 C C5 PIO . . . E 5 125.608 103.821 113.398 1 147.17 ? C5 PIO 400 R 1 
HETATM 12 O O5 PIO . . . E 5 125.215 102.709 112.591 1 147.41 ? O5 PIO 400 R 1 
HETATM 13 P P5 PIO . . . E 5 124.464 101.418 113.196 1 109.43 ? P5 PIO 400 R 1 
HETATM 14 C C6 PIO . . . E 5 124.37 104.576 113.896 1 146.77 ? C6 PIO 400 R 1 
HETATM 15 O O6 PIO . . . E 5 123.658 103.784 114.853 1 146.7 ? O6 PIO 400 R 1 
HETATM 16 O O11 PIO . . . E 5 124.795 108.812 115.243 1 118.48 ? O11 PIO 400 R 1 
HETATM 17 O O12 PIO . . . E 5 122.255 108.575 115.762 1 118.3 ? O12 PIO 400 R 1 
HETATM 18 O O13 PIO . . . E 5 123.989 107.652 117.332 1 124.97 ? O13 PIO 400 R 1 
HETATM 19 C C1A PIO . . . E 5 120.778 109.345 118.164 1 124.4 ? C1A PIO 400 R 1 
HETATM 20 O O1A PIO . . . E 5 121.321 110.422 117.981 1 124.72 ? O1A PIO 400 R 1 
HETATM 21 C C1B PIO . . . E 5 122.047 110.203 122.35 1 124.97 ? C1B PIO 400 R 1 
HETATM 22 O O1B PIO . . . E 5 122.362 109.918 123.494 1 125.12 ? O1B PIO 400 R 1 
HETATM 23 C C1C PIO . . . E 5 123.953 108.71 118.292 1 124.95 ? C1C PIO 400 R 1 
HETATM 24 C C2A PIO . . . E 5 119.279 109.21 118.019 1 123.58 ? C2A PIO 400 R 1 
HETATM 25 C C2B PIO . . . E 5 120.695 110.807 122.055 1 124.63 ? C2B PIO 400 R 1 
HETATM 26 C C2C PIO . . . E 5 122.766 108.608 119.251 1 124.92 ? C2C PIO 400 R 1 
HETATM 27 O O2C PIO . . . E 5 121.593 108.201 118.545 1 124.71 ? O2C PIO 400 R 1 
HETATM 28 C C3A PIO . . . E 5 118.741 108.078 118.888 1 122.79 ? C3A PIO 400 R 1 
HETATM 29 C C3B PIO . . . E 5 120.421 111.948 123.029 1 124.28 ? C3B PIO 400 R 1 
HETATM 30 C C3C PIO . . . E 5 122.527 109.957 119.924 1 125.05 ? C3C PIO 400 R 1 
HETATM 31 O O3C PIO . . . E 5 122.992 109.954 121.27 1 125.05 ? O3C PIO 400 R 1 
HETATM 32 O O41 PIO . . . E 5 128.851 104.637 110.317 1 142.11 ? O41 PIO 400 R 1 
HETATM 33 O O42 PIO . . . E 5 127.085 102.82 110.428 1 141.84 ? O42 PIO 400 R 1 
HETATM 34 O O43 PIO . . . E 5 129.387 102.433 111.441 1 141.92 ? O43 PIO 400 R 1 
HETATM 35 C C4A PIO . . . E 5 117.218 108.019 118.806 1 122.2 ? C4A PIO 400 R 1 
HETATM 36 C C4B PIO . . . E 5 121.005 111.648 124.404 1 124.16 ? C4B PIO 400 R 1 
HETATM 37 O O51 PIO . . . E 5 124.795 100.319 112.215 1 109.54 ? O51 PIO 400 R 1 
HETATM 38 O O52 PIO . . . E 5 125.074 101.244 114.565 1 109.38 ? O52 PIO 400 R 1 
HETATM 39 O O53 PIO . . . E 5 123.003 101.806 113.199 1 109.54 ? O53 PIO 400 R 1 
HETATM 40 C C5A PIO . . . E 5 116.655 106.881 119.649 1 121.85 ? C5A PIO 400 R 1 
#
_model_server_stats.io_time_ms              56 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           258 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           40 
#