data_6CS9
#
_model_server_result.job_id            5mkBHhotfZa-xDndw6PWbw 
_model_server_result.datetime_utc      '2024-11-27 14:54:56' 
_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          6cs9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":101}' 
#
_entry.id    6CS9 
#
_exptl.entry_id    6CS9 
_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          98.64 
_cell.angle_gamma         90 
_cell.entry_id            6CS9 
_cell.length_a            32.871 
_cell.length_b            25.538 
_cell.length_c            40.17 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6CS9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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
? 2 C N N 
? 2 D 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
disulf ? disulf1 A SG CYS 8 A CYS 8 1_555 A SG CYS 37 A CYS 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf2 A SG CYS 15 A CYS 15 1_555 A SG CYS 30 A CYS 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf3 A SG CYS 20 A CYS 20 1_555 A SG CYS 38 A CYS 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 B SG CYS 8 B CYS 8 1_555 B SG CYS 37 B CYS 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf5 B SG CYS 15 B CYS 15 1_555 B SG CYS 30 B CYS 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf6 B SG CYS 20 B CYS 20 1_555 B SG CYS 38 B CYS 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
#
_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 207 n n 
C1 C2 PIO sing 208 n n 
C1 C6 PIO sing 209 n n 
C1 H1 PIO sing 210 n n 
O1 P1 PIO sing 211 n n 
P1 O11 PIO sing 212 n n 
O11 H11 PIO sing 213 n n 
P1 O12 PIO doub 214 n n 
P1 O13 PIO sing 215 n n 
C2 O2 PIO sing 216 n n 
C2 C3 PIO sing 217 n n 
C2 H2 PIO sing 218 n n 
O2 HO2 PIO sing 219 n n 
C3 O3 PIO sing 220 n n 
C3 C4 PIO sing 221 n n 
C3 H3 PIO sing 222 n n 
O3 HO3 PIO sing 223 n n 
C4 O4 PIO sing 224 n n 
C4 C5 PIO sing 225 n n 
C4 H4 PIO sing 226 n n 
O4 P4 PIO sing 227 n n 
P4 O41 PIO sing 228 n n 
O41 H41 PIO sing 229 n n 
P4 O42 PIO doub 230 n n 
P4 O43 PIO sing 231 n n 
O43 H43 PIO sing 232 n n 
C5 O5 PIO sing 233 n n 
C5 C6 PIO sing 234 n n 
C5 H5 PIO sing 235 n n 
O5 P5 PIO sing 236 n n 
P5 O51 PIO sing 237 n n 
O51 H51 PIO sing 238 n n 
P5 O52 PIO sing 239 n n 
O52 H52 PIO sing 240 n n 
P5 O53 PIO doub 241 n n 
C6 O6 PIO sing 242 n n 
C6 H6 PIO sing 243 n n 
O6 HO6 PIO sing 244 n n 
O13 C1C PIO sing 245 n n 
C1A O1A PIO doub 246 n n 
C1A C2A PIO sing 247 n n 
C1A O2C PIO sing 248 n n 
C1B O1B PIO doub 249 n n 
C1B C2B PIO sing 250 n n 
C1B O3C PIO sing 251 n n 
C1C C2C PIO sing 252 n n 
C1C H1C PIO sing 253 n n 
C1C H1CA PIO sing 254 n n 
C2A C3A PIO sing 255 n n 
C2A H2A PIO sing 256 n n 
C2A H2AA PIO sing 257 n n 
C2B C3B PIO sing 258 n n 
C2B H2B PIO sing 259 n n 
C2B H2BA PIO sing 260 n n 
C2C O2C PIO sing 261 n n 
C2C C3C PIO sing 262 n n 
C2C H2C PIO sing 263 n n 
C3A C4A PIO sing 264 n n 
C3A H3A PIO sing 265 n n 
C3A H3AA PIO sing 266 n n 
C3B C4B PIO sing 267 n n 
C3B H3B PIO sing 268 n n 
C3B H3BA PIO sing 269 n n 
C3C O3C PIO sing 270 n n 
C3C H3C PIO sing 271 n n 
C3C H3CA PIO sing 272 n n 
C4A C5A PIO sing 273 n n 
C4A H4A PIO sing 274 n n 
C4A H4AA PIO sing 275 n n 
C4B C5B PIO sing 276 n n 
C4B H4B PIO sing 277 n n 
C4B H4BA PIO sing 278 n n 
C5A C6A PIO sing 279 n n 
C5A H5A PIO sing 280 n n 
C5A H5AA PIO sing 281 n n 
C5B C6B PIO sing 282 n n 
C5B H5B PIO sing 283 n n 
C5B H5BA PIO sing 284 n n 
C6A C7A PIO sing 285 n n 
C6A H6A PIO sing 286 n n 
C6A H6AA PIO sing 287 n n 
C6B C7B PIO sing 288 n n 
C6B H6B PIO sing 289 n n 
C6B H6BA PIO sing 290 n n 
C7A C8A PIO sing 291 n n 
C7A H7A PIO sing 292 n n 
C7A H7AA PIO sing 293 n n 
C7B C8B PIO sing 294 n n 
C7B H7B PIO sing 295 n n 
C7B H7BA PIO sing 296 n n 
C8A H8A PIO sing 297 n n 
C8A H8AA PIO sing 298 n n 
C8A H8AB PIO sing 299 n n 
C8B H8B PIO sing 300 n n 
C8B H8BA PIO sing 301 n n 
C8B H8BB PIO sing 302 n n 
#
_atom_sites.entry_id                     6CS9 
_atom_sites.fract_transf_matrix[1][1]    0.030422 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004621 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.039157 
_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]    0.02518 
_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 PIO A 1 101 1048 PIO PIO . 
D 2 PIO B 1 101 1049 PIO PIO . 
E 3 HOH A 1 201 5 HOH HOH . 
E 3 HOH A 2 202 2 HOH HOH . 
E 3 HOH A 3 203 28 HOH HOH . 
E 3 HOH A 4 204 11 HOH HOH . 
E 3 HOH A 5 205 19 HOH HOH . 
E 3 HOH A 6 206 7 HOH HOH . 
E 3 HOH A 7 207 8 HOH HOH . 
E 3 HOH A 8 208 14 HOH HOH . 
E 3 HOH A 9 209 18 HOH HOH . 
E 3 HOH A 10 210 6 HOH HOH . 
E 3 HOH A 11 211 21 HOH HOH . 
E 3 HOH A 12 212 20 HOH HOH . 
E 3 HOH A 13 213 25 HOH HOH . 
E 3 HOH A 14 214 17 HOH HOH . 
E 3 HOH A 15 215 26 HOH HOH . 
F 3 HOH B 1 201 10 HOH HOH . 
F 3 HOH B 2 202 1 HOH HOH . 
F 3 HOH B 3 203 22 HOH HOH . 
F 3 HOH B 4 204 23 HOH HOH . 
F 3 HOH B 5 205 13 HOH HOH . 
F 3 HOH B 6 206 9 HOH HOH . 
F 3 HOH B 7 207 12 HOH HOH . 
F 3 HOH B 8 208 16 HOH HOH . 
F 3 HOH B 9 209 4 HOH HOH . 
F 3 HOH B 10 210 3 HOH HOH . 
F 3 HOH B 11 211 24 HOH HOH . 
F 3 HOH B 12 212 27 HOH HOH . 
F 3 HOH B 13 213 15 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 2 5.632 7.957 26.374 1 38.72 ? C1 PIO 101 B 1 
HETATM 2 O O1 PIO . . . D 2 5.77 7.569 25.033 1 44.62 ? O1 PIO 101 B 1 
HETATM 3 P P1 PIO . . . D 2 7.284 7.246 24.464 1 50.8 ? P1 PIO 101 B 1 
HETATM 4 C C2 PIO . . . D 2 5.215 6.743 27.206 1 49.39 ? C2 PIO 101 B 1 
HETATM 5 O O2 PIO . . . D 2 4.036 6.193 26.664 1 43.96 ? O2 PIO 101 B 1 
HETATM 6 C C3 PIO . . . D 2 4.943 7.123 28.666 1 43.93 ? C3 PIO 101 B 1 
HETATM 7 O O3 PIO . . . D 2 4.416 5.998 29.323 1 42.95 ? O3 PIO 101 B 1 
HETATM 8 C C4 PIO . . . D 2 3.94 8.272 28.798 1 41.82 ? C4 PIO 101 B 1 
HETATM 9 O O4 PIO . . . D 2 3.916 8.683 30.143 1 52.23 ? O4 PIO 101 B 1 
HETATM 10 P P4 PIO . . . D 2 2.758 8.05 31.135 1 58.73 ? P4 PIO 101 B 1 
HETATM 11 C C5 PIO . . . D 2 4.302 9.471 27.917 1 43.88 ? C5 PIO 101 B 1 
HETATM 12 O O5 PIO . . . D 2 3.212 10.358 27.931 1 45.92 ? O5 PIO 101 B 1 
HETATM 13 P P5 PIO . . . D 2 3.484 11.979 27.831 1 47.42 ? P5 PIO 101 B 1 
HETATM 14 C C6 PIO . . . D 2 4.58 9.072 26.466 1 45.06 ? C6 PIO 101 B 1 
HETATM 15 O O6 PIO . . . D 2 5.047 10.189 25.753 1 40.57 ? O6 PIO 101 B 1 
HETATM 16 O O11 PIO . . . D 2 7.15 6.42 23.21 1 51.48 -1 O11 PIO 101 B 1 
HETATM 17 O O12 PIO . . . D 2 8.057 6.47 25.501 1 43.33 ? O12 PIO 101 B 1 
HETATM 18 O O13 PIO . . . D 2 8.076 8.662 24.14 1 46.11 ? O13 PIO 101 B 1 
HETATM 19 C C1A PIO . . . D 2 9.654 11.478 23.047 1 49.34 ? C1A PIO 101 B 1 
HETATM 20 O O1A PIO . . . D 2 9.148 11.427 24.113 1 59.75 ? O1A PIO 101 B 1 
HETATM 21 C C1B PIO . . . D 2 12.868 7.392 21.541 1 64.31 ? C1B PIO 101 B 1 
HETATM 22 O O1B PIO . . . D 2 13.558 6.987 22.415 1 67.53 ? O1B PIO 101 B 1 
HETATM 23 C C1C PIO . . . D 2 8.592 8.884 22.853 1 52.56 ? C1C PIO 101 B 1 
HETATM 24 C C2A PIO . . . D 2 9.397 12.673 22.129 1 52.44 ? C2A PIO 101 B 1 
HETATM 25 C C2B PIO . . . D 2 12.761 6.642 20.211 1 64.91 ? C2B PIO 101 B 1 
HETATM 26 C C2C PIO . . . D 2 10.095 9.137 22.934 1 46.53 ? C2C PIO 101 B 1 
HETATM 27 O O2C PIO . . . D 2 10.483 10.438 22.624 1 58 ? O2C PIO 101 B 1 
HETATM 28 C C3A PIO . . . D 2 10.37 12.728 20.943 1 57.46 ? C3A PIO 101 B 1 
HETATM 29 C C3B PIO . . . D 2 13.787 5.512 20.145 1 63.98 ? C3B PIO 101 B 1 
HETATM 30 C C3C PIO . . . D 2 10.769 8.239 21.891 1 45.9 ? C3C PIO 101 B 1 
HETATM 31 O O3C PIO . . . D 2 12.118 8.556 21.738 1 60.05 ? O3C PIO 101 B 1 
HETATM 32 O O41 PIO . . . D 2 1.407 8.579 30.722 1 52.16 ? O41 PIO 101 B 1 
HETATM 33 O O42 PIO . . . D 2 3.048 8.461 32.558 1 60.41 -1 O42 PIO 101 B 1 
HETATM 34 O O43 PIO . . . D 2 2.749 6.544 31.028 1 47.68 ? O43 PIO 101 B 1 
HETATM 35 C C4A PIO . . . D 2 11.807 12.363 21.323 1 60.64 ? C4A PIO 101 B 1 
HETATM 36 C C4B PIO . . . D 2 14.572 5.572 18.834 1 58.07 ? C4B PIO 101 B 1 
HETATM 37 O O51 PIO . . . D 2 2.308 12.696 28.45 1 54.82 ? O51 PIO 101 B 1 
HETATM 38 O O52 PIO . . . D 2 3.628 12.378 26.386 1 40.89 -1 O52 PIO 101 B 1 
HETATM 39 O O53 PIO . . . D 2 4.743 12.346 28.581 1 50.77 ? O53 PIO 101 B 1 
HETATM 40 C C5A PIO . . . D 2 12.801 13.323 20.666 1 62.28 ? C5A PIO 101 B 1 
HETATM 41 C C5B PIO . . . D 2 14.51 4.201 18.159 1 60.58 ? C5B PIO 101 B 1 
HETATM 42 C C6A PIO . . . D 2 12.895 13.066 19.162 1 54.76 ? C6A PIO 101 B 1 
HETATM 43 C C6B PIO . . . D 2 15.409 4.201 16.925 1 53.18 ? C6B PIO 101 B 1 
HETATM 44 C C7A PIO . . . D 2 12.6 14.354 18.393 1 55 ? C7A PIO 101 B 1 
HETATM 45 C C7B PIO . . . D 2 16.021 2.819 16.72 1 59.67 ? C7B PIO 101 B 1 
HETATM 46 C C8A PIO . . . D 2 13.183 14.258 16.983 1 54.03 ? C8A PIO 101 B 1 
HETATM 47 C C8B PIO . . . D 2 15.02 1.903 16.018 1 58.03 ? C8B PIO 101 B 1 
#
_model_server_stats.io_time_ms              113 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           365 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           47 
#