data_8OX7 # _model_server_result.job_id 6sOqxNQZZLZ_uoliLDD7Ww _model_server_result.datetime_utc '2024-11-22 00:34:02' _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 8ox7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1302}' # _entry.id 8OX7 # _exptl.entry_id 8OX7 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 826.546 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate' _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 8OX7 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OX7 _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 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,G,H _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 C 1 NAG B 403 NAG 3 n C NAG 2 C 2 NAG B 404 NAG 3 n C BMA 3 C 3 BMA B 405 BMA # 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 95 B CYS 91 1_555 A SG CYS 108 B CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 98 B CYS 94 1_555 A SG CYS 106 B CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 161 B CYS 157 1_555 A SG CYS 175 B CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 111 B ASN 107 1_555 D C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 184 B ASN 180 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 298 B ASN 294 1_555 E C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 B C SER 453 A SER 453 1_555 B N PHD 454 A PHD 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale5 B C PHD 454 A PHD 454 1_555 B N LYS 455 A LYS 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? metalc ? metalc1 B OD2 PHD 454 A PHD 454 1_555 F MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc2 B OP3 PHD 454 A PHD 454 1_555 F MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc3 B O THR 456 A THR 456 1_555 F MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc4 B OD1 ASP 893 A ASP 893 1_555 F MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? # _chem_comp.formula 'C25 H50 O22 P4' _chem_comp.formula_weight 826.546 _chem_comp.id IP9 _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'L-a-Phosphatidyl-D-myo-inositol 3,4,5-triphosphate, dioctanoyl;[(2R)-3-[[(2S,3S,5R,6S)-2,6-dihydroxy-3,4,5-triphosphonooxy-cyclohexyl]oxy-hydroxy-phosphoryl]oxy-2-octanoyloxy-propyl] octanoate' # 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 IP9 sing 197 n n C1 C2 IP9 sing 198 n n C1 C6 IP9 sing 199 n n C1 H1 IP9 sing 200 n n O1 P1 IP9 sing 201 n n C2 O2 IP9 sing 202 n n C2 C3 IP9 sing 203 n n C2 H2 IP9 sing 204 n n O2 HO2 IP9 sing 205 n n C3 O3 IP9 sing 206 n n C3 C4 IP9 sing 207 n n C3 H3 IP9 sing 208 n n O3 P3 IP9 sing 209 n n C4 O4 IP9 sing 210 n n C4 C5 IP9 sing 211 n n C4 H4 IP9 sing 212 n n O4 P4 IP9 sing 213 n n C5 O5 IP9 sing 214 n n C5 C6 IP9 sing 215 n n C5 H5 IP9 sing 216 n n O5 P5 IP9 sing 217 n n C6 O6 IP9 sing 218 n n C6 H6 IP9 sing 219 n n O6 HO6 IP9 sing 220 n n P1 O1P IP9 doub 221 n n P1 O2P IP9 sing 222 n n P1 O3P IP9 sing 223 n n O2P HO2P IP9 sing 224 n n O3P C7 IP9 sing 225 n n P3 O4P IP9 doub 226 n n P3 O5P IP9 sing 227 n n P3 O6P IP9 sing 228 n n O5P HO5P IP9 sing 229 n n O6P HO6P IP9 sing 230 n n P4 O7P IP9 sing 231 n n P4 O8P IP9 sing 232 n n P4 O9P IP9 doub 233 n n O7P HO7P IP9 sing 234 n n O8P HO8P IP9 sing 235 n n P5 OPF IP9 sing 236 n n P5 OPG IP9 doub 237 n n P5 OPH IP9 sing 238 n n OPF HOP1 IP9 sing 239 n n OPH HOP3 IP9 sing 240 n n C7 C8 IP9 sing 241 n n C7 H16 IP9 sing 242 n n C7 H17 IP9 sing 243 n n C8 C9 IP9 sing 244 n n C8 O19 IP9 sing 245 n n C9 O20 IP9 sing 246 n n C9 H18 IP9 sing 247 n n C9 H19 IP9 sing 248 n n O19 C10 IP9 sing 249 n n O20 C11 IP9 sing 250 n n C10 O21 IP9 doub 251 n n C10 C12 IP9 sing 252 n n C11 C13 IP9 sing 253 n n C11 O22 IP9 doub 254 n n C8 H20 IP9 sing 255 n n C12 C14 IP9 sing 256 n n C12 H21 IP9 sing 257 n n C12 H22 IP9 sing 258 n n C13 C15 IP9 sing 259 n n C13 H23 IP9 sing 260 n n C13 H24 IP9 sing 261 n n C14 H25 IP9 sing 262 n n C14 H26 IP9 sing 263 n n C14 C16 IP9 sing 264 n n C15 H27 IP9 sing 265 n n C15 H28 IP9 sing 266 n n C15 C17 IP9 sing 267 n n C16 H29 IP9 sing 268 n n C16 C18 IP9 sing 269 n n C16 H30 IP9 sing 270 n n C17 H31 IP9 sing 271 n n C17 H32 IP9 sing 272 n n C17 C19 IP9 sing 273 n n C18 C20 IP9 sing 274 n n C18 H33 IP9 sing 275 n n C18 H34 IP9 sing 276 n n C19 H35 IP9 sing 277 n n C19 C21 IP9 sing 278 n n C19 H36 IP9 sing 279 n n C20 C22 IP9 sing 280 n n C20 H37 IP9 sing 281 n n C20 H38 IP9 sing 282 n n C21 H39 IP9 sing 283 n n C21 H40 IP9 sing 284 n n C21 C23 IP9 sing 285 n n C22 H41 IP9 sing 286 n n C22 H42 IP9 sing 287 n n C22 C24 IP9 sing 288 n n C23 C25 IP9 sing 289 n n C23 H43 IP9 sing 290 n n C23 H44 IP9 sing 291 n n C24 H45 IP9 sing 292 n n C24 H46 IP9 sing 293 n n C24 H47 IP9 sing 294 n n C25 H48 IP9 sing 295 n n C25 H49 IP9 sing 296 n n C25 H50 IP9 sing 297 n n # _atom_sites.entry_id 8OX7 _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 # 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 D 4 NAG B 1 401 401 NAG NAG . E 4 NAG B 1 402 402 NAG NAG . F 5 MG A 1 1301 1301 MG MG . G 6 IP9 A 1 1302 1302 IP9 IP9 . H 7 HOH A 1 1401 1303 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 IP9 . . . G 6 130.02 135.832 131.366 1 29.9 ? C1 IP9 1302 A 1 HETATM 2 O O1 IP9 . . . G 6 129.807 135.487 132.709 1 29.9 ? O1 IP9 1302 A 1 HETATM 3 C C2 IP9 . . . G 6 128.81 136.671 130.942 1 29.9 ? C2 IP9 1302 A 1 HETATM 4 O O2 IP9 . . . G 6 127.931 135.809 130.259 1 29.9 ? O2 IP9 1302 A 1 HETATM 5 C C3 IP9 . . . G 6 129.198 137.865 130.058 1 29.9 ? C3 IP9 1302 A 1 HETATM 6 O O3 IP9 . . . G 6 128.064 138.323 129.35 1 29.9 ? O3 IP9 1302 A 1 HETATM 7 C C4 IP9 . . . G 6 130.349 137.5 129.111 1 29.9 ? C4 IP9 1302 A 1 HETATM 8 O O4 IP9 . . . G 6 130.572 138.572 128.228 1 29.9 ? O4 IP9 1302 A 1 HETATM 9 C C5 IP9 . . . G 6 131.638 137.215 129.896 1 29.9 ? C5 IP9 1302 A 1 HETATM 10 O O5 IP9 . . . G 6 132.466 136.37 129.132 1 29.9 ? O5 IP9 1302 A 1 HETATM 11 C C6 IP9 . . . G 6 131.379 136.544 131.256 1 29.9 ? C6 IP9 1302 A 1 HETATM 12 O O6 IP9 . . . G 6 131.459 137.522 132.264 1 29.9 ? O6 IP9 1302 A 1 HETATM 13 P P1 IP9 . . . G 6 128.613 134.403 133.042 1 29.9 ? P1 IP9 1302 A 1 HETATM 14 O O1P IP9 . . . G 6 128.191 133.713 131.768 1 29.9 ? O1P IP9 1302 A 1 HETATM 15 O O2P IP9 . . . G 6 127.423 135.123 133.625 1 29.9 ? O2P IP9 1302 A 1 HETATM 16 O O3P IP9 . . . G 6 129.158 133.289 134.125 1 29.9 ? O3P IP9 1302 A 1 HETATM 17 P P3 IP9 . . . G 6 127.468 137.526 128.031 1 29.9 ? P3 IP9 1302 A 1 HETATM 18 O O4P IP9 . . . G 6 126.13 138.119 127.66 1 29.9 ? O4P IP9 1302 A 1 HETATM 19 O O5P IP9 . . . G 6 127.277 136.066 128.366 1 29.9 ? O5P IP9 1302 A 1 HETATM 20 O O6P IP9 . . . G 6 128.423 137.654 126.868 1 29.9 ? O6P IP9 1302 A 1 HETATM 21 P P4 IP9 . . . G 6 131.396 138.298 126.827 1 29.9 ? P4 IP9 1302 A 1 HETATM 22 O O7P IP9 . . . G 6 130.885 137.03 126.185 1 29.9 ? O7P IP9 1302 A 1 HETATM 23 O O8P IP9 . . . G 6 132.868 138.151 127.12 1 29.9 ? O8P IP9 1302 A 1 HETATM 24 O O9P IP9 . . . G 6 131.195 139.462 125.887 1 29.9 ? O9P IP9 1302 A 1 HETATM 25 P P5 IP9 . . . G 6 134.098 136.399 129.378 1 29.9 ? P5 IP9 1302 A 1 HETATM 26 O OPF IP9 . . . G 6 134.667 137.71 128.892 1 29.9 ? OPF IP9 1302 A 1 HETATM 27 O OPG IP9 . . . G 6 134.405 136.243 130.848 1 29.9 ? OPG IP9 1302 A 1 HETATM 28 O OPH IP9 . . . G 6 134.734 135.263 128.613 1 29.9 ? OPH IP9 1302 A 1 HETATM 29 C C7 IP9 . . . G 6 130.533 133.126 134.33 1 29.9 ? C7 IP9 1302 A 1 HETATM 30 C C8 IP9 . . . G 6 130.841 133.377 135.803 1 29.9 ? C8 IP9 1302 A 1 HETATM 31 C C9 IP9 . . . G 6 131.456 134.764 136.001 1 29.9 ? C9 IP9 1302 A 1 HETATM 32 O O19 IP9 . . . G 6 129.638 133.224 136.505 1 29.9 ? O19 IP9 1302 A 1 HETATM 33 O O20 IP9 . . . G 6 132.791 134.738 135.582 1 29.9 ? O20 IP9 1302 A 1 HETATM 34 C C10 IP9 . . . G 6 128.936 134.386 136.838 1 29.9 ? C10 IP9 1302 A 1 HETATM 35 C C11 IP9 . . . G 6 133.784 135.024 136.536 1 29.9 ? C11 IP9 1302 A 1 HETATM 36 O O21 IP9 . . . G 6 128.365 135.011 136.012 1 29.9 ? O21 IP9 1302 A 1 HETATM 37 C C12 IP9 . . . G 6 128.915 134.816 138.298 1 29.9 ? C12 IP9 1302 A 1 HETATM 38 C C13 IP9 . . . G 6 133.735 136.268 137.43 1 29.9 ? C13 IP9 1302 A 1 HETATM 39 O O22 IP9 . . . G 6 134.705 134.284 136.63 1 29.9 ? O22 IP9 1302 A 1 HETATM 40 C C14 IP9 . . . G 6 129.538 133.678 139.095 1 29.9 ? C14 IP9 1302 A 1 HETATM 41 C C15 IP9 . . . G 6 134.148 135.921 138.866 1 29.9 ? C15 IP9 1302 A 1 HETATM 42 C C16 IP9 . . . G 6 129.468 133.995 140.583 1 29.9 ? C16 IP9 1302 A 1 HETATM 43 C C17 IP9 . . . G 6 132.974 135.353 139.668 1 29.9 ? C17 IP9 1302 A 1 HETATM 44 C C18 IP9 . . . G 6 128.052 133.714 141.078 1 29.9 ? C18 IP9 1302 A 1 HETATM 45 C C19 IP9 . . . G 6 132.628 136.24 140.863 1 29.9 ? C19 IP9 1302 A 1 HETATM 46 C C20 IP9 . . . G 6 128.057 133.474 142.583 1 29.9 ? C20 IP9 1302 A 1 HETATM 47 C C21 IP9 . . . G 6 131.968 137.533 140.381 1 29.9 ? C21 IP9 1302 A 1 HETATM 48 C C22 IP9 . . . G 6 128.628 134.662 143.358 1 29.9 ? C22 IP9 1302 A 1 HETATM 49 C C23 IP9 . . . G 6 131.938 138.563 141.509 1 29.9 ? C23 IP9 1302 A 1 HETATM 50 C C24 IP9 . . . G 6 129.956 134.277 144.003 1 29.9 ? C24 IP9 1302 A 1 HETATM 51 C C25 IP9 . . . G 6 130.488 138.807 141.922 1 29.9 ? C25 IP9 1302 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 51 #