data_8YEK # _model_server_result.job_id 14iQCQPFJuY3dsoF70FcJw _model_server_result.datetime_utc '2024-12-22 03:15:08' _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 8yek # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 8YEK # _exptl.entry_id 8YEK _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 790.145 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE _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 90 _cell.entry_id 8YEK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YEK _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E 1 1 A,B,C,D,E 1 2 A,B,C,D,E 1 3 # 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 'point symmetry operation' ? ? -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 314.20816 84.19182 0 3 'point symmetry operation' ? ? -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 84.19182 314.20816 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 248 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 223 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C15 _struct_conn.ptnr2_label_comp_id RET _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 501 _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 1.337 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C44 H88 N O8 P' _chem_comp.formula_weight 790.145 _chem_comp.id PC1 _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 3-SN-PHOSPHATIDYLCHOLINE # 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 O12 P PC1 sing 237 n n P O14 PC1 doub 238 n n P O13 PC1 sing 239 n n P O11 PC1 sing 240 n n O13 C11 PC1 sing 241 n n C11 C12 PC1 sing 242 n n C11 H111 PC1 sing 243 n n C11 H112 PC1 sing 244 n n C12 N PC1 sing 245 n n C12 H121 PC1 sing 246 n n C12 H122 PC1 sing 247 n n N C13 PC1 sing 248 n n N C14 PC1 sing 249 n n N C15 PC1 sing 250 n n C13 H131 PC1 sing 251 n n C13 H132 PC1 sing 252 n n C13 H133 PC1 sing 253 n n C14 H141 PC1 sing 254 n n C14 H142 PC1 sing 255 n n C14 H143 PC1 sing 256 n n C15 H151 PC1 sing 257 n n C15 H152 PC1 sing 258 n n C15 H153 PC1 sing 259 n n O11 C1 PC1 sing 260 n n C1 C2 PC1 sing 261 n n C1 H11 PC1 sing 262 n n C1 H12 PC1 sing 263 n n C2 O21 PC1 sing 264 n n C2 C3 PC1 sing 265 n n C2 H2 PC1 sing 266 n n O21 C21 PC1 sing 267 n n C21 O22 PC1 doub 268 n n C21 C22 PC1 sing 269 n n C22 C23 PC1 sing 270 n n C22 H221 PC1 sing 271 n n C22 H222 PC1 sing 272 n n C23 C24 PC1 sing 273 n n C23 H231 PC1 sing 274 n n C23 H232 PC1 sing 275 n n C24 C25 PC1 sing 276 n n C24 H241 PC1 sing 277 n n C24 H242 PC1 sing 278 n n C25 C26 PC1 sing 279 n n C25 H251 PC1 sing 280 n n C25 H252 PC1 sing 281 n n C26 C27 PC1 sing 282 n n C26 H261 PC1 sing 283 n n C26 H262 PC1 sing 284 n n C27 C28 PC1 sing 285 n n C27 H271 PC1 sing 286 n n C27 H272 PC1 sing 287 n n C28 C29 PC1 sing 288 n n C28 H281 PC1 sing 289 n n C28 H282 PC1 sing 290 n n C29 C2A PC1 sing 291 n n C29 H291 PC1 sing 292 n n C29 H292 PC1 sing 293 n n C2A C2B PC1 sing 294 n n C2A H2A1 PC1 sing 295 n n C2A H2A2 PC1 sing 296 n n C2B C2C PC1 sing 297 n n C2B H2B1 PC1 sing 298 n n C2B H2B2 PC1 sing 299 n n C2C C2D PC1 sing 300 n n C2C H2C1 PC1 sing 301 n n C2C H2C2 PC1 sing 302 n n C2D C2E PC1 sing 303 n n C2D H2D1 PC1 sing 304 n n C2D H2D2 PC1 sing 305 n n C2E C2F PC1 sing 306 n n C2E H2E1 PC1 sing 307 n n C2E H2E2 PC1 sing 308 n n C2F C2G PC1 sing 309 n n C2F H2F1 PC1 sing 310 n n C2F H2F2 PC1 sing 311 n n C2G C2H PC1 sing 312 n n C2G H2G1 PC1 sing 313 n n C2G H2G2 PC1 sing 314 n n C2H C2I PC1 sing 315 n n C2H H2H1 PC1 sing 316 n n C2H H2H2 PC1 sing 317 n n C2I H2I1 PC1 sing 318 n n C2I H2I2 PC1 sing 319 n n C2I H2I3 PC1 sing 320 n n C3 O31 PC1 sing 321 n n C3 H31 PC1 sing 322 n n C3 H32 PC1 sing 323 n n O31 C31 PC1 sing 324 n n C31 O32 PC1 doub 325 n n C31 C32 PC1 sing 326 n n C32 C33 PC1 sing 327 n n C32 H321 PC1 sing 328 n n C32 H322 PC1 sing 329 n n C33 C34 PC1 sing 330 n n C33 H331 PC1 sing 331 n n C33 H332 PC1 sing 332 n n C34 C35 PC1 sing 333 n n C34 H341 PC1 sing 334 n n C34 H342 PC1 sing 335 n n C35 C36 PC1 sing 336 n n C35 H351 PC1 sing 337 n n C35 H352 PC1 sing 338 n n C36 C37 PC1 sing 339 n n C36 H361 PC1 sing 340 n n C36 H362 PC1 sing 341 n n C37 C38 PC1 sing 342 n n C37 H371 PC1 sing 343 n n C37 H372 PC1 sing 344 n n C38 C39 PC1 sing 345 n n C38 H381 PC1 sing 346 n n C38 H382 PC1 sing 347 n n C39 C3A PC1 sing 348 n n C39 H391 PC1 sing 349 n n C39 H392 PC1 sing 350 n n C3A C3B PC1 sing 351 n n C3A H3A1 PC1 sing 352 n n C3A H3A2 PC1 sing 353 n n C3B C3C PC1 sing 354 n n C3B H3B1 PC1 sing 355 n n C3B H3B2 PC1 sing 356 n n C3C C3D PC1 sing 357 n n C3C H3C1 PC1 sing 358 n n C3C H3C2 PC1 sing 359 n n C3D C3E PC1 sing 360 n n C3D H3D1 PC1 sing 361 n n C3D H3D2 PC1 sing 362 n n C3E C3F PC1 sing 363 n n C3E H3E1 PC1 sing 364 n n C3E H3E2 PC1 sing 365 n n C3F C3G PC1 sing 366 n n C3F H3F1 PC1 sing 367 n n C3F H3F2 PC1 sing 368 n n C3G C3H PC1 sing 369 n n C3G H3G1 PC1 sing 370 n n C3G H3G2 PC1 sing 371 n n C3H C3I PC1 sing 372 n n C3H H3H1 PC1 sing 373 n n C3H H3H2 PC1 sing 374 n n C3I H3I1 PC1 sing 375 n n C3I H3I2 PC1 sing 376 n n C3I H3I3 PC1 sing 377 n n # _atom_sites.entry_id 8YEK _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 B 2 RET A 1 501 301 RET RET . C 3 PC1 A 1 502 302 PC1 PC1 . D 3 PC1 A 1 503 303 PC1 PC1 . E 4 HOH A 1 601 3 HOH HOH . E 4 HOH A 2 602 4 HOH HOH . E 4 HOH A 3 603 6 HOH HOH . E 4 HOH A 4 604 2 HOH HOH . E 4 HOH A 5 605 5 HOH HOH . E 4 HOH A 6 606 1 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 O O12 PC1 . . . D 3 138.101 130.894 114.543 1 113.81 ? O12 PC1 503 A 1 HETATM 2 P P PC1 . . . D 3 137.743 129.516 115.031 1 114.21 ? P PC1 503 A 1 HETATM 3 O O14 PC1 . . . D 3 137.08 128.543 114.094 1 114.06 ? O14 PC1 503 A 1 HETATM 4 O O13 PC1 . . . D 3 139.09 128.826 115.566 1 113.99 ? O13 PC1 503 A 1 HETATM 5 O O11 PC1 . . . D 3 136.86 129.62 116.37 1 111.14 ? O11 PC1 503 A 1 HETATM 6 C C1 PC1 . . . D 3 137.003 130.769 117.244 1 108.01 ? C1 PC1 503 A 1 HETATM 7 C C2 PC1 . . . D 3 135.896 130.758 118.273 1 105.78 ? C2 PC1 503 A 1 HETATM 8 O O21 PC1 . . . D 3 136.378 131.43 119.47 1 104.97 ? O21 PC1 503 A 1 HETATM 9 C C21 PC1 . . . D 3 135.755 132.539 119.893 1 103.69 ? C21 PC1 503 A 1 HETATM 10 O O22 PC1 . . . D 3 134.848 133.062 119.282 1 103.79 ? O22 PC1 503 A 1 HETATM 11 C C22 PC1 . . . D 3 136.326 133.038 121.186 1 102.46 ? C22 PC1 503 A 1 HETATM 12 C C23 PC1 . . . D 3 135.956 132.189 122.37 1 101.07 ? C23 PC1 503 A 1 HETATM 13 C C24 PC1 . . . D 3 136.213 132.817 123.732 1 99.83 ? C24 PC1 503 A 1 HETATM 14 C C25 PC1 . . . D 3 135.616 131.956 124.841 1 99 ? C25 PC1 503 A 1 HETATM 15 C C26 PC1 . . . D 3 135.767 132.377 126.277 1 98.37 ? C26 PC1 503 A 1 HETATM 16 C C27 PC1 . . . D 3 137.141 132.823 126.705 1 98.12 ? C27 PC1 503 A 1 HETATM 17 C C28 PC1 . . . D 3 138.144 131.708 126.877 1 97.68 ? C28 PC1 503 A 1 HETATM 18 C C29 PC1 . . . D 3 137.848 130.773 128.023 1 97.5 ? C29 PC1 503 A 1 HETATM 19 C C2A PC1 . . . D 3 138.756 129.559 128.103 1 96.96 ? C2A PC1 503 A 1 HETATM 20 C C2B PC1 . . . D 3 140.224 129.832 127.831 1 96.78 ? C2B PC1 503 A 1 HETATM 21 C C2C PC1 . . . D 3 141.185 128.857 128.483 1 96.73 ? C2C PC1 503 A 1 HETATM 22 C C2D PC1 . . . D 3 141.361 129.062 129.968 1 96.47 ? C2D PC1 503 A 1 HETATM 23 C C2E PC1 . . . D 3 142.488 128.258 130.582 1 96.72 ? C2E PC1 503 A 1 HETATM 24 C C3 PC1 . . . D 3 135.459 129.382 118.712 1 104.02 ? C3 PC1 503 A 1 HETATM 25 O O31 PC1 . . . D 3 136.231 129.061 119.887 1 101.25 ? O31 PC1 503 A 1 HETATM 26 C C31 PC1 . . . D 3 135.67 128.228 120.758 1 98.02 ? C31 PC1 503 A 1 HETATM 27 O O32 PC1 . . . D 3 134.815 127.434 120.459 1 98.29 ? O32 PC1 503 A 1 HETATM 28 C C32 PC1 . . . D 3 136.249 128.39 122.139 1 95.94 ? C32 PC1 503 A 1 HETATM 29 C C33 PC1 . . . D 3 135.572 127.554 123.188 1 93.98 ? C33 PC1 503 A 1 HETATM 30 C C34 PC1 . . . D 3 136.033 127.894 124.597 1 92.64 ? C34 PC1 503 A 1 HETATM 31 C C35 PC1 . . . D 3 135.21 127.255 125.691 1 92.07 ? C35 PC1 503 A 1 HETATM 32 C C36 PC1 . . . D 3 135.504 127.772 127.081 1 91.73 ? C36 PC1 503 A 1 HETATM 33 C C37 PC1 . . . D 3 134.646 127.154 128.164 1 91.92 ? C37 PC1 503 A 1 HETATM 34 C C38 PC1 . . . D 3 133.228 127.675 128.218 1 92.25 ? C38 PC1 503 A 1 HETATM 35 C C39 PC1 . . . D 3 132.36 127.014 129.267 1 92.53 ? C39 PC1 503 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 593 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 35 #