data_2YGQ # _model_server_result.job_id Dx-szNPkLMoxRe443WGXWg _model_server_result.datetime_utc '2024-11-26 02:59:56' _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 2ygq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1275}' # _entry.id 2YGQ # _exptl.entry_id 2YGQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 734.039 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE _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 2YGQ _cell.length_a 178.007 _cell.length_b 178.007 _cell.length_c 178.007 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YGQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_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 1,2,3 # 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 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 3 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GU4 _pdbx_entity_branch_link.comp_id_2 YYJ _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 2 n B GU4 1 B 1 GU4 A 1279 SCR 2 n B YYJ 2 B 2 YYJ A 1279 SCR # 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 109 A CYS 140 1_555 A SG CYS 146 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 151 A CYS 182 1_555 A SG CYS 161 A CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 155 A CYS 186 1_555 A SG CYS 167 A CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 169 A CYS 200 1_555 A SG CYS 178 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 183 A CYS 214 1_555 A SG CYS 193 A CYS 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf6 A SG CYS 187 A CYS 218 1_555 A SG CYS 199 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 A SG CYS 201 A CYS 232 1_555 A SG CYS 210 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 A SG CYS 215 A CYS 246 1_555 A SG CYS 225 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 A SG CYS 219 A CYS 250 1_555 A SG CYS 231 A CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 A SG CYS 233 A CYS 264 1_555 A SG CYS 242 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 57 A ASN 88 1_555 D C1 NAG . A NAG 1276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 214 A ASN 245 1_555 E C1 NAG . A NAG 1277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale3 A OG1 THR 224 A THR 255 1_555 F C1 FUC . A FUC 1278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 B C1 GU4 . B GU4 1 1_555 B O2 YYJ . B YYJ 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 sing # _chem_comp.formula 'C40 H80 N O8 P' _chem_comp.formula_weight 734.039 _chem_comp.id PCF _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 N C12 PCF sing 328 n n N C13 PCF sing 329 n n N C14 PCF sing 330 n n N C15 PCF sing 331 n n P O11 PCF sing 332 n n P O12 PCF doub 333 n n P O13 PCF sing 334 n n P O14 PCF sing 335 n n O11 C1 PCF sing 336 n n O13 C11 PCF sing 337 n n C11 C12 PCF sing 338 n n C11 H111 PCF sing 339 n n C11 H112 PCF sing 340 n n C12 H121 PCF sing 341 n n C12 H122 PCF sing 342 n n C13 H131 PCF sing 343 n n C13 H132 PCF sing 344 n n C13 H133 PCF sing 345 n n C14 H141 PCF sing 346 n n C14 H142 PCF sing 347 n n C14 H143 PCF sing 348 n n C15 H151 PCF sing 349 n n C15 H152 PCF sing 350 n n C15 H153 PCF sing 351 n n C1 C2 PCF sing 352 n n C1 H11 PCF sing 353 n n C1 H12 PCF sing 354 n n C2 C3 PCF sing 355 n n C2 O21 PCF sing 356 n n C2 H21 PCF sing 357 n n C3 O31 PCF sing 358 n n C3 H31 PCF sing 359 n n C3 H32 PCF sing 360 n n O31 C31 PCF sing 361 n n O32 C31 PCF doub 362 n n C31 C32 PCF sing 363 n n C32 C33 PCF sing 364 n n C32 H321 PCF sing 365 n n C32 H322 PCF sing 366 n n C33 C34 PCF sing 367 n n C33 H331 PCF sing 368 n n C33 H332 PCF sing 369 n n C34 C35 PCF sing 370 n n C34 H341 PCF sing 371 n n C34 H342 PCF sing 372 n n C35 C36 PCF sing 373 n n C35 H351 PCF sing 374 n n C35 H352 PCF sing 375 n n C36 C37 PCF sing 376 n n C36 H361 PCF sing 377 n n C36 H362 PCF sing 378 n n C37 C38 PCF sing 379 n n C37 H371 PCF sing 380 n n C37 H372 PCF sing 381 n n C38 C39 PCF sing 382 n n C38 H381 PCF sing 383 n n C38 H382 PCF sing 384 n n C39 C40 PCF sing 385 n n C39 H391 PCF sing 386 n n C39 H392 PCF sing 387 n n C40 C41 PCF sing 388 n n C40 H401 PCF sing 389 n n C40 H402 PCF sing 390 n n C41 C42 PCF sing 391 n n C41 H411 PCF sing 392 n n C41 H412 PCF sing 393 n n C42 C43 PCF sing 394 n n C42 H421 PCF sing 395 n n C42 H422 PCF sing 396 n n C43 C44 PCF sing 397 n n C43 H431 PCF sing 398 n n C43 H432 PCF sing 399 n n O21 C21 PCF sing 400 n n O22 C21 PCF doub 401 n n C21 C22 PCF sing 402 n n C22 C23 PCF sing 403 n n C22 H221 PCF sing 404 n n C22 H222 PCF sing 405 n n C23 C24 PCF sing 406 n n C23 H231 PCF sing 407 n n C23 H232 PCF sing 408 n n C24 C25 PCF sing 409 n n C24 H241 PCF sing 410 n n C24 H242 PCF sing 411 n n C25 C26 PCF sing 412 n n C25 H251 PCF sing 413 n n C25 H252 PCF sing 414 n n C26 C27 PCF sing 415 n n C26 H261 PCF sing 416 n n C26 H262 PCF sing 417 n n C27 C28 PCF sing 418 n n C27 H271 PCF sing 419 n n C27 H272 PCF sing 420 n n C28 C29 PCF sing 421 n n C28 H281 PCF sing 422 n n C28 H282 PCF sing 423 n n C29 C30 PCF sing 424 n n C29 H291 PCF sing 425 n n C29 H292 PCF sing 426 n n C30 C47 PCF sing 427 n n C30 H301 PCF sing 428 n n C30 H302 PCF sing 429 n n C47 C48 PCF sing 430 n n C47 H471 PCF sing 431 n n C47 H472 PCF sing 432 n n C48 C49 PCF sing 433 n n C48 H481 PCF sing 434 n n C48 H482 PCF sing 435 n n C49 C50 PCF sing 436 n n C49 H491 PCF sing 437 n n C49 H492 PCF sing 438 n n C50 C51 PCF sing 439 n n C50 H501 PCF sing 440 n n C50 H502 PCF sing 441 n n C51 C52 PCF sing 442 n n C51 H511 PCF sing 443 n n C51 H512 PCF sing 444 n n C52 H521 PCF sing 445 n n C52 H522 PCF sing 446 n n C52 H523 PCF sing 447 n n C44 C45 PCF sing 448 n n C44 H441 PCF sing 449 n n C44 H442 PCF sing 450 n n C45 C46 PCF sing 451 n n C45 H451 PCF sing 452 n n C45 H452 PCF sing 453 n n C46 H461 PCF sing 454 n n C46 H462 PCF sing 455 n n C46 H463 PCF sing 456 n n # _atom_sites.entry_id 2YGQ _atom_sites.fract_transf_matrix[1][1] 0.005618 _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] 0.005618 _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] 0.005618 _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 3 PCF A 1 1275 1275 PCF PCF . D 4 NAG A 1 1276 1276 NAG NAG . E 4 NAG A 1 1277 1277 NAG NAG . F 5 FUC A 1 1278 1278 FUC FUC . # 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 N N PCF . . . C 3 38.891 26.305 10.086 1 348.47 ? N PCF 1275 A 1 HETATM 2 P P PCF . . . C 3 40.076 22.201 8.929 1 309.76 ? P PCF 1275 A 1 HETATM 3 O O11 PCF . . . C 3 38.582 21.644 8.747 1 283.8 ? O11 PCF 1275 A 1 HETATM 4 O O12 PCF . . . C 3 40.736 21.437 10.046 1 325.89 ? O12 PCF 1275 A 1 HETATM 5 O O13 PCF . . . C 3 39.829 23.715 9.403 1 314.99 ? O13 PCF 1275 A 1 HETATM 6 O O14 PCF . . . C 3 40.729 22.244 7.572 1 307.79 ? O14 PCF 1275 A 1 HETATM 7 C C11 PCF . . . C 3 39.151 23.947 10.634 1 329.9 ? C11 PCF 1275 A 1 HETATM 8 C C12 PCF . . . C 3 39.374 25.375 11.112 1 343.3 ? C12 PCF 1275 A 1 HETATM 9 C C13 PCF . . . C 3 38.186 27.417 10.733 1 347.58 ? C13 PCF 1275 A 1 HETATM 10 C C14 PCF . . . C 3 37.972 25.598 9.188 1 344.6 ? C14 PCF 1275 A 1 HETATM 11 C C15 PCF . . . C 3 40.028 26.813 9.311 1 362.18 ? C15 PCF 1275 A 1 HETATM 12 C C1 PCF . . . C 3 38.377 20.24 8.677 1 270.8 ? C1 PCF 1275 A 1 HETATM 13 C C2 PCF . . . C 3 37.848 19.812 7.32 1 252.15 ? C2 PCF 1275 A 1 HETATM 14 C C3 PCF . . . C 3 38.341 18.402 7.153 1 252.71 ? C3 PCF 1275 A 1 HETATM 15 O O31 PCF . . . C 3 37.308 17.597 7.692 1 242.89 ? O31 PCF 1275 A 1 HETATM 16 O O32 PCF . . . C 3 38.292 17.139 9.693 1 261.31 ? O32 PCF 1275 A 1 HETATM 17 C C31 PCF . . . C 3 37.643 16.703 8.765 1 244.99 ? C31 PCF 1275 A 1 HETATM 18 C C32 PCF . . . C 3 37.177 15.274 8.692 1 223.32 ? C32 PCF 1275 A 1 HETATM 19 C C33 PCF . . . C 3 37.317 14.861 7.235 1 200.51 ? C33 PCF 1275 A 1 HETATM 20 C C34 PCF . . . C 3 36.754 13.48 6.951 1 184.1 ? C34 PCF 1275 A 1 HETATM 21 C C35 PCF . . . C 3 37.27 12.46 7.948 1 185.96 ? C35 PCF 1275 A 1 HETATM 22 C C36 PCF . . . C 3 36.15 12.093 8.905 1 186.13 ? C36 PCF 1275 A 1 HETATM 23 C C37 PCF . . . C 3 35.356 10.9 8.39 1 175.3 ? C37 PCF 1275 A 1 HETATM 24 C C38 PCF . . . C 3 36.113 9.61 8.67 1 163.79 ? C38 PCF 1275 A 1 HETATM 25 C C39 PCF . . . C 3 35.167 8.426 8.718 1 156.15 ? C39 PCF 1275 A 1 HETATM 26 C C40 PCF . . . C 3 34.441 8.269 7.392 1 144.5 ? C40 PCF 1275 A 1 HETATM 27 C C41 PCF . . . C 3 33.805 6.89 7.306 1 132.86 ? C41 PCF 1275 A 1 HETATM 28 C C42 PCF . . . C 3 32.606 6.804 8.234 1 136.02 ? C42 PCF 1275 A 1 HETATM 29 C C43 PCF . . . C 3 31.322 7.064 7.467 1 138.42 ? C43 PCF 1275 A 1 HETATM 30 O O21 PCF . . . C 3 36.433 19.7 7.326 1 232.72 ? O21 PCF 1275 A 1 HETATM 31 O O22 PCF . . . C 3 36.19 20.861 5.36 1 225.81 ? O22 PCF 1275 A 1 HETATM 32 C C21 PCF . . . C 3 35.875 19.88 5.999 1 220.85 ? C21 PCF 1275 A 1 HETATM 33 C C22 PCF . . . C 3 34.927 18.863 5.41 1 202.53 ? C22 PCF 1275 A 1 HETATM 34 C C23 PCF . . . C 3 34.22 18.119 6.53 1 196.43 ? C23 PCF 1275 A 1 HETATM 35 C C24 PCF . . . C 3 32.921 17.491 6.047 1 182.52 ? C24 PCF 1275 A 1 HETATM 36 C C25 PCF . . . C 3 33.139 16.179 5.306 1 180.07 ? C25 PCF 1275 A 1 HETATM 37 C C26 PCF . . . C 3 33.09 15.004 6.275 1 170.05 ? C26 PCF 1275 A 1 HETATM 38 C C27 PCF . . . C 3 32.526 13.744 5.627 1 155.1 ? C27 PCF 1275 A 1 HETATM 39 C C28 PCF . . . C 3 33.606 12.935 4.921 1 143.64 ? C28 PCF 1275 A 1 HETATM 40 C C29 PCF . . . C 3 33.421 11.439 5.15 1 131.01 ? C29 PCF 1275 A 1 HETATM 41 C C30 PCF . . . C 3 32.475 10.8 4.143 1 121.21 ? C30 PCF 1275 A 1 HETATM 42 C C47 PCF . . . C 3 32.11 9.394 4.6 1 115.2 ? C47 PCF 1275 A 1 HETATM 43 C C48 PCF . . . C 3 30.829 8.926 3.92 1 109.7 ? C48 PCF 1275 A 1 HETATM 44 C C49 PCF . . . C 3 31.063 7.704 3.049 1 106.12 ? C49 PCF 1275 A 1 HETATM 45 C C50 PCF . . . C 3 30.653 6.44 3.79 1 104.48 ? C50 PCF 1275 A 1 HETATM 46 C C51 PCF . . . C 3 29.137 6.294 3.826 1 104.4 ? C51 PCF 1275 A 1 HETATM 47 C C52 PCF . . . C 3 28.584 5.958 2.461 1 102.36 ? C52 PCF 1275 A 1 HETATM 48 C C44 PCF . . . C 3 30.508 5.784 7.378 1 138.23 ? C44 PCF 1275 A 1 HETATM 49 C C45 PCF . . . C 3 29.916 5.437 8.736 1 140.16 ? C45 PCF 1275 A 1 HETATM 50 C C46 PCF . . . C 3 28.739 6.328 9.052 1 137.5 ? C46 PCF 1275 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 50 #