data_6NWD # _model_server_result.job_id JcyUYifuhYCwVGt9fKUDng _model_server_result.datetime_utc '2024-11-25 10:52:46' _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 6nwd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1302}' # _entry.id 6NWD # _exptl.entry_id 6NWD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 678.94 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE _entity.pdbx_number_of_molecules 3 _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 6NWD _cell.length_a 54.25 _cell.length_b 129.25 _cell.length_c 82.65 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NWD _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 41.325 # 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 ? 3 E 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 257 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 257 _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 1301 _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 1.43 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C36 H73 N O8 P 1' _chem_comp.formula_weight 678.94 _chem_comp.id PX4 _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE _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 O1 P1 PX4 sing 332 n n O1 H1P PX4 sing 333 n n O2 P1 PX4 doub 334 n n P1 O3 PX4 sing 335 n n P1 O4 PX4 sing 336 n n O3 C1 PX4 sing 337 n n C1 C2 PX4 sing 338 n n C1 H1 PX4 sing 339 n n C1 H2 PX4 sing 340 n n C2 N1 PX4 sing 341 n n C2 H3 PX4 sing 342 n n C2 H4 PX4 sing 343 n n N1 C3 PX4 sing 344 n n N1 C4 PX4 sing 345 n n N1 C5 PX4 sing 346 n n C3 H5 PX4 sing 347 n n C3 H6 PX4 sing 348 n n C3 H7 PX4 sing 349 n n C4 H8 PX4 sing 350 n n C4 H9 PX4 sing 351 n n C4 H10 PX4 sing 352 n n C5 H11 PX4 sing 353 n n C5 H12 PX4 sing 354 n n C5 H13 PX4 sing 355 n n O4 C6 PX4 sing 356 n n C6 C7 PX4 sing 357 n n C6 H14 PX4 sing 358 n n C6 H15 PX4 sing 359 n n C7 C8 PX4 sing 360 n n C7 O7 PX4 sing 361 n n C7 H16 PX4 sing 362 n n C8 O5 PX4 sing 363 n n C8 H17 PX4 sing 364 n n C8 H18 PX4 sing 365 n n O5 C9 PX4 sing 366 n n C9 O6 PX4 doub 367 n n C9 C10 PX4 sing 368 n n C10 C11 PX4 sing 369 n n C10 H19 PX4 sing 370 n n C10 H20 PX4 sing 371 n n C11 C12 PX4 sing 372 n n C11 H21 PX4 sing 373 n n C11 H22 PX4 sing 374 n n C12 C13 PX4 sing 375 n n C12 H23 PX4 sing 376 n n C12 H24 PX4 sing 377 n n C13 C14 PX4 sing 378 n n C13 H25 PX4 sing 379 n n C13 H26 PX4 sing 380 n n C14 C15 PX4 sing 381 n n C14 H27 PX4 sing 382 n n C14 H28 PX4 sing 383 n n C15 C16 PX4 sing 384 n n C15 H29 PX4 sing 385 n n C15 H30 PX4 sing 386 n n C16 C17 PX4 sing 387 n n C16 H31 PX4 sing 388 n n C16 H32 PX4 sing 389 n n C17 C18 PX4 sing 390 n n C17 H33 PX4 sing 391 n n C17 H34 PX4 sing 392 n n C18 C19 PX4 sing 393 n n C18 H35 PX4 sing 394 n n C18 H36 PX4 sing 395 n n C19 C20 PX4 sing 396 n n C19 H37 PX4 sing 397 n n C19 H38 PX4 sing 398 n n C20 C21 PX4 sing 399 n n C20 H39 PX4 sing 400 n n C20 H40 PX4 sing 401 n n C21 C22 PX4 sing 402 n n C21 H41 PX4 sing 403 n n C21 H42 PX4 sing 404 n n C22 H43 PX4 sing 405 n n C22 H44 PX4 sing 406 n n C22 H45 PX4 sing 407 n n O7 C23 PX4 sing 408 n n C23 O8 PX4 doub 409 n n C23 C24 PX4 sing 410 n n C24 C25 PX4 sing 411 n n C24 H46 PX4 sing 412 n n C24 H47 PX4 sing 413 n n C25 C26 PX4 sing 414 n n C25 H48 PX4 sing 415 n n C25 H49 PX4 sing 416 n n C26 C27 PX4 sing 417 n n C26 H50 PX4 sing 418 n n C26 H51 PX4 sing 419 n n C27 C28 PX4 sing 420 n n C27 H52 PX4 sing 421 n n C27 H53 PX4 sing 422 n n C28 C29 PX4 sing 423 n n C28 H54 PX4 sing 424 n n C28 H55 PX4 sing 425 n n C29 C30 PX4 sing 426 n n C29 H56 PX4 sing 427 n n C29 H57 PX4 sing 428 n n C30 C31 PX4 sing 429 n n C30 H58 PX4 sing 430 n n C30 H59 PX4 sing 431 n n C31 C32 PX4 sing 432 n n C31 H60 PX4 sing 433 n n C31 H61 PX4 sing 434 n n C32 C33 PX4 sing 435 n n C32 H62 PX4 sing 436 n n C32 H63 PX4 sing 437 n n C33 C34 PX4 sing 438 n n C33 H64 PX4 sing 439 n n C33 H65 PX4 sing 440 n n C34 C35 PX4 sing 441 n n C34 H66 PX4 sing 442 n n C34 H67 PX4 sing 443 n n C35 C36 PX4 sing 444 n n C35 H68 PX4 sing 445 n n C35 H69 PX4 sing 446 n n C36 H70 PX4 sing 447 n n C36 H71 PX4 sing 448 n n C36 H72 PX4 sing 449 n n # _atom_sites.entry_id 6NWD _atom_sites.fract_transf_matrix[1][1] 0.018433 _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] 0.007737 _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] 0.012099 _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 1301 1301 RET RET . C 3 PX4 A 1 1302 1401 PX4 PX4 . D 3 PX4 A 1 1303 1402 PX4 PX4 . E 3 PX4 A 1 1304 1403 PX4 PX4 . F 4 D10 A 1 1305 1404 D10 D10 . G 5 D12 A 1 1306 1405 D12 D12 . H 6 HOH A 1 1401 402 HOH HOH . H 6 HOH A 2 1402 411 HOH HOH . H 6 HOH A 3 1403 502 HOH HOH . H 6 HOH A 4 1404 501 HOH HOH . H 6 HOH A 5 1405 414 HOH HOH . H 6 HOH A 6 1406 420 HOH HOH . H 6 HOH A 7 1407 413 HOH HOH . H 6 HOH A 8 1408 412 HOH HOH . H 6 HOH A 9 1409 417 HOH HOH . H 6 HOH A 10 1410 418 HOH HOH . H 6 HOH A 11 1411 419 HOH HOH . H 6 HOH A 12 1412 410 HOH HOH . H 6 HOH A 13 1413 416 HOH HOH . H 6 HOH A 14 1414 415 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 O1 PX4 . . . C 3 7.843 54.45 11.141 1 66.28 ? O1 PX4 1302 A 1 HETATM 2 O O2 PX4 . . . C 3 7.273 53.978 8.784 1 73.22 ? O2 PX4 1302 A 1 HETATM 3 P P1 PX4 . . . C 3 7.625 53.347 10.125 1 76.73 ? P1 PX4 1302 A 1 HETATM 4 O O3 PX4 . . . C 3 8.951 52.49 9.984 1 56.8 ? O3 PX4 1302 A 1 HETATM 5 O O4 PX4 . . . C 3 6.411 52.408 10.599 1 72.38 ? O4 PX4 1302 A 1 HETATM 6 C C6 PX4 . . . C 3 6.626 50.997 10.785 1 58.86 ? C6 PX4 1302 A 1 HETATM 7 C C7 PX4 . . . C 3 5.501 50.221 10.089 1 66.43 ? C7 PX4 1302 A 1 HETATM 8 C C8 PX4 . . . C 3 5.929 48.791 9.83 1 53.04 ? C8 PX4 1302 A 1 HETATM 9 O O5 PX4 . . . C 3 5.376 48.348 8.601 1 57.38 ? O5 PX4 1302 A 1 HETATM 10 C C9 PX4 . . . C 3 4.234 47.477 8.729 1 61.29 ? C9 PX4 1302 A 1 HETATM 11 O O6 PX4 . . . C 3 3.156 47.84 8.337 1 74.08 ? O6 PX4 1302 A 1 HETATM 12 C C10 PX4 . . . C 3 4.382 46.064 9.357 1 55.55 ? C10 PX4 1302 A 1 HETATM 13 C C11 PX4 . . . C 3 3.567 45.063 8.493 1 49.78 ? C11 PX4 1302 A 1 HETATM 14 C C12 PX4 . . . C 3 3.267 43.748 9.306 1 52.92 ? C12 PX4 1302 A 1 HETATM 15 C C13 PX4 . . . C 3 2.985 42.591 8.316 1 45.82 ? C13 PX4 1302 A 1 HETATM 16 C C14 PX4 . . . C 3 2.088 41.54 8.978 1 53.4 ? C14 PX4 1302 A 1 HETATM 17 C C15 PX4 . . . C 3 2.267 40.176 8.253 1 47.47 ? C15 PX4 1302 A 1 HETATM 18 C C16 PX4 . . . C 3 3.703 39.637 8.551 1 60.68 ? C16 PX4 1302 A 1 HETATM 19 O O7 PX4 . . . C 3 4.287 50.247 10.854 1 68.54 ? O7 PX4 1302 A 1 HETATM 20 C C23 PX4 . . . C 3 4.393 50.259 12.285 1 58.52 ? C23 PX4 1302 A 1 HETATM 21 O O8 PX4 . . . C 3 4.254 51.311 12.897 1 58.79 ? O8 PX4 1302 A 1 HETATM 22 C C24 PX4 . . . C 3 4.652 48.974 13.063 1 53.89 ? C24 PX4 1302 A 1 HETATM 23 C C25 PX4 . . . C 3 3.31 48.369 13.512 1 49.78 ? C25 PX4 1302 A 1 HETATM 24 C C26 PX4 . . . C 3 3.493 46.835 13.751 1 51.81 ? C26 PX4 1302 A 1 HETATM 25 C C27 PX4 . . . C 3 2.129 46.141 13.504 1 58.57 ? C27 PX4 1302 A 1 HETATM 26 C C28 PX4 . . . C 3 2.346 44.889 12.646 1 57.12 ? C28 PX4 1302 A 1 HETATM 27 C C29 PX4 . . . C 3 3.093 43.845 13.446 1 54.74 ? C29 PX4 1302 A 1 HETATM 28 C C30 PX4 . . . C 3 2.362 42.5 13.255 1 50.93 ? C30 PX4 1302 A 1 HETATM 29 C C31 PX4 . . . C 3 3.395 41.361 13.117 1 51.56 ? C31 PX4 1302 A 1 HETATM 30 C C32 PX4 . . . C 3 2.726 40.033 13.557 1 45.14 ? C32 PX4 1302 A 1 HETATM 31 C C33 PX4 . . . C 3 3.757 38.866 13.398 1 52.37 ? C33 PX4 1302 A 1 HETATM 32 C C34 PX4 . . . C 3 3.107 37.718 12.608 1 47.23 ? C34 PX4 1302 A 1 HETATM 33 C C35 PX4 . . . C 3 3.782 36.376 12.991 1 55.12 ? C35 PX4 1302 A 1 HETATM 34 C C36 PX4 . . . C 3 3.323 35.291 12.026 1 48.24 ? C36 PX4 1302 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 34 #