data_4NFD # _model_server_result.job_id Tj5agRB_rVPJGK0Aqgr2dg _model_server_result.datetime_utc '2024-11-05 04:43:29' _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 4nfd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4NFD # _exptl.entry_id 4NFD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.27 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'N-acetyl-alpha-neuraminic acid' _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 90.6 _cell.angle_gamma 90 _cell.entry_id 4NFD _cell.length_a 33.58 _cell.length_b 39.571 _cell.length_c 41.481 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NFD _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C11 H19 N O9' _chem_comp.formula_weight 309.27 _chem_comp.id SIA _chem_comp.mon_nstd_flag . _chem_comp.name 'N-acetyl-alpha-neuraminic acid' _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms 'N-acetylneuraminic acid;sialic acid;alpha-sialic acid;O-SIALIC ACID' # 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 C2 SIA sing 290 n n C1 O1A SIA doub 291 n n C1 O1B SIA sing 292 n n C2 C3 SIA sing 293 n n C2 O2 SIA sing 294 n n C2 O6 SIA sing 295 n n C3 C4 SIA sing 296 n n C3 H32 SIA sing 297 n n C3 H31 SIA sing 298 n n C4 C5 SIA sing 299 n n C4 O4 SIA sing 300 n n C4 H4 SIA sing 301 n n C5 C6 SIA sing 302 n n C5 N5 SIA sing 303 n n C5 H5 SIA sing 304 n n C6 C7 SIA sing 305 n n C6 O6 SIA sing 306 n n C6 H6 SIA sing 307 n n C7 C8 SIA sing 308 n n C7 O7 SIA sing 309 n n C7 H7 SIA sing 310 n n C8 C9 SIA sing 311 n n C8 O8 SIA sing 312 n n C8 H8 SIA sing 313 n n C9 O9 SIA sing 314 n n C9 H92 SIA sing 315 n n C9 H91 SIA sing 316 n n C10 C11 SIA sing 317 n n C10 N5 SIA sing 318 n n C10 O10 SIA doub 319 n n C11 H111 SIA sing 320 n n C11 H113 SIA sing 321 n n C11 H112 SIA sing 322 n n N5 HN5 SIA sing 323 n n O1B HO1B SIA sing 324 n n O2 HO2 SIA sing 325 n n O4 HO4 SIA sing 326 n n O7 HO7 SIA sing 327 n n O8 HO8 SIA sing 328 n n O9 HO9 SIA sing 329 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version SIA DNeup5Aca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 SIA 'N-acetyl-a-D-neuraminic acid' 'COMMON NAME' GMML 1 SIA a-D-Neup5Ac 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 SIA Neu5Ac 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 4NFD _atom_sites.fract_transf_matrix[1][1] 0.02978 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000312 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025271 _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] 0.024109 _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 SIA A 1 201 1 SIA SIA . C 3 HOH A 1 301 1 HOH HOH . C 3 HOH A 2 302 2 HOH HOH . C 3 HOH A 3 303 3 HOH HOH . C 3 HOH A 4 304 4 HOH HOH . C 3 HOH A 5 305 5 HOH HOH . C 3 HOH A 6 306 6 HOH HOH . C 3 HOH A 7 307 7 HOH HOH . C 3 HOH A 8 308 8 HOH HOH . C 3 HOH A 9 309 9 HOH HOH . C 3 HOH A 10 310 10 HOH HOH . C 3 HOH A 11 311 11 HOH HOH . C 3 HOH A 12 312 12 HOH HOH . C 3 HOH A 13 313 13 HOH HOH . C 3 HOH A 14 314 14 HOH HOH . C 3 HOH A 15 315 15 HOH HOH . C 3 HOH A 16 316 16 HOH HOH . C 3 HOH A 17 317 17 HOH HOH . C 3 HOH A 18 318 18 HOH HOH . C 3 HOH A 19 319 19 HOH HOH . C 3 HOH A 20 320 20 HOH HOH . C 3 HOH A 21 321 21 HOH HOH . C 3 HOH A 22 322 22 HOH HOH . C 3 HOH A 23 323 23 HOH HOH . C 3 HOH A 24 324 24 HOH HOH . C 3 HOH A 25 325 25 HOH HOH . C 3 HOH A 26 326 26 HOH HOH . C 3 HOH A 27 327 27 HOH HOH . C 3 HOH A 28 328 28 HOH HOH . C 3 HOH A 29 329 29 HOH HOH . C 3 HOH A 30 330 30 HOH HOH . C 3 HOH A 31 331 31 HOH HOH . C 3 HOH A 32 332 32 HOH HOH . C 3 HOH A 33 333 33 HOH HOH . C 3 HOH A 34 334 34 HOH HOH . C 3 HOH A 35 335 35 HOH HOH . C 3 HOH A 36 336 36 HOH HOH . C 3 HOH A 37 337 37 HOH HOH . C 3 HOH A 38 338 38 HOH HOH . C 3 HOH A 39 339 39 HOH HOH . C 3 HOH A 40 340 40 HOH HOH . C 3 HOH A 41 341 41 HOH HOH . C 3 HOH A 42 342 42 HOH HOH . C 3 HOH A 43 343 43 HOH HOH . C 3 HOH A 44 344 44 HOH HOH . C 3 HOH A 45 345 45 HOH HOH . C 3 HOH A 46 346 46 HOH HOH . C 3 HOH A 47 347 47 HOH HOH . C 3 HOH A 48 348 48 HOH HOH . C 3 HOH A 49 349 49 HOH HOH . C 3 HOH A 50 350 50 HOH HOH . C 3 HOH A 51 351 51 HOH HOH . C 3 HOH A 52 352 52 HOH HOH . C 3 HOH A 53 353 53 HOH HOH . C 3 HOH A 54 354 54 HOH HOH . C 3 HOH A 55 355 55 HOH HOH . C 3 HOH A 56 356 56 HOH HOH . C 3 HOH A 57 357 57 HOH HOH . C 3 HOH A 58 358 58 HOH HOH . C 3 HOH A 59 359 59 HOH HOH . C 3 HOH A 60 360 60 HOH HOH . C 3 HOH A 61 361 61 HOH HOH . C 3 HOH A 62 362 62 HOH HOH . C 3 HOH A 63 363 63 HOH HOH . C 3 HOH A 64 364 64 HOH HOH . C 3 HOH A 65 365 65 HOH HOH . C 3 HOH A 66 366 66 HOH HOH . C 3 HOH A 67 367 67 HOH HOH . C 3 HOH A 68 368 68 HOH HOH . C 3 HOH A 69 369 69 HOH HOH . C 3 HOH A 70 370 70 HOH HOH . C 3 HOH A 71 371 71 HOH HOH . C 3 HOH A 72 372 72 HOH HOH . C 3 HOH A 73 373 73 HOH HOH . C 3 HOH A 74 374 74 HOH HOH . C 3 HOH A 75 375 75 HOH HOH . C 3 HOH A 76 376 76 HOH HOH . C 3 HOH A 77 377 77 HOH HOH . C 3 HOH A 78 378 78 HOH HOH . C 3 HOH A 79 379 79 HOH HOH . C 3 HOH A 80 380 80 HOH HOH . C 3 HOH A 81 381 81 HOH HOH . C 3 HOH A 82 382 82 HOH HOH . C 3 HOH A 83 383 83 HOH HOH . C 3 HOH A 84 384 84 HOH HOH . C 3 HOH A 85 385 85 HOH HOH . C 3 HOH A 86 386 86 HOH HOH . C 3 HOH A 87 387 87 HOH HOH . C 3 HOH A 88 388 88 HOH HOH . C 3 HOH A 89 389 89 HOH HOH . C 3 HOH A 90 390 90 HOH HOH . C 3 HOH A 91 391 91 HOH HOH . C 3 HOH A 92 392 92 HOH HOH . C 3 HOH A 93 393 93 HOH HOH . C 3 HOH A 94 394 94 HOH HOH . C 3 HOH A 95 395 95 HOH HOH . C 3 HOH A 96 396 96 HOH HOH . C 3 HOH A 97 397 97 HOH HOH . C 3 HOH A 98 398 98 HOH HOH . C 3 HOH A 99 399 99 HOH HOH . C 3 HOH A 100 400 100 HOH HOH . C 3 HOH A 101 401 101 HOH HOH . C 3 HOH A 102 402 102 HOH HOH . C 3 HOH A 103 403 103 HOH HOH . C 3 HOH A 104 404 104 HOH HOH . C 3 HOH A 105 405 105 HOH HOH . C 3 HOH A 106 406 106 HOH HOH . C 3 HOH A 107 407 107 HOH HOH . C 3 HOH A 108 408 108 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 SIA . . . B 2 20.629 8.065 17.742 1 20.46 ? C1 SIA 201 A 1 HETATM 2 C C2 SIA . . . B 2 22.142 8.094 17.823 1 21.87 ? C2 SIA 201 A 1 HETATM 3 C C3 SIA . . . B 2 22.624 8.271 19.261 1 19.4 ? C3 SIA 201 A 1 HETATM 4 C C4 SIA . . . B 2 22.537 7.009 20.116 1 18.44 ? C4 SIA 201 A 1 HETATM 5 C C5 SIA . . . B 2 22.975 5.77 19.347 1 16.16 ? C5 SIA 201 A 1 HETATM 6 C C6 SIA . . . B 2 22.221 5.757 18.022 1 16.47 ? C6 SIA 201 A 1 HETATM 7 C C7 SIA . . . B 2 22.442 4.506 17.184 1 13.07 ? C7 SIA 201 A 1 HETATM 8 C C8 SIA . . . B 2 21.683 4.613 15.86 1 14.85 ? C8 SIA 201 A 1 HETATM 9 C C9 SIA . . . B 2 21.724 3.315 15.063 1 17.69 ? C9 SIA 201 A 1 HETATM 10 C C10 SIA . . . B 2 23.637 3.939 20.826 1 17.16 ? C10 SIA 201 A 1 HETATM 11 C C11 SIA . . . B 2 23.121 2.852 21.722 1 14.73 ? C11 SIA 201 A 1 HETATM 12 N N5 SIA . . . B 2 22.704 4.583 20.132 1 13.09 ? N5 SIA 201 A 1 HETATM 13 O O1A SIA . . . B 2 20.086 7.622 16.706 1 24.96 ? O1A SIA 201 A 1 HETATM 14 O O1B SIA . . . B 2 19.967 8.475 18.708 1 28.01 ? O1B SIA 201 A 1 HETATM 15 O O2 SIA . . . B 2 22.649 9.196 17.072 1 15.23 ? O2 SIA 201 A 1 HETATM 16 O O4 SIA . . . B 2 23.355 7.17 21.276 1 19.7 ? O4 SIA 201 A 1 HETATM 17 O O6 SIA . . . B 2 22.658 6.885 17.281 1 14.1 ? O6 SIA 201 A 1 HETATM 18 O O7 SIA . . . B 2 23.838 4.37 16.922 1 13.46 ? O7 SIA 201 A 1 HETATM 19 O O8 SIA . . . B 2 20.323 4.979 16.096 1 15.1 ? O8 SIA 201 A 1 HETATM 20 O O9 SIA . . . B 2 21.088 2.259 15.783 1 13.92 ? O9 SIA 201 A 1 HETATM 21 O O10 SIA . . . B 2 24.822 4.202 20.747 1 18.61 ? O10 SIA 201 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 219 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 21 #