data_4D63 # _model_server_result.job_id 0V4riCqIYD1p8pjw-K8clQ _model_server_result.datetime_utc '2025-02-20 02:31:23' _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 4d63 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1455}' # _entry.id 4D63 # _exptl.entry_id 4D63 _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 _cell.angle_gamma 90 _cell.entry_id 4D63 _cell.length_a 98.46 _cell.length_b 98.46 _cell.length_c 98.46 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D63 _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 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 _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 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 4D63 _atom_sites.fract_transf_matrix[1][1] 0.010156 _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] 0.010156 _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] 0.010156 _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 1455 1455 SIA SIA . C 3 HOH A 1 2001 2001 HOH HOH . C 3 HOH A 2 2002 2002 HOH HOH . C 3 HOH A 3 2003 2003 HOH HOH . C 3 HOH A 4 2004 2004 HOH HOH . C 3 HOH A 5 2005 2005 HOH HOH . C 3 HOH A 6 2006 2006 HOH HOH . C 3 HOH A 7 2007 2007 HOH HOH . C 3 HOH A 8 2008 2008 HOH HOH . C 3 HOH A 9 2009 2009 HOH HOH . C 3 HOH A 10 2010 2010 HOH HOH . C 3 HOH A 11 2011 2011 HOH HOH . C 3 HOH A 12 2012 2012 HOH HOH . C 3 HOH A 13 2013 2013 HOH HOH . C 3 HOH A 14 2014 2014 HOH HOH . C 3 HOH A 15 2015 2015 HOH HOH . C 3 HOH A 16 2016 2016 HOH HOH . C 3 HOH A 17 2017 2017 HOH HOH . C 3 HOH A 18 2018 2018 HOH HOH . C 3 HOH A 19 2019 2019 HOH HOH . C 3 HOH A 20 2020 2020 HOH HOH . C 3 HOH A 21 2021 2021 HOH HOH . C 3 HOH A 22 2022 2022 HOH HOH . C 3 HOH A 23 2023 2023 HOH HOH . C 3 HOH A 24 2024 2024 HOH HOH . C 3 HOH A 25 2025 2025 HOH HOH . C 3 HOH A 26 2026 2026 HOH HOH . C 3 HOH A 27 2027 2027 HOH HOH . C 3 HOH A 28 2028 2028 HOH HOH . C 3 HOH A 29 2029 2029 HOH HOH . C 3 HOH A 30 2030 2030 HOH HOH . C 3 HOH A 31 2031 2031 HOH HOH . C 3 HOH A 32 2032 2032 HOH HOH . C 3 HOH A 33 2033 2033 HOH HOH . C 3 HOH A 34 2034 2034 HOH HOH . C 3 HOH A 35 2035 2035 HOH HOH . C 3 HOH A 36 2036 2036 HOH HOH . C 3 HOH A 37 2037 2037 HOH HOH . C 3 HOH A 38 2038 2038 HOH HOH . C 3 HOH A 39 2039 2039 HOH HOH . C 3 HOH A 40 2040 2040 HOH HOH . C 3 HOH A 41 2041 2041 HOH HOH . C 3 HOH A 42 2042 2042 HOH HOH . C 3 HOH A 43 2043 2043 HOH HOH . C 3 HOH A 44 2044 2044 HOH HOH . C 3 HOH A 45 2045 2045 HOH HOH . C 3 HOH A 46 2046 2046 HOH HOH . C 3 HOH A 47 2047 2047 HOH HOH . C 3 HOH A 48 2048 2048 HOH HOH . C 3 HOH A 49 2049 2049 HOH HOH . C 3 HOH A 50 2050 2050 HOH HOH . C 3 HOH A 51 2051 2051 HOH HOH . C 3 HOH A 52 2052 2052 HOH HOH . C 3 HOH A 53 2053 2053 HOH HOH . C 3 HOH A 54 2054 2054 HOH HOH . C 3 HOH A 55 2055 2055 HOH HOH . C 3 HOH A 56 2056 2056 HOH HOH . C 3 HOH A 57 2057 2057 HOH HOH . C 3 HOH A 58 2058 2058 HOH HOH . C 3 HOH A 59 2059 2059 HOH HOH . C 3 HOH A 60 2060 2060 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 47.605 12.214 31.617 0.67 54.64 ? C1 SIA 1455 A 1 HETATM 2 C C2 SIA . . . B 2 46.96 12.294 32.996 0.67 59.87 ? C2 SIA 1455 A 1 HETATM 3 C C3 SIA . . . B 2 46.446 13.717 33.295 0.67 60.32 ? C3 SIA 1455 A 1 HETATM 4 C C4 SIA . . . B 2 45.131 14.037 32.571 0.67 58.63 ? C4 SIA 1455 A 1 HETATM 5 C C5 SIA . . . B 2 44.113 12.968 32.938 0.67 57.4 ? C5 SIA 1455 A 1 HETATM 6 C C6 SIA . . . B 2 44.657 11.607 32.474 0.67 58.57 ? C6 SIA 1455 A 1 HETATM 7 C C7 SIA . . . B 2 43.752 10.42 32.806 0.67 58.64 ? C7 SIA 1455 A 1 HETATM 8 C C8 SIA . . . B 2 44.458 9.058 32.656 0.67 59.15 ? C8 SIA 1455 A 1 HETATM 9 C C9 SIA . . . B 2 44.514 8.266 33.967 0.67 59.51 ? C9 SIA 1455 A 1 HETATM 10 C C10 SIA . . . B 2 41.709 13.431 33.123 0.67 51.68 ? C10 SIA 1455 A 1 HETATM 11 C C11 SIA . . . B 2 40.452 13.967 32.474 0.67 50.39 ? C11 SIA 1455 A 1 HETATM 12 N N5 SIA . . . B 2 42.819 13.35 32.386 0.67 53.43 ? N5 SIA 1455 A 1 HETATM 13 O O1A SIA . . . B 2 47.913 13.285 31.042 0.67 51.28 ? O1A SIA 1455 A 1 HETATM 14 O O1B SIA . . . B 2 47.834 11.089 31.103 0.67 45.54 ? O1B SIA 1455 A 1 HETATM 15 O O2 SIA . . . B 2 47.931 11.873 33.982 0.67 61.31 ? O2 SIA 1455 A 1 HETATM 16 O O4 SIA . . . B 2 44.599 15.337 32.916 0.67 54.31 ? O4 SIA 1455 A 1 HETATM 17 O O6 SIA . . . B 2 45.887 11.362 33.157 0.67 59.88 ? O6 SIA 1455 A 1 HETATM 18 O O7 SIA . . . B 2 43.287 10.596 34.157 0.67 57.09 ? O7 SIA 1455 A 1 HETATM 19 O O8 SIA . . . B 2 43.812 8.224 31.688 0.67 55.84 ? O8 SIA 1455 A 1 HETATM 20 O O9 SIA . . . B 2 45.488 7.219 33.856 0.67 60.42 ? O9 SIA 1455 A 1 HETATM 21 O O10 SIA . . . B 2 41.699 13.097 34.285 0.67 49.17 ? O10 SIA 1455 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 21 #