data_5EGC # _model_server_result.job_id 1RQjb0KsnSMyTgBZzkZCgQ _model_server_result.datetime_utc '2025-03-01 03:16:25' _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 5egc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 5EGC # _exptl.entry_id 5EGC _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 111.06 _cell.angle_gamma 90 _cell.entry_id 5EGC _cell.length_a 455.627 _cell.length_b 261.749 _cell.length_c 450.98 _cell.Z_PDB 240 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EGC _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 60-meric 60 'complete icosahedral assembly' 1 ? monomeric 1 'icosahedral asymmetric unit' 2 ? pentameric 5 'icosahedral pentamer' 3 ? hexameric 6 'icosahedral 23 hexamer' 4 ? monomeric 1 'icosahedral asymmetric unit, std point frame' 5 ? 30-meric 30 'crystal asymmetric unit, crystal frame' 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 (1-60) A,B,C,D 2 1 A,B,C,D 3 (1-5) A,B,C,D 4 (1,2,6,10,23,24) A,B,C,D 5 P A,B,C,D 6 (X0)(1-10,21-25,31-35,41-50) # 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] P 'transform to point frame' ? ? 0 -1 0 0.358314 0 -0.933601 0.933601 0 0.358314 -0.45103 450.97972 0.49838 X0 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.976089 0.176919 -0.126295 -0.176919 0.309017 -0.934456 -0.126295 0.934456 0.332928 49.357 364.28941 260.69594 3 'point symmetry operation' ? ? 0.9374 0.109342 -0.330645 -0.109342 -0.809017 -0.577526 -0.330645 0.577526 -0.746417 129.05872 224.51993 681.66791 4 'point symmetry operation' ? ? 0.9374 -0.109342 -0.330645 0.109342 -0.809017 0.577526 -0.330645 -0.577526 -0.746417 128.96008 -226.15177 681.14695 5 'point symmetry operation' ? ? 0.976089 -0.176919 -0.126295 0.176919 0.309017 0.934456 -0.126295 -0.934456 0.332928 49.19741 -364.91272 259.85301 6 'point symmetry operation' ? ? 0.743222 0 0.669045 0 -1 0 0.669045 0 -0.743222 -323.18459 -0.90206 842.0704 7 'point symmetry operation' ? ? 0.640954 0.756683 0.128878 0.176919 -0.309017 0.934456 0.746912 -0.576142 -0.331937 -112.08417 -365.19147 681.33738 8 'point symmetry operation' ? ? 0.47548 0.467656 -0.745129 0.109342 0.809017 0.577526 0.872905 -0.356076 0.333537 228.80091 -225.42199 421.78562 9 'point symmetry operation' ? ? 0.47548 -0.467656 -0.745129 -0.109342 0.809017 -0.577526 0.872905 0.356076 0.333537 228.37906 225.24971 422.10682 10 'point symmetry operation' ? ? 0.640954 -0.756683 0.128878 -0.176919 -0.309017 -0.934456 0.746912 0.576142 -0.331937 -112.76674 364.01066 681.8571 11 'point symmetry operation' ? ? -0.743222 0 -0.669045 0 -1 0 -0.669045 0 0.743222 -0.93058 -0.90206 -0.35715 12 'point symmetry operation' ? ? -0.640954 -0.756683 -0.128878 0.176919 -0.309017 0.934456 -0.746912 0.576142 0.331937 -212.031 -365.19147 160.37586 13 'point symmetry operation' ? ? -0.47548 -0.467656 0.745129 0.109342 0.809017 0.577526 -0.872905 0.356076 -0.333537 -552.91608 -225.42199 419.92763 14 'point symmetry operation' ? ? -0.47548 0.467656 0.745129 -0.109342 0.809017 -0.577526 -0.872905 -0.356076 -0.333537 -552.49422 225.24971 419.60643 15 'point symmetry operation' ? ? -0.640954 0.756683 -0.128878 -0.176919 -0.309017 -0.934456 -0.746912 -0.576142 0.331937 -211.34842 364.01066 159.85615 16 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 -324.11516 0 841.71324 17 'point symmetry operation' ? ? -0.976089 -0.176919 0.126295 -0.176919 0.309017 -0.934456 0.126295 -0.934456 -0.332928 -373.47216 364.28941 581.0173 18 'point symmetry operation' ? ? -0.9374 -0.109342 0.330645 -0.109342 -0.809017 -0.577526 0.330645 -0.577526 0.746417 -453.17388 224.51993 160.04534 19 'point symmetry operation' ? ? -0.9374 0.109342 0.330645 0.109342 -0.809017 0.577526 0.330645 0.577526 0.746417 -453.07525 -226.15177 160.5663 20 'point symmetry operation' ? ? -0.976089 0.176919 0.126295 0.176919 0.309017 0.934456 0.126295 0.934456 -0.332928 -373.31257 -364.91272 581.86024 21 'point symmetry operation' ? ? 0.334522 -0.358314 -0.871611 -0.933601 0 -0.358314 0.128389 0.933601 -0.334522 258.81601 -0.94941 582.87 22 'point symmetry operation' ? ? 0.499996 -0.866024 0.002396 -0.866024 -0.5 -0.001383 0.002396 -0.001383 -0.999996 -82.42843 -140.44014 842.09932 23 'point symmetry operation' ? ? 0.640954 -0.176919 0.746912 -0.756683 -0.309017 0.576142 0.128878 -0.934456 -0.331937 -372.60895 -365.68985 581.01868 24 'point symmetry operation' ? ? 0.562597 0.756683 0.333041 -0.756683 0.309017 0.576142 0.333041 -0.576142 0.74642 -210.70594 -365.4111 160.43265 25 'point symmetry operation' ? ? 0.373211 0.644574 -0.667261 -0.866024 0.5 -0.001383 0.332739 0.578381 0.744823 179.53615 -139.98911 161.57683 26 'point symmetry operation' ? ? -0.334522 0.358314 0.871611 -0.933601 0 -0.358314 -0.128389 -0.933601 0.334522 -582.93117 -0.94941 258.84325 27 'point symmetry operation' ? ? -0.499996 0.866024 -0.002396 -0.866024 -0.5 -0.001383 -0.002396 0.001383 0.999996 -241.68674 -140.44014 -0.38607 28 'point symmetry operation' ? ? -0.640954 0.176919 -0.746912 -0.756683 -0.309017 0.576142 -0.128878 0.934456 0.331937 48.49378 -365.68985 260.69457 29 'point symmetry operation' ? ? -0.562597 -0.756683 -0.333041 -0.756683 0.309017 0.576142 -0.333041 0.576142 -0.74642 -113.40923 -365.4111 681.28059 30 'point symmetry operation' ? ? -0.373211 -0.644574 0.667261 -0.866024 0.5 -0.001383 -0.332739 -0.578381 -0.744823 -503.65131 -139.98911 680.13641 31 'point symmetry operation' ? ? 0.334522 0.358314 -0.871611 0.933601 0 0.358314 0.128389 -0.933601 -0.334522 259.13923 0.04735 582.02783 32 'point symmetry operation' ? ? 0.373211 -0.644574 -0.667261 0.866024 0.5 0.001383 0.332739 -0.578381 0.744823 178.9547 139.53808 161.0551 33 'point symmetry operation' ? ? 0.562597 -0.756683 0.333041 0.756683 0.309017 -0.576142 0.333041 0.576142 0.74642 -211.38851 364.78779 160.95237 34 'point symmetry operation' ? ? 0.640954 0.176919 0.746912 0.756683 -0.309017 -0.576142 0.128878 0.934456 -0.331937 -372.44935 364.50904 581.86161 35 'point symmetry operation' ? ? 0.499996 0.866024 0.002396 0.866024 -0.5 0.001383 0.002396 0.001383 -0.999996 -81.64722 139.08705 842.10056 36 'point symmetry operation' ? ? -0.334522 -0.358314 0.871611 0.933601 0 0.358314 -0.128389 0.933601 0.334522 -583.25439 0.04735 259.68541 37 'point symmetry operation' ? ? -0.373211 0.644574 0.667261 0.866024 0.5 0.001383 -0.332739 0.578381 -0.744823 -503.06986 139.53808 680.65815 38 'point symmetry operation' ? ? -0.562597 0.756683 -0.333041 0.756683 0.309017 -0.576142 -0.333041 -0.576142 -0.74642 -112.72665 364.78779 680.76088 39 'point symmetry operation' ? ? -0.640954 -0.176919 -0.746912 0.756683 -0.309017 -0.576142 -0.128878 -0.934456 0.331937 48.33419 364.50904 259.85163 40 'point symmetry operation' ? ? -0.499996 -0.866024 -0.002396 0.866024 -0.5 0.001383 -0.002396 -0.001383 0.999996 -242.46794 139.08705 -0.38732 41 'point symmetry operation' ? ? 0.334522 -0.933601 0.128389 -0.358314 0 0.933601 -0.871611 -0.358314 -0.334522 -162.30009 -451.43075 420.22972 42 'point symmetry operation' ? ? 0.47548 -0.109342 0.872905 -0.467656 0.809017 0.356076 -0.745129 -0.577526 0.333537 -452.41965 -225.73001 159.47106 43 'point symmetry operation' ? ? 0.373211 0.866024 0.332739 -0.644574 0.5 -0.578381 -0.667261 0.001383 0.744823 -241.2206 138.73168 -0.74099 44 'point symmetry operation' ? ? 0.169048 0.644574 -0.745618 -0.644574 -0.5 -0.578381 -0.745618 0.578381 0.330952 179.42716 138.28065 161.00118 45 'point symmetry operation' ? ? 0.145137 -0.467656 -0.871914 -0.467656 -0.809017 0.356076 -0.871914 0.356076 -0.33612 228.20272 -226.45979 421.17539 46 'point symmetry operation' ? ? 0.334522 0.933601 0.128389 0.358314 0 -0.933601 -0.871611 0.358314 -0.334522 -161.45792 450.52869 420.55294 47 'point symmetry operation' ? ? 0.145137 0.467656 -0.871914 0.467656 -0.809017 -0.356076 -0.871914 -0.356076 -0.33612 228.62457 224.82795 420.85419 48 'point symmetry operation' ? ? 0.169048 -0.644574 -0.745618 0.644574 -0.5 0.578381 -0.745618 -0.578381 0.330952 178.84571 -139.63374 160.47944 49 'point symmetry operation' ? ? 0.373211 -0.866024 0.332739 0.644574 0.5 0.578381 -0.667261 -0.001383 0.744823 -242.0018 -139.18271 -0.74224 50 'point symmetry operation' ? ? 0.47548 0.109342 0.872905 0.467656 0.809017 -0.356076 -0.745129 0.577526 0.333537 -452.32102 225.55773 159.99202 51 'point symmetry operation' ? ? -0.334522 0.933601 -0.128389 -0.358314 0 0.933601 0.871611 0.358314 0.334522 -161.81508 -451.43075 421.48352 52 'point symmetry operation' ? ? -0.47548 0.109342 -0.872905 -0.467656 0.809017 0.356076 0.745129 0.577526 -0.333537 128.30449 -225.73001 682.24218 53 'point symmetry operation' ? ? -0.373211 -0.866024 -0.332739 -0.644574 0.5 -0.578381 0.667261 -0.001383 -0.744823 -82.89457 138.73168 842.45424 54 'point symmetry operation' ? ? -0.169048 -0.644574 0.745618 -0.644574 -0.5 -0.578381 0.745618 -0.578381 -0.330952 -503.54232 138.28065 680.71207 55 'point symmetry operation' ? ? -0.145137 0.467656 0.871914 -0.467656 -0.809017 0.356076 0.871914 -0.356076 0.33612 -552.31788 -226.45979 420.53786 56 'point symmetry operation' ? ? -0.334522 -0.933601 -0.128389 0.358314 0 -0.933601 0.871611 -0.358314 0.334522 -162.65724 450.52869 421.1603 57 'point symmetry operation' ? ? -0.145137 -0.467656 0.871914 0.467656 -0.809017 -0.356076 0.871914 0.356076 0.33612 -552.73973 224.82795 420.85906 58 'point symmetry operation' ? ? -0.169048 0.644574 0.745618 0.644574 -0.5 0.578381 0.745618 0.578381 -0.330952 -502.96088 -139.63374 681.2338 59 'point symmetry operation' ? ? -0.373211 0.866024 -0.332739 0.644574 0.5 0.578381 0.667261 0.001383 -0.744823 -82.11336 -139.18271 842.45548 60 'point symmetry operation' ? ? -0.47548 -0.109342 -0.872905 0.467656 0.809017 -0.356076 0.745129 -0.577526 -0.333537 128.20585 225.55773 681.72122 # _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 5EGC _atom_sites.fract_transf_matrix[1][1] 0.002195 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000845 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00382 _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] 0.002376 _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 1 801 737 SIA SIA . C 3 MG A 1 802 1 MG MG . D 4 HOH A 1 901 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 C C1 SIA . . . B 2 -58.678 -34.841 488.171 0.55 32.8 ? C1 SIA 801 A 1 HETATM 2 C C2 SIA . . . B 2 -57.974 -34.75 486.756 0.55 30.69 ? C2 SIA 801 A 1 HETATM 3 C C3 SIA . . . B 2 -58.891 -34.707 485.524 0.55 32.21 ? C3 SIA 801 A 1 HETATM 4 C C4 SIA . . . B 2 -59.74 -33.451 485.357 0.55 27.76 ? C4 SIA 801 A 1 HETATM 5 C C5 SIA . . . B 2 -58.918 -32.182 485.645 0.55 30.1 ? C5 SIA 801 A 1 HETATM 6 C C6 SIA . . . B 2 -58.037 -32.32 486.916 0.55 30.89 ? C6 SIA 801 A 1 HETATM 7 C C7 SIA . . . B 2 -57.058 -31.126 487.118 0.55 33.41 ? C7 SIA 801 A 1 HETATM 8 C C8 SIA . . . B 2 -56.747 -30.951 488.623 0.55 32.62 ? C8 SIA 801 A 1 HETATM 9 C C9 SIA . . . B 2 -55.721 -29.838 488.881 0.55 33.57 ? C9 SIA 801 A 1 HETATM 10 C C10 SIA . . . B 2 -59.743 -29.925 484.947 0.55 35.59 ? C10 SIA 801 A 1 HETATM 11 C C11 SIA . . . B 2 -60.693 -28.799 485.367 0.55 28.6 ? C11 SIA 801 A 1 HETATM 12 N N5 SIA . . . B 2 -59.738 -30.983 485.81 0.55 31.41 ? N5 SIA 801 A 1 HETATM 13 O O1A SIA . . . B 2 -59.898 -35.12 488.172 0.55 35.7 ? O1A SIA 801 A 1 HETATM 14 O O1B SIA . . . B 2 -57.89 -34.58 489.137 0.55 32.99 ? O1B SIA 801 A 1 HETATM 15 O O2 SIA . . . B 2 -57.078 -35.786 486.569 0.55 32.86 ? O2 SIA 801 A 1 HETATM 16 O O4 SIA . . . B 2 -60.187 -33.388 483.994 0.55 26.87 ? O4 SIA 801 A 1 HETATM 17 O O6 SIA . . . B 2 -57.221 -33.49 486.835 0.55 34.78 ? O6 SIA 801 A 1 HETATM 18 O O7 SIA . . . B 2 -55.878 -31.252 486.323 0.55 39.7 ? O7 SIA 801 A 1 HETATM 19 O O8 SIA . . . B 2 -57.986 -30.752 489.309 0.55 35.1 ? O8 SIA 801 A 1 HETATM 20 O O9 SIA . . . B 2 -56.107 -28.99 489.977 0.55 19.74 ? O9 SIA 801 A 1 HETATM 21 O O10 SIA . . . B 2 -59.064 -29.854 483.909 0.55 35.56 ? O10 SIA 801 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #