data_2YK7 # _model_server_result.job_id SPfwtb2alDdvGJMwRjgXrg _model_server_result.datetime_utc '2024-11-22 12:19:54' _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 2yk7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1371}' # _entry.id 2YK7 # _exptl.entry_id 2YK7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 632.442 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-MONOPHOSPHATE-3-FLUORO-N-ACETYL-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 2YK7 _cell.length_a 42.762 _cell.length_b 101.413 _cell.length_c 166.57 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YK7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _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 _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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 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 'C20 H30 F N4 O16 P' _chem_comp.formula_weight 632.442 _chem_comp.id CSF _chem_comp.mon_nstd_flag n _chem_comp.name "CYTIDINE-5'-MONOPHOSPHATE-3-FLUORO-N-ACETYL-NEURAMINIC ACID" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms CMP-3FNEUAC # 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 C5A C4A CSF sing 107 n n C5A C6A CSF sing 108 n n C5A N5A CSF sing 109 n n C5A H5A CSF sing 110 n n C4A C3A CSF sing 111 n n C4A O4A CSF sing 112 n n C4A H4A CSF sing 113 n n C2A O6A CSF sing 114 n n C2A C3A CSF sing 115 n n C2A C1A CSF sing 116 n n C2A O1A CSF sing 117 n n O6A C6A CSF sing 118 n n C6A C7A CSF sing 119 n n C6A H6A CSF sing 120 n n C3A F3A CSF sing 121 n n C3A H3A CSF sing 122 n n O4A H4 CSF sing 123 n n N5A C10 CSF sing 124 n n N5A H3 CSF sing 125 n n C7A C8A CSF sing 126 n n C7A O7A CSF sing 127 n n C7A H7A CSF sing 128 n n C8A C9A CSF sing 129 n n C8A O8A CSF sing 130 n n C8A H8A CSF sing 131 n n C9A O9A CSF sing 132 n n C9A H9A1 CSF sing 133 n n C9A H9A2 CSF sing 134 n n O9A H9A CSF sing 135 n n O8A H2 CSF sing 136 n n O7A H1 CSF sing 137 n n C1A OBA CSF sing 138 n n C1A OAA CSF doub 139 n n OBA HBA CSF sing 140 n n O1A PA CSF sing 141 n n O2A PA CSF doub 142 n n N1 C2 CSF sing 143 n n N1 C6 CSF sing 144 n n N1 C1' CSF sing 145 n n C2 N3 CSF sing 146 n n C2 O2 CSF doub 147 n n N3 C4 CSF doub 148 n n C4 C5 CSF sing 149 n n C4 N4 CSF sing 150 n n C5 C6 CSF doub 151 n n C5 H7 CSF sing 152 n n C6 H6 CSF sing 153 n n C3' C2' CSF sing 154 n n C3' C4' CSF sing 155 n n C3' O3' CSF sing 156 n n C3' H3' CSF sing 157 n n C2' C1' CSF sing 158 n n C2' O2' CSF sing 159 n n C2' H2' CSF sing 160 n n C1' O4' CSF sing 161 n n C1' H1' CSF sing 162 n n O4' C4' CSF sing 163 n n C4' C5' CSF sing 164 n n C4' H4' CSF sing 165 n n PA O5' CSF sing 166 n n PA O3A CSF sing 167 n n O5' C5' CSF sing 168 n n C5' H5' CSF sing 169 n n C5' "H5''" CSF sing 170 n n O3' HO3' CSF sing 171 n n O2' H8 CSF sing 172 n n N4 H41 CSF sing 173 n n N4 H42 CSF sing 174 n n O3A H5 CSF sing 175 n n C10 O10 CSF doub 176 n n C10 C11 CSF sing 177 n n C11 H111 CSF sing 178 n n C11 H112 CSF sing 179 n n C11 H113 CSF sing 180 n n # _atom_sites.entry_id 2YK7 _atom_sites.fract_transf_matrix[1][1] 0.023385 _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] 0.009861 _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] 0.006003 _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 CSF A 1 1371 1371 CSF CSF . C 3 1PE A 1 1372 1372 1PE 1PE . D 4 EDO A 1 1373 1373 EDO EDO . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2024 2024 HOH HOH . E 5 HOH A 25 2025 2025 HOH HOH . E 5 HOH A 26 2026 2026 HOH HOH . E 5 HOH A 27 2027 2027 HOH HOH . E 5 HOH A 28 2028 2028 HOH HOH . E 5 HOH A 29 2029 2029 HOH HOH . E 5 HOH A 30 2030 2030 HOH HOH . E 5 HOH A 31 2031 2031 HOH HOH . E 5 HOH A 32 2032 2032 HOH HOH . E 5 HOH A 33 2033 2033 HOH HOH . E 5 HOH A 34 2034 2034 HOH HOH . E 5 HOH A 35 2035 2035 HOH HOH . E 5 HOH A 36 2036 2036 HOH HOH . E 5 HOH A 37 2037 2037 HOH HOH . E 5 HOH A 38 2038 2038 HOH HOH . E 5 HOH A 39 2039 2039 HOH HOH . E 5 HOH A 40 2040 2040 HOH HOH . E 5 HOH A 41 2041 2041 HOH HOH . E 5 HOH A 42 2042 2042 HOH HOH . E 5 HOH A 43 2043 2043 HOH HOH . E 5 HOH A 44 2044 2044 HOH HOH . E 5 HOH A 45 2045 2045 HOH HOH . E 5 HOH A 46 2046 2046 HOH HOH . E 5 HOH A 47 2047 2047 HOH HOH . E 5 HOH A 48 2048 2048 HOH HOH . E 5 HOH A 49 2049 2049 HOH HOH . E 5 HOH A 50 2050 2050 HOH HOH . E 5 HOH A 51 2051 2051 HOH HOH . E 5 HOH A 52 2052 2052 HOH HOH . E 5 HOH A 53 2053 2053 HOH HOH . E 5 HOH A 54 2054 2054 HOH HOH . E 5 HOH A 55 2055 2055 HOH HOH . E 5 HOH A 56 2056 2056 HOH HOH . E 5 HOH A 57 2057 2057 HOH HOH . E 5 HOH A 58 2058 2058 HOH HOH . E 5 HOH A 59 2059 2059 HOH HOH . E 5 HOH A 60 2060 2060 HOH HOH . E 5 HOH A 61 2061 2061 HOH HOH . E 5 HOH A 62 2062 2062 HOH HOH . E 5 HOH A 63 2063 2063 HOH HOH . E 5 HOH A 64 2064 2064 HOH HOH . E 5 HOH A 65 2065 2065 HOH HOH . E 5 HOH A 66 2066 2066 HOH HOH . E 5 HOH A 67 2067 2067 HOH HOH . E 5 HOH A 68 2068 2068 HOH HOH . E 5 HOH A 69 2069 2069 HOH HOH . E 5 HOH A 70 2070 2070 HOH HOH . E 5 HOH A 71 2071 2071 HOH HOH . E 5 HOH A 72 2072 2072 HOH HOH . E 5 HOH A 73 2073 2073 HOH HOH . E 5 HOH A 74 2074 2074 HOH HOH . E 5 HOH A 75 2075 2075 HOH HOH . E 5 HOH A 76 2076 2076 HOH HOH . E 5 HOH A 77 2077 2077 HOH HOH . E 5 HOH A 78 2078 2078 HOH HOH . E 5 HOH A 79 2079 2079 HOH HOH . E 5 HOH A 80 2080 2080 HOH HOH . E 5 HOH A 81 2081 2081 HOH HOH . E 5 HOH A 82 2082 2082 HOH HOH . E 5 HOH A 83 2083 2083 HOH HOH . E 5 HOH A 84 2084 2084 HOH HOH . E 5 HOH A 85 2085 2085 HOH HOH . E 5 HOH A 86 2086 2086 HOH HOH . E 5 HOH A 87 2087 2087 HOH HOH . E 5 HOH A 88 2088 2088 HOH HOH . E 5 HOH A 89 2089 2089 HOH HOH . E 5 HOH A 90 2090 2090 HOH HOH . E 5 HOH A 91 2091 2091 HOH HOH . E 5 HOH A 92 2092 2092 HOH HOH . E 5 HOH A 93 2093 2093 HOH HOH . E 5 HOH A 94 2094 2094 HOH HOH . E 5 HOH A 95 2095 2095 HOH HOH . E 5 HOH A 96 2096 2096 HOH HOH . E 5 HOH A 97 2097 2097 HOH HOH . E 5 HOH A 98 2098 2098 HOH HOH . E 5 HOH A 99 2099 2099 HOH HOH . E 5 HOH A 100 2100 2100 HOH HOH . E 5 HOH A 101 2101 2101 HOH HOH . E 5 HOH A 102 2102 2102 HOH HOH . E 5 HOH A 103 2103 2103 HOH HOH . E 5 HOH A 104 2104 2104 HOH HOH . E 5 HOH A 105 2105 2105 HOH HOH . E 5 HOH A 106 2106 2106 HOH HOH . E 5 HOH A 107 2107 2107 HOH HOH . E 5 HOH A 108 2108 2108 HOH HOH . E 5 HOH A 109 2109 2109 HOH HOH . E 5 HOH A 110 2110 2110 HOH HOH . E 5 HOH A 111 2111 2111 HOH HOH . E 5 HOH A 112 2112 2112 HOH HOH . E 5 HOH A 113 2113 2113 HOH HOH . E 5 HOH A 114 2114 2114 HOH HOH . E 5 HOH A 115 2115 2115 HOH HOH . E 5 HOH A 116 2116 2116 HOH HOH . E 5 HOH A 117 2117 2117 HOH HOH . E 5 HOH A 118 2118 2118 HOH HOH . E 5 HOH A 119 2119 2119 HOH HOH . E 5 HOH A 120 2120 2120 HOH HOH . E 5 HOH A 121 2121 2121 HOH HOH . E 5 HOH A 122 2122 2122 HOH HOH . E 5 HOH A 123 2123 2123 HOH HOH . E 5 HOH A 124 2124 2124 HOH HOH . E 5 HOH A 125 2125 2125 HOH HOH . E 5 HOH A 126 2126 2126 HOH HOH . E 5 HOH A 127 2127 2127 HOH HOH . E 5 HOH A 128 2128 2128 HOH HOH . E 5 HOH A 129 2129 2129 HOH HOH . E 5 HOH A 130 2130 2130 HOH HOH . E 5 HOH A 131 2131 2131 HOH HOH . E 5 HOH A 132 2132 2132 HOH HOH . E 5 HOH A 133 2133 2133 HOH HOH . E 5 HOH A 134 2134 2134 HOH HOH . E 5 HOH A 135 2135 2135 HOH HOH . E 5 HOH A 136 2136 2136 HOH HOH . E 5 HOH A 137 2137 2137 HOH HOH . E 5 HOH A 138 2138 2138 HOH HOH . E 5 HOH A 139 2139 2139 HOH HOH . E 5 HOH A 140 2140 2140 HOH HOH . E 5 HOH A 141 2141 2141 HOH HOH . E 5 HOH A 142 2142 2142 HOH HOH . E 5 HOH A 143 2143 2143 HOH HOH . E 5 HOH A 144 2144 2144 HOH HOH . E 5 HOH A 145 2145 2145 HOH HOH . E 5 HOH A 146 2146 2146 HOH HOH . E 5 HOH A 147 2147 2147 HOH HOH . E 5 HOH A 148 2148 2148 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 C5A CSF . . . B 2 -6.679 -5.771 18.027 1 47.05 ? C5A CSF 1371 A 1 HETATM 2 C C4A CSF . . . B 2 -8.143 -5.675 18.383 1 43.98 ? C4A CSF 1371 A 1 HETATM 3 C C2A CSF . . . B 2 -6.924 -6.663 20.516 1 39.74 ? C2A CSF 1371 A 1 HETATM 4 O O6A CSF . . . B 2 -5.744 -6.017 19.969 1 45.74 ? O6A CSF 1371 A 1 HETATM 5 C C6A CSF . . . B 2 -6.134 -4.878 19.12 1 47.91 ? C6A CSF 1371 A 1 HETATM 6 C C3A CSF . . . B 2 -8.149 -6.761 19.45 1 43.48 ? C3A CSF 1371 A 1 HETATM 7 O O4A CSF . . . B 2 -9.027 -5.928 17.266 1 44.62 ? O4A CSF 1371 A 1 HETATM 8 N N5A CSF . . . B 2 -6.285 -5.56 16.611 1 46.61 ? N5A CSF 1371 A 1 HETATM 9 C C7A CSF . . . B 2 -5.272 -3.646 18.88 1 50.55 ? C7A CSF 1371 A 1 HETATM 10 C C8A CSF . . . B 2 -6.154 -2.489 19.272 1 51.97 ? C8A CSF 1371 A 1 HETATM 11 C C9A CSF . . . B 2 -5.579 -1.1 18.921 1 53.97 ? C9A CSF 1371 A 1 HETATM 12 O O9A CSF . . . B 2 -4.669 -0.588 19.921 1 51.97 ? O9A CSF 1371 A 1 HETATM 13 O O8A CSF . . . B 2 -7.43 -2.729 18.652 1 53.31 ? O8A CSF 1371 A 1 HETATM 14 O O7A CSF . . . B 2 -4.171 -3.669 19.761 1 53.7 ? O7A CSF 1371 A 1 HETATM 15 C C1A CSF . . . B 2 -6.48 -7.927 20.996 1 36.44 ? C1A CSF 1371 A 1 HETATM 16 O OBA CSF . . . B 2 -5.297 -7.99 21.436 1 43.36 ? OBA CSF 1371 A 1 HETATM 17 O OAA CSF . . . B 2 -7.381 -8.713 21.228 1 40.27 ? OAA CSF 1371 A 1 HETATM 18 O O1A CSF . . . B 2 -7.475 -6.022 21.797 1 40.63 ? O1A CSF 1371 A 1 HETATM 19 O O2A CSF . . . B 2 -7.741 -6.343 24.452 1 36.95 ? O2A CSF 1371 A 1 HETATM 20 N N1 CSF . . . B 2 -10.862 -2.517 24.16 1 33.38 ? N1 CSF 1371 A 1 HETATM 21 C C2 CSF . . . B 2 -12.109 -2.111 24.677 1 28.52 ? C2 CSF 1371 A 1 HETATM 22 N N3 CSF . . . B 2 -12.766 -3.013 25.531 1 28.03 ? N3 CSF 1371 A 1 HETATM 23 C C4 CSF . . . B 2 -12.271 -4.29 25.827 1 28.44 ? C4 CSF 1371 A 1 HETATM 24 C C5 CSF . . . B 2 -11.034 -4.704 25.315 1 29.51 ? C5 CSF 1371 A 1 HETATM 25 C C6 CSF . . . B 2 -10.321 -3.829 24.48 1 31.68 ? C6 CSF 1371 A 1 HETATM 26 C C3' CSF . . . B 2 -7.826 -1.364 23.878 1 33.02 ? C3' CSF 1371 A 1 HETATM 27 C C2' CSF . . . B 2 -9.18 -0.637 23.96 1 33.15 ? C2' CSF 1371 A 1 HETATM 28 C C1' CSF . . . B 2 -10.113 -1.59 23.254 1 33.02 ? C1' CSF 1371 A 1 HETATM 29 O O4' CSF . . . B 2 -9.275 -2.449 22.394 1 34.18 ? O4' CSF 1371 A 1 HETATM 30 C C4' CSF . . . B 2 -7.916 -1.956 22.467 1 35.55 ? C4' CSF 1371 A 1 HETATM 31 P PA CSF . . . B 2 -6.84 -5.621 23.31 1 39.21 ? PA CSF 1371 A 1 HETATM 32 O O5' CSF . . . B 2 -7.233 -4.104 23.455 1 41.2 ? O5' CSF 1371 A 1 HETATM 33 C C5' CSF . . . B 2 -7.047 -3.231 22.319 1 39.24 ? C5' CSF 1371 A 1 HETATM 34 O O3' CSF . . . B 2 -6.735 -0.425 24.054 1 29.77 ? O3' CSF 1371 A 1 HETATM 35 O O2' CSF . . . B 2 -9.168 0.622 23.225 1 29.31 ? O2' CSF 1371 A 1 HETATM 36 N N4 CSF . . . B 2 -13.002 -5.094 26.571 1 26.48 ? N4 CSF 1371 A 1 HETATM 37 O O2 CSF . . . B 2 -12.573 -0.971 24.453 1 29.22 ? O2 CSF 1371 A 1 HETATM 38 O O3A CSF . . . B 2 -5.345 -5.76 23.529 1 35.38 ? O3A CSF 1371 A 1 HETATM 39 C C10 CSF . . . B 2 -6.039 -6.644 15.841 1 46.47 ? C10 CSF 1371 A 1 HETATM 40 O O10 CSF . . . B 2 -6.13 -7.827 16.226 1 43.96 ? O10 CSF 1371 A 1 HETATM 41 C C11 CSF . . . B 2 -5.64 -6.311 14.384 1 47.92 ? C11 CSF 1371 A 1 HETATM 42 F F3A CSF . . . B 2 -8.315 -7.98 18.799 1 45.76 ? F3A CSF 1371 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 497 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 42 #