data_2XJE # _model_server_result.job_id LbRDwuvfpLDWZ0IfZ9GhtA _model_server_result.datetime_utc '2024-11-23 04:56:48' _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 2xje # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1489}' # _entry.id 2XJE # _exptl.entry_id 2XJE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 2XJE _cell.length_a 91.65 _cell.length_b 127.61 _cell.length_c 130.47 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XJE _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _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 _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_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 130.47 # _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A OD1 ASN 71 A ASN 52 1_555 F MG MG . A MG 1493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc2 A O ASP 73 A ASP 54 1_555 F MG MG . A MG 1493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc3 A OD1 ASP 370 A ASP 351 1_555 F MG MG . A MG 1493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc4 B O2P U5P . A U5P 1489 1_555 F MG MG . A MG 1493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc5 C O3G ATP . A ATP 1490 1_555 E MG MG . A MG 1492 3_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc6 C O1B ATP . A ATP 1490 1_555 E MG MG . A MG 1492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc7 C O1B ATP . A ATP 1490 1_555 E MG MG . A MG 1492 3_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc8 C O2B ATP . A ATP 1490 1_555 E MG MG . A MG 1492 3_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc9 C O3G ATP . A ATP 1490 1_555 E MG MG . A MG 1492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc10 E MG MG . A MG 1492 1_555 G O HOH . A HOH 2175 3_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc11 E MG MG . A MG 1492 1_555 G O HOH . A HOH 2175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc12 F MG MG . A MG 1493 1_555 G O HOH . A HOH 2138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc13 F MG MG . A MG 1493 1_555 G O HOH . A HOH 2140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _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 N1 C2 U5P sing 420 n n N1 C6 U5P sing 421 n n N1 C1' U5P sing 422 n n C2 N3 U5P sing 423 n n C2 O2 U5P doub 424 n n N3 C4 U5P sing 425 n n N3 HN3 U5P sing 426 n n C4 C5 U5P sing 427 n n C4 O4 U5P doub 428 n n C5 C6 U5P doub 429 n n C5 H5 U5P sing 430 n n C6 H6 U5P sing 431 n n C1' C2' U5P sing 432 n n C1' O4' U5P sing 433 n n C1' H1' U5P sing 434 n n C2' O2' U5P sing 435 n n C2' C3' U5P sing 436 n n C2' H2' U5P sing 437 n n O2' HO2' U5P sing 438 n n C3' C4' U5P sing 439 n n C3' O3' U5P sing 440 n n C3' H3' U5P sing 441 n n C4' O4' U5P sing 442 n n C4' C5' U5P sing 443 n n C4' H4' U5P sing 444 n n O3' HO3' U5P sing 445 n n C5' O5' U5P sing 446 n n C5' "H5'1" U5P sing 447 n n C5' "H5'2" U5P sing 448 n n O5' P U5P sing 449 n n P O1P U5P doub 450 n n P O2P U5P sing 451 n n P O3P U5P sing 452 n n O2P HOP2 U5P sing 453 n n O3P HOP3 U5P sing 454 n n # _atom_sites.entry_id 2XJE _atom_sites.fract_transf_matrix[1][1] 0.010911 _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] 0.007836 _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] 0.007665 _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 U5P A 1 1489 1489 U5P U5P . C 3 ATP A 1 1490 1490 ATP ATP . D 4 GOL A 1 1491 1491 GOL GOL . E 5 MG A 1 1492 1492 MG MG . F 5 MG A 1 1493 1493 MG MG . G 6 HOH A 1 2001 2001 HOH HOH . G 6 HOH A 2 2002 2002 HOH HOH . G 6 HOH A 3 2003 2003 HOH HOH . G 6 HOH A 4 2004 2004 HOH HOH . G 6 HOH A 5 2005 2005 HOH HOH . G 6 HOH A 6 2006 2006 HOH HOH . G 6 HOH A 7 2007 2007 HOH HOH . G 6 HOH A 8 2008 2008 HOH HOH . G 6 HOH A 9 2009 2009 HOH HOH . G 6 HOH A 10 2010 2010 HOH HOH . G 6 HOH A 11 2011 2011 HOH HOH . G 6 HOH A 12 2012 2012 HOH HOH . G 6 HOH A 13 2013 2013 HOH HOH . G 6 HOH A 14 2014 2014 HOH HOH . G 6 HOH A 15 2015 2015 HOH HOH . G 6 HOH A 16 2016 2016 HOH HOH . G 6 HOH A 17 2017 2017 HOH HOH . G 6 HOH A 18 2018 2018 HOH HOH . G 6 HOH A 19 2019 2019 HOH HOH . G 6 HOH A 20 2020 2020 HOH HOH . G 6 HOH A 21 2021 2021 HOH HOH . G 6 HOH A 22 2022 2022 HOH HOH . G 6 HOH A 23 2023 2023 HOH HOH . G 6 HOH A 24 2024 2024 HOH HOH . G 6 HOH A 25 2025 2025 HOH HOH . G 6 HOH A 26 2026 2026 HOH HOH . G 6 HOH A 27 2027 2027 HOH HOH . G 6 HOH A 28 2028 2028 HOH HOH . G 6 HOH A 29 2029 2029 HOH HOH . G 6 HOH A 30 2030 2030 HOH HOH . G 6 HOH A 31 2031 2031 HOH HOH . G 6 HOH A 32 2032 2032 HOH HOH . G 6 HOH A 33 2033 2033 HOH HOH . G 6 HOH A 34 2034 2034 HOH HOH . G 6 HOH A 35 2035 2035 HOH HOH . G 6 HOH A 36 2036 2036 HOH HOH . G 6 HOH A 37 2037 2037 HOH HOH . G 6 HOH A 38 2038 2038 HOH HOH . G 6 HOH A 39 2039 2039 HOH HOH . G 6 HOH A 40 2040 2040 HOH HOH . G 6 HOH A 41 2041 2041 HOH HOH . G 6 HOH A 42 2042 2042 HOH HOH . G 6 HOH A 43 2043 2043 HOH HOH . G 6 HOH A 44 2044 2044 HOH HOH . G 6 HOH A 45 2045 2045 HOH HOH . G 6 HOH A 46 2046 2046 HOH HOH . G 6 HOH A 47 2047 2047 HOH HOH . G 6 HOH A 48 2048 2048 HOH HOH . G 6 HOH A 49 2049 2049 HOH HOH . G 6 HOH A 50 2050 2050 HOH HOH . G 6 HOH A 51 2051 2051 HOH HOH . G 6 HOH A 52 2052 2052 HOH HOH . G 6 HOH A 53 2053 2053 HOH HOH . G 6 HOH A 54 2054 2054 HOH HOH . G 6 HOH A 55 2055 2055 HOH HOH . G 6 HOH A 56 2056 2056 HOH HOH . G 6 HOH A 57 2057 2057 HOH HOH . G 6 HOH A 58 2058 2058 HOH HOH . G 6 HOH A 59 2059 2059 HOH HOH . G 6 HOH A 60 2060 2060 HOH HOH . G 6 HOH A 61 2061 2061 HOH HOH . G 6 HOH A 62 2062 2062 HOH HOH . G 6 HOH A 63 2063 2063 HOH HOH . G 6 HOH A 64 2064 2064 HOH HOH . G 6 HOH A 65 2065 2065 HOH HOH . G 6 HOH A 66 2066 2066 HOH HOH . G 6 HOH A 67 2067 2067 HOH HOH . G 6 HOH A 68 2068 2068 HOH HOH . G 6 HOH A 69 2069 2069 HOH HOH . G 6 HOH A 70 2070 2070 HOH HOH . G 6 HOH A 71 2071 2071 HOH HOH . G 6 HOH A 72 2072 2072 HOH HOH . G 6 HOH A 73 2073 2073 HOH HOH . G 6 HOH A 74 2074 2074 HOH HOH . G 6 HOH A 75 2075 2075 HOH HOH . G 6 HOH A 76 2076 2076 HOH HOH . G 6 HOH A 77 2077 2077 HOH HOH . G 6 HOH A 78 2078 2078 HOH HOH . G 6 HOH A 79 2079 2079 HOH HOH . G 6 HOH A 80 2080 2080 HOH HOH . G 6 HOH A 81 2081 2081 HOH HOH . G 6 HOH A 82 2082 2082 HOH HOH . G 6 HOH A 83 2083 2083 HOH HOH . G 6 HOH A 84 2084 2084 HOH HOH . G 6 HOH A 85 2085 2085 HOH HOH . G 6 HOH A 86 2086 2086 HOH HOH . G 6 HOH A 87 2087 2087 HOH HOH . G 6 HOH A 88 2088 2088 HOH HOH . G 6 HOH A 89 2089 2089 HOH HOH . G 6 HOH A 90 2090 2090 HOH HOH . G 6 HOH A 91 2091 2091 HOH HOH . G 6 HOH A 92 2092 2092 HOH HOH . G 6 HOH A 93 2093 2093 HOH HOH . G 6 HOH A 94 2094 2094 HOH HOH . G 6 HOH A 95 2095 2095 HOH HOH . G 6 HOH A 96 2096 2096 HOH HOH . G 6 HOH A 97 2097 2097 HOH HOH . G 6 HOH A 98 2098 2098 HOH HOH . G 6 HOH A 99 2099 2099 HOH HOH . G 6 HOH A 100 2100 2100 HOH HOH . G 6 HOH A 101 2101 2101 HOH HOH . G 6 HOH A 102 2102 2102 HOH HOH . G 6 HOH A 103 2103 2103 HOH HOH . G 6 HOH A 104 2104 2104 HOH HOH . G 6 HOH A 105 2105 2105 HOH HOH . G 6 HOH A 106 2106 2106 HOH HOH . G 6 HOH A 107 2107 2107 HOH HOH . G 6 HOH A 108 2108 2108 HOH HOH . G 6 HOH A 109 2109 2109 HOH HOH . G 6 HOH A 110 2110 2110 HOH HOH . G 6 HOH A 111 2111 2111 HOH HOH . G 6 HOH A 112 2112 2112 HOH HOH . G 6 HOH A 113 2113 2113 HOH HOH . G 6 HOH A 114 2114 2114 HOH HOH . G 6 HOH A 115 2115 2115 HOH HOH . G 6 HOH A 116 2116 2116 HOH HOH . G 6 HOH A 117 2117 2117 HOH HOH . G 6 HOH A 118 2118 2118 HOH HOH . G 6 HOH A 119 2119 2119 HOH HOH . G 6 HOH A 120 2120 2120 HOH HOH . G 6 HOH A 121 2121 2121 HOH HOH . G 6 HOH A 122 2122 2122 HOH HOH . G 6 HOH A 123 2123 2123 HOH HOH . G 6 HOH A 124 2124 2124 HOH HOH . G 6 HOH A 125 2125 2125 HOH HOH . G 6 HOH A 126 2126 2126 HOH HOH . G 6 HOH A 127 2127 2127 HOH HOH . G 6 HOH A 128 2128 2128 HOH HOH . G 6 HOH A 129 2129 2129 HOH HOH . G 6 HOH A 130 2130 2130 HOH HOH . G 6 HOH A 131 2131 2131 HOH HOH . G 6 HOH A 132 2132 2132 HOH HOH . G 6 HOH A 133 2133 2133 HOH HOH . G 6 HOH A 134 2134 2134 HOH HOH . G 6 HOH A 135 2135 2135 HOH HOH . G 6 HOH A 136 2136 2136 HOH HOH . G 6 HOH A 137 2137 2137 HOH HOH . G 6 HOH A 138 2138 2138 HOH HOH . G 6 HOH A 139 2139 2139 HOH HOH . G 6 HOH A 140 2140 2140 HOH HOH . G 6 HOH A 141 2141 2141 HOH HOH . G 6 HOH A 142 2142 2142 HOH HOH . G 6 HOH A 143 2143 2143 HOH HOH . G 6 HOH A 144 2144 2144 HOH HOH . G 6 HOH A 145 2145 2145 HOH HOH . G 6 HOH A 146 2146 2146 HOH HOH . G 6 HOH A 147 2147 2147 HOH HOH . G 6 HOH A 148 2148 2148 HOH HOH . G 6 HOH A 149 2149 2149 HOH HOH . G 6 HOH A 150 2150 2150 HOH HOH . G 6 HOH A 151 2151 2151 HOH HOH . G 6 HOH A 152 2152 2152 HOH HOH . G 6 HOH A 153 2153 2153 HOH HOH . G 6 HOH A 154 2154 2154 HOH HOH . G 6 HOH A 155 2155 2155 HOH HOH . G 6 HOH A 156 2156 2156 HOH HOH . G 6 HOH A 157 2157 2157 HOH HOH . G 6 HOH A 158 2158 2158 HOH HOH . G 6 HOH A 159 2159 2159 HOH HOH . G 6 HOH A 160 2160 2160 HOH HOH . G 6 HOH A 161 2161 2161 HOH HOH . G 6 HOH A 162 2162 2162 HOH HOH . G 6 HOH A 163 2163 2163 HOH HOH . G 6 HOH A 164 2164 2164 HOH HOH . G 6 HOH A 165 2165 2165 HOH HOH . G 6 HOH A 166 2166 2166 HOH HOH . G 6 HOH A 167 2167 2167 HOH HOH . G 6 HOH A 168 2168 2168 HOH HOH . G 6 HOH A 169 2169 2169 HOH HOH . G 6 HOH A 170 2170 2170 HOH HOH . G 6 HOH A 171 2171 2171 HOH HOH . G 6 HOH A 172 2172 2172 HOH HOH . G 6 HOH A 173 2173 2173 HOH HOH . G 6 HOH A 174 2174 2174 HOH HOH . G 6 HOH A 175 2175 2175 HOH HOH . G 6 HOH A 176 2176 2176 HOH HOH . G 6 HOH A 177 2177 2177 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 N N1 U5P . . . B 2 1.099 14.178 41.669 1 57.09 ? N1 U5P 1489 A 1 HETATM 2 C C2 U5P . . . B 2 0.329 15.192 42.285 1 56.83 ? C2 U5P 1489 A 1 HETATM 3 N N3 U5P . . . B 2 -0.942 14.983 42.659 1 56.3 ? N3 U5P 1489 A 1 HETATM 4 C C4 U5P . . . B 2 -1.53 13.801 42.464 1 57.1 ? C4 U5P 1489 A 1 HETATM 5 C C5 U5P . . . B 2 -0.815 12.771 41.859 1 57.76 ? C5 U5P 1489 A 1 HETATM 6 C C6 U5P . . . B 2 0.506 12.989 41.474 1 57.36 ? C6 U5P 1489 A 1 HETATM 7 O O2 U5P . . . B 2 0.829 16.303 42.503 1 58.32 ? O2 U5P 1489 A 1 HETATM 8 O O4 U5P . . . B 2 -2.719 13.633 42.822 1 57.57 ? O4 U5P 1489 A 1 HETATM 9 C C1' U5P . . . B 2 2.515 14.352 41.224 1 55.91 ? C1' U5P 1489 A 1 HETATM 10 C C2' U5P . . . B 2 2.634 15.133 39.938 1 53.33 ? C2' U5P 1489 A 1 HETATM 11 O O2' U5P . . . B 2 2.407 14.218 38.876 1 52.98 ? O2' U5P 1489 A 1 HETATM 12 C C3' U5P . . . B 2 4.064 15.651 39.958 1 52.83 ? C3' U5P 1489 A 1 HETATM 13 C C4' U5P . . . B 2 4.524 15.59 41.439 1 51.08 ? C4' U5P 1489 A 1 HETATM 14 O O3' U5P . . . B 2 4.819 14.794 39.071 1 52.16 ? O3' U5P 1489 A 1 HETATM 15 O O4' U5P . . . B 2 3.416 15.012 42.137 1 55.19 ? O4' U5P 1489 A 1 HETATM 16 C C5' U5P . . . B 2 4.884 16.906 42.186 1 45.73 ? C5' U5P 1489 A 1 HETATM 17 O O5' U5P . . . B 2 6.302 17.187 42.137 1 40.77 ? O5' U5P 1489 A 1 HETATM 18 P P U5P . . . B 2 7.139 18.336 42.973 1 36.19 ? P U5P 1489 A 1 HETATM 19 O O1P U5P . . . B 2 8.265 18.762 42.023 1 32.75 ? O1P U5P 1489 A 1 HETATM 20 O O2P U5P . . . B 2 6.116 19.42 43.239 1 34.38 ? O2P U5P 1489 A 1 HETATM 21 O O3P U5P . . . B 2 7.683 17.692 44.235 1 31.19 ? O3P U5P 1489 A 1 # _model_server_stats.io_time_ms 80 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 21 #