data_1SYL # _model_server_result.job_id I0Ly5DtM3Oh-Yg6BPCm_iQ _model_server_result.datetime_utc '2024-11-25 06:21:03' _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 1syl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":777}' # _entry.id 1SYL # _exptl.entry_id 1SYL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 468.142 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-5'-TRIPHOSPHATE" _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 120 _cell.entry_id 1SYL _cell.length_a 76.421 _cell.length_b 76.421 _cell.length_c 100.259 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SYL _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _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,D,E,F _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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 76.421 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 38.2105 66.182527 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 C O1A DUT . A DUT 777 1_555 B MG MG . A MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc2 C O1B DUT . A DUT 777 1_555 B MG MG . A MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc3 C O2G DUT . A DUT 777 1_555 B MG MG . A MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc4 B MG MG . A MG 997 1_555 F O HOH . A HOH 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc5 B MG MG . A MG 997 1_555 F O HOH . A HOH 1033 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc6 B MG MG . A MG 997 1_555 F O HOH . A HOH 1083 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? # _chem_comp.formula 'C9 H15 N2 O14 P3' _chem_comp.formula_weight 468.142 _chem_comp.id DUT _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-5'-TRIPHOSPHATE" _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 DUT sing 83 n n N1 C6 DUT sing 84 n n N1 C1' DUT sing 85 n n C2 N3 DUT sing 86 n n C2 O2 DUT doub 87 n n N3 C4 DUT sing 88 n n N3 HN3 DUT sing 89 n n C4 C5 DUT sing 90 n n C4 O4 DUT doub 91 n n C5 C6 DUT doub 92 n n C5 H5 DUT sing 93 n n C6 H6 DUT sing 94 n n C1' C2' DUT sing 95 n n C1' O4' DUT sing 96 n n C1' H1' DUT sing 97 n n C2' C3' DUT sing 98 n n C2' "H2'1" DUT sing 99 n n C2' "H2'2" DUT sing 100 n n C3' C4' DUT sing 101 n n C3' O3' DUT sing 102 n n C3' H3' DUT sing 103 n n C4' O4' DUT sing 104 n n C4' C5' DUT sing 105 n n C4' H4' DUT sing 106 n n O3' HO3' DUT sing 107 n n C5' O5' DUT sing 108 n n C5' "H5'1" DUT sing 109 n n C5' "H5'2" DUT sing 110 n n O5' PA DUT sing 111 n n PA O1A DUT doub 112 n n PA O2A DUT sing 113 n n PA O3A DUT sing 114 n n O2A HOA2 DUT sing 115 n n O3A PB DUT sing 116 n n PB O1B DUT doub 117 n n PB O2B DUT sing 118 n n PB O3B DUT sing 119 n n O2B HOB2 DUT sing 120 n n O3B PG DUT sing 121 n n PG O1G DUT doub 122 n n PG O2G DUT sing 123 n n PG O3G DUT sing 124 n n O2G HOG2 DUT sing 125 n n O3G HOG3 DUT sing 126 n n # _atom_sites.entry_id 1SYL _atom_sites.fract_transf_matrix[1][1] 0.013085 _atom_sites.fract_transf_matrix[1][2] 0.007555 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01511 _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] 0.009974 _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 MG A 1 997 997 MG MG . C 3 DUT A 1 777 777 DUT DUT . D 4 TRS A 1 501 501 TRS TRS . E 4 TRS A 1 502 502 TRS TRS . F 5 HOH A 1 998 1 HOH HOH . F 5 HOH A 2 999 2 HOH HOH . F 5 HOH A 3 1000 3 HOH HOH . F 5 HOH A 4 1001 4 HOH HOH . F 5 HOH A 5 1002 5 HOH HOH . F 5 HOH A 6 1003 6 HOH HOH . F 5 HOH A 7 1004 7 HOH HOH . F 5 HOH A 8 1005 8 HOH HOH . F 5 HOH A 9 1006 9 HOH HOH . F 5 HOH A 10 1007 10 HOH HOH . F 5 HOH A 11 1008 11 HOH HOH . F 5 HOH A 12 1009 12 HOH HOH . F 5 HOH A 13 1010 13 HOH HOH . F 5 HOH A 14 1011 14 HOH HOH . F 5 HOH A 15 1012 15 HOH HOH . F 5 HOH A 16 1013 16 HOH HOH . F 5 HOH A 17 1014 17 HOH HOH . F 5 HOH A 18 1015 18 HOH HOH . F 5 HOH A 19 1016 19 HOH HOH . F 5 HOH A 20 1017 20 HOH HOH . F 5 HOH A 21 1018 21 HOH HOH . F 5 HOH A 22 1019 22 HOH HOH . F 5 HOH A 23 1020 23 HOH HOH . F 5 HOH A 24 1021 24 HOH HOH . F 5 HOH A 25 1022 25 HOH HOH . F 5 HOH A 26 1023 26 HOH HOH . F 5 HOH A 27 1024 28 HOH HOH . F 5 HOH A 28 1025 29 HOH HOH . F 5 HOH A 29 1026 30 HOH HOH . F 5 HOH A 30 1027 31 HOH HOH . F 5 HOH A 31 1028 32 HOH HOH . F 5 HOH A 32 1029 33 HOH HOH . F 5 HOH A 33 1030 34 HOH HOH . F 5 HOH A 34 1031 35 HOH HOH . F 5 HOH A 35 1032 36 HOH HOH . F 5 HOH A 36 1033 37 HOH HOH . F 5 HOH A 37 1034 38 HOH HOH . F 5 HOH A 38 1035 39 HOH HOH . F 5 HOH A 39 1036 40 HOH HOH . F 5 HOH A 40 1037 41 HOH HOH . F 5 HOH A 41 1038 42 HOH HOH . F 5 HOH A 42 1039 43 HOH HOH . F 5 HOH A 43 1040 44 HOH HOH . F 5 HOH A 44 1041 45 HOH HOH . F 5 HOH A 45 1042 46 HOH HOH . F 5 HOH A 46 1043 47 HOH HOH . F 5 HOH A 47 1044 48 HOH HOH . F 5 HOH A 48 1045 49 HOH HOH . F 5 HOH A 49 1046 50 HOH HOH . F 5 HOH A 50 1047 51 HOH HOH . F 5 HOH A 51 1048 52 HOH HOH . F 5 HOH A 52 1049 53 HOH HOH . F 5 HOH A 53 1050 54 HOH HOH . F 5 HOH A 54 1051 55 HOH HOH . F 5 HOH A 55 1052 56 HOH HOH . F 5 HOH A 56 1053 57 HOH HOH . F 5 HOH A 57 1054 58 HOH HOH . F 5 HOH A 58 1055 59 HOH HOH . F 5 HOH A 59 1056 60 HOH HOH . F 5 HOH A 60 1057 61 HOH HOH . F 5 HOH A 61 1058 62 HOH HOH . F 5 HOH A 62 1059 63 HOH HOH . F 5 HOH A 63 1060 64 HOH HOH . F 5 HOH A 64 1061 65 HOH HOH . F 5 HOH A 65 1062 66 HOH HOH . F 5 HOH A 66 1063 67 HOH HOH . F 5 HOH A 67 1064 68 HOH HOH . F 5 HOH A 68 1065 69 HOH HOH . F 5 HOH A 69 1066 70 HOH HOH . F 5 HOH A 70 1067 71 HOH HOH . F 5 HOH A 71 1068 72 HOH HOH . F 5 HOH A 72 1069 74 HOH HOH . F 5 HOH A 73 1070 76 HOH HOH . F 5 HOH A 74 1071 77 HOH HOH . F 5 HOH A 75 1072 78 HOH HOH . F 5 HOH A 76 1073 80 HOH HOH . F 5 HOH A 77 1074 81 HOH HOH . F 5 HOH A 78 1075 82 HOH HOH . F 5 HOH A 79 1076 83 HOH HOH . F 5 HOH A 80 1077 84 HOH HOH . F 5 HOH A 81 1078 87 HOH HOH . F 5 HOH A 82 1079 89 HOH HOH . F 5 HOH A 83 1080 90 HOH HOH . F 5 HOH A 84 1081 91 HOH HOH . F 5 HOH A 85 1082 92 HOH HOH . F 5 HOH A 86 1083 94 HOH HOH . F 5 HOH A 87 1084 95 HOH HOH . F 5 HOH A 88 1085 96 HOH HOH . F 5 HOH A 89 1086 97 HOH HOH . F 5 HOH A 90 1087 98 HOH HOH . F 5 HOH A 91 1088 99 HOH HOH . F 5 HOH A 92 1089 100 HOH HOH . F 5 HOH A 93 1090 101 HOH HOH . F 5 HOH A 94 1091 102 HOH HOH . F 5 HOH A 95 1092 103 HOH HOH . F 5 HOH A 96 1093 105 HOH HOH . F 5 HOH A 97 1094 106 HOH HOH . F 5 HOH A 98 1095 107 HOH HOH . F 5 HOH A 99 1096 108 HOH HOH . F 5 HOH A 100 1097 109 HOH HOH . F 5 HOH A 101 1098 111 HOH HOH . F 5 HOH A 102 1099 112 HOH HOH . F 5 HOH A 103 1100 113 HOH HOH . F 5 HOH A 104 1101 114 HOH HOH . F 5 HOH A 105 1102 115 HOH HOH . F 5 HOH A 106 1103 116 HOH HOH . F 5 HOH A 107 1104 117 HOH HOH . F 5 HOH A 108 1105 119 HOH HOH . F 5 HOH A 109 1106 120 HOH HOH . F 5 HOH A 110 1107 122 HOH HOH . F 5 HOH A 111 1108 123 HOH HOH . F 5 HOH A 112 1109 124 HOH HOH . F 5 HOH A 113 1110 125 HOH HOH . F 5 HOH A 114 1111 127 HOH HOH . F 5 HOH A 115 1112 128 HOH HOH . F 5 HOH A 116 1113 129 HOH HOH . F 5 HOH A 117 1114 130 HOH HOH . F 5 HOH A 118 1115 133 HOH HOH . F 5 HOH A 119 1116 134 HOH HOH . F 5 HOH A 120 1117 135 HOH HOH . F 5 HOH A 121 1118 136 HOH HOH . F 5 HOH A 122 1119 137 HOH HOH . F 5 HOH A 123 1120 138 HOH HOH . F 5 HOH A 124 1121 139 HOH HOH . F 5 HOH A 125 1122 140 HOH HOH . F 5 HOH A 126 1123 141 HOH HOH . F 5 HOH A 127 1124 142 HOH HOH . F 5 HOH A 128 1125 143 HOH HOH . F 5 HOH A 129 1126 144 HOH HOH . F 5 HOH A 130 1127 145 HOH HOH . F 5 HOH A 131 1128 146 HOH HOH . F 5 HOH A 132 1129 147 HOH HOH . F 5 HOH A 133 1130 148 HOH HOH . F 5 HOH A 134 1131 149 HOH HOH . F 5 HOH A 135 1132 150 HOH HOH . F 5 HOH A 136 1133 151 HOH HOH . F 5 HOH A 137 1134 152 HOH HOH . F 5 HOH A 138 1135 153 HOH HOH . F 5 HOH A 139 1136 154 HOH HOH . F 5 HOH A 140 1137 155 HOH HOH . F 5 HOH A 141 1138 158 HOH HOH . F 5 HOH A 142 1139 160 HOH HOH . F 5 HOH A 143 1140 162 HOH HOH . F 5 HOH A 144 1141 163 HOH HOH . F 5 HOH A 145 1142 164 HOH HOH . F 5 HOH A 146 1143 166 HOH HOH . F 5 HOH A 147 1144 167 HOH HOH . F 5 HOH A 148 1145 168 HOH HOH . F 5 HOH A 149 1146 169 HOH HOH . F 5 HOH A 150 1147 170 HOH HOH . F 5 HOH A 151 1148 171 HOH HOH . F 5 HOH A 152 1149 172 HOH HOH . F 5 HOH A 153 1150 173 HOH HOH . F 5 HOH A 154 1151 174 HOH HOH . F 5 HOH A 155 1152 175 HOH HOH . F 5 HOH A 156 1153 176 HOH HOH . F 5 HOH A 157 1154 179 HOH HOH . F 5 HOH A 158 1155 181 HOH HOH . F 5 HOH A 159 1156 182 HOH HOH . F 5 HOH A 160 1157 183 HOH HOH . F 5 HOH A 161 1158 184 HOH HOH . F 5 HOH A 162 1159 185 HOH HOH . F 5 HOH A 163 1160 186 HOH HOH . F 5 HOH A 164 1161 187 HOH HOH . F 5 HOH A 165 1162 196 HOH HOH . F 5 HOH A 166 1163 199 HOH HOH . F 5 HOH A 167 1164 206 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 DUT . . . C 3 52.133 22.24 45.502 1 26.59 ? N1 DUT 777 A 1 HETATM 2 C C2 DUT . . . C 3 52.328 20.952 46.012 1 27.9 ? C2 DUT 777 A 1 HETATM 3 N N3 DUT . . . C 3 51.327 20.376 46.722 1 33.84 ? N3 DUT 777 A 1 HETATM 4 C C4 DUT . . . C 3 50.161 21.007 46.969 1 31.35 ? C4 DUT 777 A 1 HETATM 5 C C5 DUT . . . C 3 49.951 22.296 46.473 1 24.76 ? C5 DUT 777 A 1 HETATM 6 C C6 DUT . . . C 3 50.952 22.901 45.742 1 28.63 ? C6 DUT 777 A 1 HETATM 7 O O2 DUT . . . C 3 53.394 20.344 45.807 1 28.48 ? O2 DUT 777 A 1 HETATM 8 O O4 DUT . . . C 3 49.274 20.415 47.643 1 26.85 ? O4 DUT 777 A 1 HETATM 9 C C1' DUT . . . C 3 53.184 22.891 44.747 1 27.57 ? C1' DUT 777 A 1 HETATM 10 C C2' DUT . . . C 3 52.791 23.003 43.28 1 26.77 ? C2' DUT 777 A 1 HETATM 11 C C3' DUT . . . C 3 52.404 24.447 43.082 1 31.83 ? C3' DUT 777 A 1 HETATM 12 C C4' DUT . . . C 3 53.255 25.142 44.157 1 26.57 ? C4' DUT 777 A 1 HETATM 13 O O4' DUT . . . C 3 53.282 24.223 45.269 1 27.56 ? O4' DUT 777 A 1 HETATM 14 O O3' DUT . . . C 3 52.65 24.86 41.751 1 30.72 ? O3' DUT 777 A 1 HETATM 15 C C5' DUT . . . C 3 52.703 26.472 44.591 1 28.24 ? C5' DUT 777 A 1 HETATM 16 O O5' DUT . . . C 3 51.326 26.318 44.931 1 25.89 ? O5' DUT 777 A 1 HETATM 17 P PA DUT . . . C 3 50.469 27.591 45.4 1 29.83 ? PA DUT 777 A 1 HETATM 18 O O1A DUT . . . C 3 50.689 28.57 44.272 1 34.52 ? O1A DUT 777 A 1 HETATM 19 O O2A DUT . . . C 3 49.084 27.106 45.786 1 33.96 ? O2A DUT 777 A 1 HETATM 20 O O3A DUT . . . C 3 51.168 28.036 46.762 1 31.94 ? O3A DUT 777 A 1 HETATM 21 P PB DUT . . . C 3 51.855 29.446 47.135 1 31.21 ? PB DUT 777 A 1 HETATM 22 O O1B DUT . . . C 3 51.285 30.589 46.273 1 31 ? O1B DUT 777 A 1 HETATM 23 O O2B DUT . . . C 3 51.734 29.623 48.6 1 25.77 ? O2B DUT 777 A 1 HETATM 24 O O3B DUT . . . C 3 53.401 29.331 46.787 1 39.71 ? O3B DUT 777 A 1 HETATM 25 P PG DUT . . . C 3 54.063 30.214 45.596 1 37.58 ? PG DUT 777 A 1 HETATM 26 O O1G DUT . . . C 3 54.278 31.574 46.213 1 38.79 ? O1G DUT 777 A 1 HETATM 27 O O2G DUT . . . C 3 53.161 30.257 44.312 1 33.21 ? O2G DUT 777 A 1 HETATM 28 O O3G DUT . . . C 3 55.306 29.467 45.196 1 37.44 ? O3G DUT 777 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 45 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 366 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #