data_3TPY # _model_server_result.job_id y5oPdIxwOUay7I1C100UDw _model_server_result.datetime_utc '2024-10-19 00:45:46' _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 3tpy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":777}' # _entry.id 3TPY # _exptl.entry_id 3TPY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-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 3TPY _cell.length_a 60.559 _cell.length_b 60.559 _cell.length_c 63.635 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TPY _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _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,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_775 -y+2,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 60.559 104.891265 0 3 'crystal symmetry operation' 3_575 -x+y,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -60.559 104.891265 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 E OP1 UMP . A UMP 154 1_555 B MG MG . A MG 999 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc2 F O HOH . A HOH 223 1_555 B MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc3 F O HOH . A HOH 225 1_555 B MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc4 F O HOH . A HOH 245 1_555 B MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? metalc ? metalc5 D O2G DUP . A DUP 777 1_555 B MG MG . A MG 999 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc6 D O1A DUP . A DUP 777 1_555 B MG MG . A MG 999 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc7 D O1B DUP . A DUP 777 1_555 B MG MG . A MG 999 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.303 ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DUP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-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 O4 C4 DUP doub 83 n n C4 C5 DUP sing 84 n y C4 N3 DUP sing 85 n y C5 C6 DUP doub 86 n y C5 H5 DUP sing 87 n n C6 N1 DUP sing 88 n y C6 H6 DUP sing 89 n n N3 C2 DUP sing 90 n y N3 HN3 DUP sing 91 n n C2 O2 DUP doub 92 n n C2 N1 DUP sing 93 n y N1 C1' DUP sing 94 n n C1' C2' DUP sing 95 n n C1' O4' DUP sing 96 n n C1' H1' DUP sing 97 n n C2' C3' DUP sing 98 n n C2' "H2'1" DUP sing 99 n n C2' "H2'2" DUP sing 100 n n C3' O3' DUP sing 101 n n C3' C4' DUP sing 102 n n C3' H1 DUP sing 103 n n O3' H3' DUP sing 104 n n O4' C4' DUP sing 105 n n C4' C5' DUP sing 106 n n C4' H4' DUP sing 107 n n C5' O5' DUP sing 108 n n C5' "H5'1" DUP sing 109 n n C5' "H5'2" DUP sing 110 n n O5' PA DUP sing 111 n n PA O1A DUP doub 112 n n PA O2A DUP sing 113 n n PA N3A DUP sing 114 n n O2A H2A DUP sing 115 n n N3A PB DUP sing 116 n n N3A H3A DUP sing 117 n n PB O1B DUP doub 118 n n PB O2B DUP sing 119 n n PB O3B DUP sing 120 n n O2B H2B DUP sing 121 n n O3B PG DUP sing 122 n n PG O2G DUP doub 123 n n PG O1G DUP sing 124 n n PG O3G DUP sing 125 n n O1G H1G DUP sing 126 n n O3G H3G DUP sing 127 n n # _atom_sites.entry_id 3TPY _atom_sites.fract_transf_matrix[1][1] 0.016513 _atom_sites.fract_transf_matrix[1][2] 0.009534 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019067 _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] 0.015715 _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 1 999 999 MG MG . C 3 TRS A 1 153 1 TRS TRS . D 4 DUP A 1 777 777 DUP DUP . E 5 UMP A 1 154 777 UMP UMP . F 6 HOH A 1 155 1 HOH HOH . F 6 HOH A 2 156 2 HOH HOH . F 6 HOH A 3 157 3 HOH HOH . F 6 HOH A 4 158 4 HOH HOH . F 6 HOH A 5 159 5 HOH HOH . F 6 HOH A 6 160 6 HOH HOH . F 6 HOH A 7 161 7 HOH HOH . F 6 HOH A 8 162 8 HOH HOH . F 6 HOH A 9 163 9 HOH HOH . F 6 HOH A 10 164 10 HOH HOH . F 6 HOH A 11 165 11 HOH HOH . F 6 HOH A 12 166 12 HOH HOH . F 6 HOH A 13 167 13 HOH HOH . F 6 HOH A 14 168 14 HOH HOH . F 6 HOH A 15 169 15 HOH HOH . F 6 HOH A 16 170 16 HOH HOH . F 6 HOH A 17 171 17 HOH HOH . F 6 HOH A 18 172 18 HOH HOH . F 6 HOH A 19 173 19 HOH HOH . F 6 HOH A 20 174 20 HOH HOH . F 6 HOH A 21 175 21 HOH HOH . F 6 HOH A 22 176 22 HOH HOH . F 6 HOH A 23 177 23 HOH HOH . F 6 HOH A 24 178 24 HOH HOH . F 6 HOH A 25 179 25 HOH HOH . F 6 HOH A 26 180 26 HOH HOH . F 6 HOH A 27 181 27 HOH HOH . F 6 HOH A 28 182 28 HOH HOH . F 6 HOH A 29 183 29 HOH HOH . F 6 HOH A 30 184 30 HOH HOH . F 6 HOH A 31 185 31 HOH HOH . F 6 HOH A 32 186 32 HOH HOH . F 6 HOH A 33 187 33 HOH HOH . F 6 HOH A 34 188 34 HOH HOH . F 6 HOH A 35 189 35 HOH HOH . F 6 HOH A 36 190 36 HOH HOH . F 6 HOH A 37 191 37 HOH HOH . F 6 HOH A 38 192 38 HOH HOH . F 6 HOH A 39 193 39 HOH HOH . F 6 HOH A 40 194 40 HOH HOH . F 6 HOH A 41 195 41 HOH HOH . F 6 HOH A 42 196 42 HOH HOH . F 6 HOH A 43 197 43 HOH HOH . F 6 HOH A 44 198 44 HOH HOH . F 6 HOH A 45 199 45 HOH HOH . F 6 HOH A 46 200 46 HOH HOH . F 6 HOH A 47 201 47 HOH HOH . F 6 HOH A 48 202 48 HOH HOH . F 6 HOH A 49 203 49 HOH HOH . F 6 HOH A 50 204 50 HOH HOH . F 6 HOH A 51 205 52 HOH HOH . F 6 HOH A 52 206 53 HOH HOH . F 6 HOH A 53 207 54 HOH HOH . F 6 HOH A 54 208 55 HOH HOH . F 6 HOH A 55 209 56 HOH HOH . F 6 HOH A 56 210 57 HOH HOH . F 6 HOH A 57 211 58 HOH HOH . F 6 HOH A 58 212 59 HOH HOH . F 6 HOH A 59 213 61 HOH HOH . F 6 HOH A 60 214 62 HOH HOH . F 6 HOH A 61 215 64 HOH HOH . F 6 HOH A 62 216 65 HOH HOH . F 6 HOH A 63 217 66 HOH HOH . F 6 HOH A 64 218 67 HOH HOH . F 6 HOH A 65 219 70 HOH HOH . F 6 HOH A 66 220 72 HOH HOH . F 6 HOH A 67 221 73 HOH HOH . F 6 HOH A 68 222 74 HOH HOH . F 6 HOH A 69 223 75 HOH HOH . F 6 HOH A 70 224 76 HOH HOH . F 6 HOH A 71 225 77 HOH HOH . F 6 HOH A 72 226 78 HOH HOH . F 6 HOH A 73 227 79 HOH HOH . F 6 HOH A 74 228 80 HOH HOH . F 6 HOH A 75 229 81 HOH HOH . F 6 HOH A 76 230 82 HOH HOH . F 6 HOH A 77 231 83 HOH HOH . F 6 HOH A 78 232 84 HOH HOH . F 6 HOH A 79 233 85 HOH HOH . F 6 HOH A 80 234 86 HOH HOH . F 6 HOH A 81 235 87 HOH HOH . F 6 HOH A 82 236 89 HOH HOH . F 6 HOH A 83 237 90 HOH HOH . F 6 HOH A 84 238 91 HOH HOH . F 6 HOH A 85 239 92 HOH HOH . F 6 HOH A 86 240 93 HOH HOH . F 6 HOH A 87 241 94 HOH HOH . F 6 HOH A 88 242 95 HOH HOH . F 6 HOH A 89 243 96 HOH HOH . F 6 HOH A 90 244 97 HOH HOH . F 6 HOH A 91 245 98 HOH HOH . F 6 HOH A 92 246 99 HOH HOH . F 6 HOH A 93 247 100 HOH HOH . F 6 HOH A 94 248 101 HOH HOH . F 6 HOH A 95 249 102 HOH HOH . F 6 HOH A 96 250 103 HOH HOH . F 6 HOH A 97 251 104 HOH HOH . F 6 HOH A 98 252 105 HOH HOH . F 6 HOH A 99 253 106 HOH HOH . F 6 HOH A 100 254 107 HOH HOH . F 6 HOH A 101 255 108 HOH HOH . F 6 HOH A 102 256 109 HOH HOH . F 6 HOH A 103 257 110 HOH HOH . F 6 HOH A 104 258 111 HOH HOH . F 6 HOH A 105 259 112 HOH HOH . F 6 HOH A 106 260 113 HOH HOH . F 6 HOH A 107 261 114 HOH HOH . F 6 HOH A 108 262 115 HOH HOH . F 6 HOH A 109 263 116 HOH HOH . F 6 HOH A 110 264 117 HOH HOH . F 6 HOH A 111 265 118 HOH HOH . F 6 HOH A 112 266 119 HOH HOH . F 6 HOH A 113 267 120 HOH HOH . F 6 HOH A 114 268 121 HOH HOH . F 6 HOH A 115 269 122 HOH HOH . F 6 HOH A 116 270 123 HOH HOH . F 6 HOH A 117 271 124 HOH HOH . F 6 HOH A 118 272 125 HOH HOH . F 6 HOH A 119 273 126 HOH HOH . F 6 HOH A 120 274 127 HOH HOH . F 6 HOH A 121 275 128 HOH HOH . F 6 HOH A 122 276 129 HOH HOH . F 6 HOH A 123 277 130 HOH HOH . F 6 HOH A 124 278 131 HOH HOH . F 6 HOH A 125 279 132 HOH HOH . F 6 HOH A 126 280 133 HOH HOH . F 6 HOH A 127 281 134 HOH HOH . F 6 HOH A 128 282 135 HOH HOH . F 6 HOH A 129 283 136 HOH HOH . F 6 HOH A 130 284 138 HOH HOH . F 6 HOH A 131 285 139 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 O O4 DUP . B . D 4 -2.266 59.647 28.856 0.7 17.19 ? O4 DUP 777 A 1 HETATM 2 C C4 DUP . B . D 4 -3.11 58.953 29.403 0.7 20.3 ? C4 DUP 777 A 1 HETATM 3 C C5 DUP . B . D 4 -4.291 59.485 29.885 0.7 15.28 ? C5 DUP 777 A 1 HETATM 4 C C6 DUP . B . D 4 -5.212 58.637 30.479 0.7 21.27 ? C6 DUP 777 A 1 HETATM 5 N N3 DUP . B . D 4 -2.877 57.611 29.502 0.7 17.44 ? N3 DUP 777 A 1 HETATM 6 C C2 DUP . B . D 4 -3.775 56.771 30.109 0.7 20.7 ? C2 DUP 777 A 1 HETATM 7 O O2 DUP . B . D 4 -3.52 55.561 30.195 0.7 17 ? O2 DUP 777 A 1 HETATM 8 N N1 DUP . B . D 4 -4.954 57.287 30.591 0.7 15.71 ? N1 DUP 777 A 1 HETATM 9 C C1' DUP . B . D 4 -5.922 56.416 31.254 0.7 14.74 ? C1' DUP 777 A 1 HETATM 10 C C2' DUP . B . D 4 -5.752 56.66 32.77 0.7 19.76 ? C2' DUP 777 A 1 HETATM 11 C C3' DUP . B . D 4 -6.955 57.519 33.12 0.7 16.35 ? C3' DUP 777 A 1 HETATM 12 O O3' DUP . B . D 4 -7.368 57.394 34.483 0.7 20.5 ? O3' DUP 777 A 1 HETATM 13 O O4' DUP . B . D 4 -7.267 56.824 30.927 0.7 15.79 ? O4' DUP 777 A 1 HETATM 14 C C4' DUP . B . D 4 -7.974 57.028 32.119 0.7 13.65 ? C4' DUP 777 A 1 HETATM 15 C C5' DUP . B . D 4 -9.09 58.041 31.894 0.7 21.22 ? C5' DUP 777 A 1 HETATM 16 O O5' DUP . B . D 4 -8.492 59.222 31.387 0.7 23.43 ? O5' DUP 777 A 1 HETATM 17 P PA DUP . B . D 4 -9.339 60.563 31.137 0.7 19.64 ? PA DUP 777 A 1 HETATM 18 O O1A DUP . B . D 4 -10.369 60.851 32.163 0.7 24.08 ? O1A DUP 777 A 1 HETATM 19 O O2A DUP . B . D 4 -8.354 61.615 30.709 0.7 18.61 ? O2A DUP 777 A 1 HETATM 20 N N3A DUP . B . D 4 -10.138 59.99 29.803 0.7 26.73 ? N3A DUP 777 A 1 HETATM 21 P PB DUP . B . D 4 -11.768 59.969 29.491 0.7 27.76 ? PB DUP 777 A 1 HETATM 22 O O1B DUP . B . D 4 -12.532 61.121 30.145 0.7 33.19 ? O1B DUP 777 A 1 HETATM 23 O O2B DUP . B . D 4 -11.81 59.939 28.028 0.7 23.21 ? O2B DUP 777 A 1 HETATM 24 O O3B DUP . B . D 4 -12.329 58.613 30.198 0.7 37.24 ? O3B DUP 777 A 1 HETATM 25 P PG DUP . B . D 4 -13.098 58.529 31.62 0.7 33.91 ? PG DUP 777 A 1 HETATM 26 O O2G DUP . B . D 4 -12.411 59.357 32.669 0.7 29.19 ? O2G DUP 777 A 1 HETATM 27 O O1G DUP . B . D 4 -14.503 59.067 31.417 0.7 39.06 ? O1G DUP 777 A 1 HETATM 28 O O3G DUP . B . D 4 -13.092 57.06 32.005 0.7 46.53 ? O3G DUP 777 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #