data_3THQ # _model_server_result.job_id hBtvtB8pfDl_3X-P86kuzg _model_server_result.datetime_utc '2024-11-29 21:11:26' _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 3thq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1000}' # _entry.id 3THQ # _exptl.entry_id 3THQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 339.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "6-AMINOURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 115.32 _cell.angle_gamma 90 _cell.entry_id 3THQ _cell.length_a 59.621 _cell.length_b 64.343 _cell.length_c 61.255 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3THQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C9 H14 N3 O9 P' _chem_comp.formula_weight 339.196 _chem_comp.id NUP _chem_comp.mon_nstd_flag . _chem_comp.name "6-AMINOURIDINE 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 O4 C4 NUP doub 270 n n C4 N2 NUP sing 271 n n C4 C5 NUP sing 272 n n N2 C2 NUP sing 273 n n N2 HN2 NUP sing 274 n n C2 O2 NUP doub 275 n n C2 N1 NUP sing 276 n n C5 C6 NUP doub 277 n n C5 H5 NUP sing 278 n n C6 N1 NUP sing 279 n n C6 N3 NUP sing 280 n n N3 HN31 NUP sing 281 n n N3 HN32 NUP sing 282 n n N1 C1' NUP sing 283 n n C1' C2' NUP sing 284 n n C1' O4' NUP sing 285 n n C1' H1' NUP sing 286 n n O4' C4' NUP sing 287 n n C2' O2' NUP sing 288 n n C2' C3' NUP sing 289 n n C2' H2' NUP sing 290 n n O2' HO2' NUP sing 291 n n C3' O3' NUP sing 292 n n C3' C4' NUP sing 293 n n C3' H3' NUP sing 294 n n O3' HO3' NUP sing 295 n n C4' C5' NUP sing 296 n n C4' H4' NUP sing 297 n n C5' O5' NUP sing 298 n n C5' "H5'1" NUP sing 299 n n C5' "H5'2" NUP sing 300 n n O5' P NUP sing 301 n n P O1P NUP doub 302 n n P O2P NUP sing 303 n n P O3P NUP sing 304 n n O2P HO2P NUP sing 305 n n O3P HO3P NUP sing 306 n n # _atom_sites.entry_id 3THQ _atom_sites.fract_transf_matrix[1][1] 0.016773 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007935 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015542 _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] 0.01806 _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 C 2 NUP A 1 1000 1000 NUP NUP . D 2 NUP B 1 1000 1000 NUP NUP . E 3 EPE B 1 3380 3380 EPE EPE . F 4 HOH A 1 248 3 HOH HOH . F 4 HOH A 2 249 7 HOH HOH . F 4 HOH A 3 250 8 HOH HOH . F 4 HOH A 4 251 12 HOH HOH . F 4 HOH A 5 252 13 HOH HOH . F 4 HOH A 6 253 14 HOH HOH . F 4 HOH A 7 254 15 HOH HOH . F 4 HOH A 8 255 16 HOH HOH . F 4 HOH A 9 256 18 HOH HOH . F 4 HOH A 10 257 23 HOH HOH . F 4 HOH A 11 258 27 HOH HOH . F 4 HOH A 12 259 30 HOH HOH . F 4 HOH A 13 260 31 HOH HOH . F 4 HOH A 14 261 32 HOH HOH . F 4 HOH A 15 262 33 HOH HOH . F 4 HOH A 16 263 35 HOH HOH . F 4 HOH A 17 264 36 HOH HOH . F 4 HOH A 18 265 37 HOH HOH . F 4 HOH A 19 266 40 HOH HOH . F 4 HOH A 20 267 43 HOH HOH . F 4 HOH A 21 268 50 HOH HOH . F 4 HOH A 22 269 52 HOH HOH . F 4 HOH A 23 270 53 HOH HOH . F 4 HOH A 24 271 58 HOH HOH . F 4 HOH A 25 272 59 HOH HOH . F 4 HOH A 26 273 60 HOH HOH . F 4 HOH A 27 274 62 HOH HOH . F 4 HOH A 28 275 65 HOH HOH . F 4 HOH A 29 276 66 HOH HOH . F 4 HOH A 30 277 68 HOH HOH . F 4 HOH A 31 278 70 HOH HOH . F 4 HOH A 32 279 71 HOH HOH . F 4 HOH A 33 280 72 HOH HOH . F 4 HOH A 34 281 73 HOH HOH . F 4 HOH A 35 282 75 HOH HOH . F 4 HOH A 36 283 76 HOH HOH . F 4 HOH A 37 284 77 HOH HOH . F 4 HOH A 38 285 80 HOH HOH . F 4 HOH A 39 286 81 HOH HOH . F 4 HOH A 40 287 83 HOH HOH . F 4 HOH A 41 288 84 HOH HOH . F 4 HOH A 42 289 87 HOH HOH . F 4 HOH A 43 290 88 HOH HOH . F 4 HOH A 44 291 90 HOH HOH . F 4 HOH A 45 292 92 HOH HOH . F 4 HOH A 46 293 94 HOH HOH . F 4 HOH A 47 294 95 HOH HOH . F 4 HOH A 48 295 96 HOH HOH . F 4 HOH A 49 296 97 HOH HOH . F 4 HOH A 50 297 99 HOH HOH . F 4 HOH A 51 298 100 HOH HOH . F 4 HOH A 52 299 101 HOH HOH . F 4 HOH A 53 300 102 HOH HOH . F 4 HOH A 54 301 104 HOH HOH . F 4 HOH A 55 302 105 HOH HOH . F 4 HOH A 56 303 106 HOH HOH . F 4 HOH A 57 304 109 HOH HOH . F 4 HOH A 58 305 111 HOH HOH . F 4 HOH A 59 306 113 HOH HOH . F 4 HOH A 60 307 115 HOH HOH . F 4 HOH A 61 308 122 HOH HOH . F 4 HOH A 62 309 124 HOH HOH . F 4 HOH A 63 310 128 HOH HOH . F 4 HOH A 64 311 129 HOH HOH . F 4 HOH A 65 312 130 HOH HOH . F 4 HOH A 66 313 132 HOH HOH . F 4 HOH A 67 314 133 HOH HOH . F 4 HOH A 68 315 134 HOH HOH . F 4 HOH A 69 316 138 HOH HOH . F 4 HOH A 70 317 139 HOH HOH . F 4 HOH A 71 318 141 HOH HOH . F 4 HOH A 72 319 146 HOH HOH . F 4 HOH A 73 320 147 HOH HOH . F 4 HOH A 74 321 149 HOH HOH . F 4 HOH A 75 322 152 HOH HOH . F 4 HOH A 76 323 153 HOH HOH . F 4 HOH A 77 324 155 HOH HOH . F 4 HOH A 78 325 156 HOH HOH . F 4 HOH A 79 326 161 HOH HOH . F 4 HOH A 80 327 162 HOH HOH . F 4 HOH A 81 328 163 HOH HOH . F 4 HOH A 82 329 166 HOH HOH . F 4 HOH A 83 330 167 HOH HOH . F 4 HOH A 84 331 169 HOH HOH . F 4 HOH A 85 332 170 HOH HOH . F 4 HOH A 86 333 172 HOH HOH . F 4 HOH A 87 334 174 HOH HOH . F 4 HOH A 88 335 175 HOH HOH . F 4 HOH A 89 336 176 HOH HOH . F 4 HOH A 90 337 178 HOH HOH . F 4 HOH A 91 338 179 HOH HOH . F 4 HOH A 92 339 180 HOH HOH . F 4 HOH A 93 340 181 HOH HOH . F 4 HOH A 94 341 185 HOH HOH . F 4 HOH A 95 342 186 HOH HOH . F 4 HOH A 96 343 187 HOH HOH . F 4 HOH A 97 344 188 HOH HOH . F 4 HOH A 98 345 189 HOH HOH . F 4 HOH A 99 346 190 HOH HOH . F 4 HOH A 100 347 191 HOH HOH . F 4 HOH A 101 348 195 HOH HOH . F 4 HOH A 102 349 196 HOH HOH . F 4 HOH A 103 350 197 HOH HOH . F 4 HOH A 104 351 198 HOH HOH . F 4 HOH A 105 352 199 HOH HOH . F 4 HOH A 106 353 202 HOH HOH . F 4 HOH A 107 354 203 HOH HOH . F 4 HOH A 108 355 207 HOH HOH . F 4 HOH A 109 356 211 HOH HOH . F 4 HOH A 110 357 212 HOH HOH . G 4 HOH B 1 248 1 HOH HOH . G 4 HOH B 2 249 2 HOH HOH . G 4 HOH B 3 250 4 HOH HOH . G 4 HOH B 4 251 5 HOH HOH . G 4 HOH B 5 252 6 HOH HOH . G 4 HOH B 6 253 9 HOH HOH . G 4 HOH B 7 254 10 HOH HOH . G 4 HOH B 8 255 11 HOH HOH . G 4 HOH B 9 256 17 HOH HOH . G 4 HOH B 10 257 19 HOH HOH . G 4 HOH B 11 258 20 HOH HOH . G 4 HOH B 12 259 21 HOH HOH . G 4 HOH B 13 260 22 HOH HOH . G 4 HOH B 14 261 24 HOH HOH . G 4 HOH B 15 262 25 HOH HOH . G 4 HOH B 16 263 26 HOH HOH . G 4 HOH B 17 264 28 HOH HOH . G 4 HOH B 18 265 29 HOH HOH . G 4 HOH B 19 266 34 HOH HOH . G 4 HOH B 20 267 38 HOH HOH . G 4 HOH B 21 268 39 HOH HOH . G 4 HOH B 22 269 41 HOH HOH . G 4 HOH B 23 270 42 HOH HOH . G 4 HOH B 24 271 44 HOH HOH . G 4 HOH B 25 272 45 HOH HOH . G 4 HOH B 26 273 46 HOH HOH . G 4 HOH B 27 274 47 HOH HOH . G 4 HOH B 28 275 48 HOH HOH . G 4 HOH B 29 276 49 HOH HOH . G 4 HOH B 30 277 51 HOH HOH . G 4 HOH B 31 278 54 HOH HOH . G 4 HOH B 32 279 55 HOH HOH . G 4 HOH B 33 280 56 HOH HOH . G 4 HOH B 34 281 57 HOH HOH . G 4 HOH B 35 282 61 HOH HOH . G 4 HOH B 36 283 63 HOH HOH . G 4 HOH B 37 284 64 HOH HOH . G 4 HOH B 38 285 67 HOH HOH . G 4 HOH B 39 286 69 HOH HOH . G 4 HOH B 40 287 74 HOH HOH . G 4 HOH B 41 288 78 HOH HOH . G 4 HOH B 42 289 79 HOH HOH . G 4 HOH B 43 290 82 HOH HOH . G 4 HOH B 44 291 85 HOH HOH . G 4 HOH B 45 292 86 HOH HOH . G 4 HOH B 46 293 89 HOH HOH . G 4 HOH B 47 294 91 HOH HOH . G 4 HOH B 48 295 93 HOH HOH . G 4 HOH B 49 296 98 HOH HOH . G 4 HOH B 50 297 103 HOH HOH . G 4 HOH B 51 298 107 HOH HOH . G 4 HOH B 52 299 108 HOH HOH . G 4 HOH B 53 300 110 HOH HOH . G 4 HOH B 54 301 112 HOH HOH . G 4 HOH B 55 302 114 HOH HOH . G 4 HOH B 56 303 116 HOH HOH . G 4 HOH B 57 304 117 HOH HOH . G 4 HOH B 58 305 118 HOH HOH . G 4 HOH B 59 306 119 HOH HOH . G 4 HOH B 60 307 120 HOH HOH . G 4 HOH B 61 308 121 HOH HOH . G 4 HOH B 62 309 123 HOH HOH . G 4 HOH B 63 310 125 HOH HOH . G 4 HOH B 64 311 126 HOH HOH . G 4 HOH B 65 312 127 HOH HOH . G 4 HOH B 66 313 131 HOH HOH . G 4 HOH B 67 314 135 HOH HOH . G 4 HOH B 68 315 136 HOH HOH . G 4 HOH B 69 316 137 HOH HOH . G 4 HOH B 70 317 140 HOH HOH . G 4 HOH B 71 318 142 HOH HOH . G 4 HOH B 72 319 143 HOH HOH . G 4 HOH B 73 320 144 HOH HOH . G 4 HOH B 74 321 145 HOH HOH . G 4 HOH B 75 322 148 HOH HOH . G 4 HOH B 76 323 150 HOH HOH . G 4 HOH B 77 324 151 HOH HOH . G 4 HOH B 78 325 154 HOH HOH . G 4 HOH B 79 326 157 HOH HOH . G 4 HOH B 80 327 158 HOH HOH . G 4 HOH B 81 328 159 HOH HOH . G 4 HOH B 82 329 160 HOH HOH . G 4 HOH B 83 330 164 HOH HOH . G 4 HOH B 84 331 165 HOH HOH . G 4 HOH B 85 332 168 HOH HOH . G 4 HOH B 86 333 171 HOH HOH . G 4 HOH B 87 334 173 HOH HOH . G 4 HOH B 88 335 177 HOH HOH . G 4 HOH B 89 336 182 HOH HOH . G 4 HOH B 90 337 183 HOH HOH . G 4 HOH B 91 338 184 HOH HOH . G 4 HOH B 92 339 192 HOH HOH . G 4 HOH B 93 340 193 HOH HOH . G 4 HOH B 94 341 194 HOH HOH . G 4 HOH B 95 342 200 HOH HOH . G 4 HOH B 96 343 201 HOH HOH . G 4 HOH B 97 344 204 HOH HOH . G 4 HOH B 98 345 205 HOH HOH . G 4 HOH B 99 346 206 HOH HOH . G 4 HOH B 100 347 208 HOH HOH . G 4 HOH B 101 348 209 HOH HOH . G 4 HOH B 102 349 210 HOH HOH . G 4 HOH B 103 350 213 HOH HOH . G 4 HOH B 104 351 214 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 NUP . . . C 2 16.259 -7.548 5.746 1 10.51 ? O4 NUP 1000 A 1 HETATM 2 C C4 NUP . . . C 2 17.096 -7.606 6.793 1 9.29 ? C4 NUP 1000 A 1 HETATM 3 N N2 NUP . . . C 2 18.155 -8.436 6.711 1 7.58 ? N2 NUP 1000 A 1 HETATM 4 C C2 NUP . . . C 2 19.027 -8.529 7.719 1 7.82 ? C2 NUP 1000 A 1 HETATM 5 O O2 NUP . . . C 2 19.986 -9.319 7.554 1 7.95 ? O2 NUP 1000 A 1 HETATM 6 C C5 NUP . . . C 2 16.883 -6.82 7.909 1 10.14 ? C5 NUP 1000 A 1 HETATM 7 C C6 NUP . . . C 2 17.818 -6.937 8.933 1 10.73 ? C6 NUP 1000 A 1 HETATM 8 N N3 NUP . . . C 2 17.609 -6.129 9.997 1 15.48 ? N3 NUP 1000 A 1 HETATM 9 N N1 NUP . . . C 2 18.854 -7.808 8.84 1 8.41 ? N1 NUP 1000 A 1 HETATM 10 C C1' NUP . . . C 2 19.834 -7.89 9.931 1 6.42 ? C1' NUP 1000 A 1 HETATM 11 O O4' NUP . . . C 2 21.084 -7.405 9.476 1 7.85 ? O4' NUP 1000 A 1 HETATM 12 C C2' NUP . . . C 2 20.144 -9.287 10.452 1 6.99 ? C2' NUP 1000 A 1 HETATM 13 O O2' NUP . . . C 2 19.285 -9.599 11.542 1 10.69 ? O2' NUP 1000 A 1 HETATM 14 C C3' NUP . . . C 2 21.58 -9.154 10.951 1 6.78 ? C3' NUP 1000 A 1 HETATM 15 O O3' NUP . . . C 2 21.556 -8.509 12.26 1 8.22 ? O3' NUP 1000 A 1 HETATM 16 C C4' NUP . . . C 2 22.175 -8.21 9.936 1 6.52 ? C4' NUP 1000 A 1 HETATM 17 C C5' NUP . . . C 2 22.833 -8.882 8.731 1 8.77 ? C5' NUP 1000 A 1 HETATM 18 O O5' NUP . . . C 2 24.005 -9.533 9.264 1 8.79 ? O5' NUP 1000 A 1 HETATM 19 P P NUP . . . C 2 25 -10.372 8.314 1 7.48 ? P NUP 1000 A 1 HETATM 20 O O1P NUP . . . C 2 24.197 -11.166 7.308 1 7.8 ? O1P NUP 1000 A 1 HETATM 21 O O2P NUP . . . C 2 25.648 -11.279 9.336 1 7.01 ? O2P NUP 1000 A 1 HETATM 22 O O3P NUP . . . C 2 25.943 -9.391 7.672 1 7.19 ? O3P NUP 1000 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #