data_3LTY # _model_server_result.job_id YlwS0LSu-wWH8rVFqBKQnQ _model_server_result.datetime_utc '2024-11-27 10:59:34' _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 3lty # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":229}' # _entry.id 3LTY # _exptl.entry_id 3LTY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 340.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "6-HYDROXYURIDINE-5'-PHOSPHATE" _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 90 _cell.angle_gamma 90 _cell.entry_id 3LTY _cell.length_a 56.581 _cell.length_b 56.605 _cell.length_c 127.209 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LTY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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,F _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 H13 N2 O10 P' _chem_comp.formula_weight 340.181 _chem_comp.id BMP _chem_comp.mon_nstd_flag . _chem_comp.name "6-HYDROXYURIDINE-5'-PHOSPHATE" _chem_comp.type 'rna linking' _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 P OP1 BMP doub 70 n n P OP2 BMP sing 71 n n P OP3 BMP sing 72 n n P O5' BMP sing 73 n n OP2 HOP2 BMP sing 74 n n OP3 HOP3 BMP sing 75 n n O5' C5' BMP sing 76 n n C5' C4' BMP sing 77 n n C5' H5' BMP sing 78 n n C5' "H5''" BMP sing 79 n n C4' O4' BMP sing 80 n n C4' C3' BMP sing 81 n n C4' H4' BMP sing 82 n n O4' C1' BMP sing 83 n n C3' O3' BMP sing 84 n n C3' C2' BMP sing 85 n n C3' H3' BMP sing 86 n n O3' HO3' BMP sing 87 n n C2' O2' BMP sing 88 n n C2' C1' BMP sing 89 n n C2' H2' BMP sing 90 n n O2' HO2' BMP sing 91 n n C1' N1 BMP sing 92 n n C1' H1' BMP sing 93 n n N1 C2 BMP sing 94 n n N1 C6 BMP sing 95 n n C2 O2 BMP doub 96 n n C2 N3 BMP sing 97 n n N3 C4 BMP sing 98 n n N3 HN3 BMP sing 99 n n C4 O4 BMP doub 100 n n C4 C5 BMP sing 101 n n C5 C6 BMP doub 102 n n C5 H51 BMP sing 103 n n C6 O1 BMP sing 104 n n O1 HO1 BMP sing 105 n n # _atom_sites.entry_id 3LTY _atom_sites.fract_transf_matrix[1][1] 0.017674 _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] 0.017666 _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] 0.007861 _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 BMP A 1 229 1 BMP BMP . D 2 BMP B 1 229 2 BMP BMP . E 3 HOH A 1 230 4 HOH HOH . E 3 HOH A 2 231 231 HOH HOH . E 3 HOH A 3 232 232 HOH HOH . E 3 HOH A 4 233 233 HOH HOH . E 3 HOH A 5 234 5 HOH HOH . E 3 HOH A 6 235 235 HOH HOH . E 3 HOH A 7 236 6 HOH HOH . E 3 HOH A 8 237 7 HOH HOH . E 3 HOH A 9 238 8 HOH HOH . E 3 HOH A 10 239 239 HOH HOH . E 3 HOH A 11 240 240 HOH HOH . E 3 HOH A 12 241 9 HOH HOH . E 3 HOH A 13 242 11 HOH HOH . E 3 HOH A 14 243 243 HOH HOH . E 3 HOH A 15 244 244 HOH HOH . E 3 HOH A 16 245 16 HOH HOH . E 3 HOH A 17 246 246 HOH HOH . E 3 HOH A 18 247 18 HOH HOH . E 3 HOH A 19 248 248 HOH HOH . E 3 HOH A 20 249 249 HOH HOH . E 3 HOH A 21 250 21 HOH HOH . E 3 HOH A 22 251 23 HOH HOH . E 3 HOH A 23 252 26 HOH HOH . E 3 HOH A 24 253 27 HOH HOH . E 3 HOH A 25 254 254 HOH HOH . E 3 HOH A 26 255 28 HOH HOH . E 3 HOH A 27 256 30 HOH HOH . E 3 HOH A 28 257 31 HOH HOH . E 3 HOH A 29 258 33 HOH HOH . E 3 HOH A 30 259 34 HOH HOH . E 3 HOH A 31 260 35 HOH HOH . E 3 HOH A 32 261 38 HOH HOH . E 3 HOH A 33 262 42 HOH HOH . E 3 HOH A 34 263 43 HOH HOH . E 3 HOH A 35 264 45 HOH HOH . E 3 HOH A 36 265 46 HOH HOH . E 3 HOH A 37 266 47 HOH HOH . E 3 HOH A 38 267 48 HOH HOH . E 3 HOH A 39 268 52 HOH HOH . E 3 HOH A 40 269 53 HOH HOH . E 3 HOH A 41 270 54 HOH HOH . E 3 HOH A 42 271 57 HOH HOH . E 3 HOH A 43 272 59 HOH HOH . E 3 HOH A 44 273 62 HOH HOH . E 3 HOH A 45 274 63 HOH HOH . E 3 HOH A 46 275 64 HOH HOH . E 3 HOH A 47 276 65 HOH HOH . E 3 HOH A 48 277 68 HOH HOH . E 3 HOH A 49 278 71 HOH HOH . E 3 HOH A 50 279 72 HOH HOH . E 3 HOH A 51 280 74 HOH HOH . E 3 HOH A 52 281 76 HOH HOH . E 3 HOH A 53 282 80 HOH HOH . E 3 HOH A 54 283 82 HOH HOH . E 3 HOH A 55 284 83 HOH HOH . E 3 HOH A 56 285 85 HOH HOH . E 3 HOH A 57 286 86 HOH HOH . E 3 HOH A 58 287 88 HOH HOH . E 3 HOH A 59 288 90 HOH HOH . E 3 HOH A 60 289 91 HOH HOH . E 3 HOH A 61 290 92 HOH HOH . E 3 HOH A 62 291 94 HOH HOH . E 3 HOH A 63 292 98 HOH HOH . E 3 HOH A 64 293 99 HOH HOH . E 3 HOH A 65 294 100 HOH HOH . E 3 HOH A 66 295 101 HOH HOH . E 3 HOH A 67 296 104 HOH HOH . E 3 HOH A 68 297 105 HOH HOH . E 3 HOH A 69 298 107 HOH HOH . E 3 HOH A 70 299 109 HOH HOH . E 3 HOH A 71 300 110 HOH HOH . E 3 HOH A 72 301 111 HOH HOH . E 3 HOH A 73 302 113 HOH HOH . E 3 HOH A 74 303 115 HOH HOH . E 3 HOH A 75 304 116 HOH HOH . E 3 HOH A 76 305 123 HOH HOH . E 3 HOH A 77 306 126 HOH HOH . E 3 HOH A 78 307 127 HOH HOH . E 3 HOH A 79 308 128 HOH HOH . E 3 HOH A 80 309 130 HOH HOH . E 3 HOH A 81 310 131 HOH HOH . E 3 HOH A 82 311 134 HOH HOH . E 3 HOH A 83 312 135 HOH HOH . E 3 HOH A 84 313 136 HOH HOH . E 3 HOH A 85 314 140 HOH HOH . E 3 HOH A 86 315 143 HOH HOH . E 3 HOH A 87 316 144 HOH HOH . E 3 HOH A 88 317 147 HOH HOH . E 3 HOH A 89 318 148 HOH HOH . E 3 HOH A 90 319 151 HOH HOH . E 3 HOH A 91 320 152 HOH HOH . E 3 HOH A 92 321 156 HOH HOH . E 3 HOH A 93 322 157 HOH HOH . E 3 HOH A 94 323 158 HOH HOH . E 3 HOH A 95 324 159 HOH HOH . E 3 HOH A 96 325 161 HOH HOH . E 3 HOH A 97 326 162 HOH HOH . E 3 HOH A 98 327 164 HOH HOH . E 3 HOH A 99 328 168 HOH HOH . E 3 HOH A 100 329 172 HOH HOH . E 3 HOH A 101 330 173 HOH HOH . E 3 HOH A 102 331 176 HOH HOH . E 3 HOH A 103 332 177 HOH HOH . E 3 HOH A 104 333 178 HOH HOH . E 3 HOH A 105 334 179 HOH HOH . E 3 HOH A 106 335 180 HOH HOH . E 3 HOH A 107 336 181 HOH HOH . E 3 HOH A 108 337 185 HOH HOH . E 3 HOH A 109 338 194 HOH HOH . E 3 HOH A 110 339 197 HOH HOH . E 3 HOH A 111 340 198 HOH HOH . E 3 HOH A 112 341 205 HOH HOH . E 3 HOH A 113 342 207 HOH HOH . E 3 HOH A 114 343 209 HOH HOH . E 3 HOH A 115 344 212 HOH HOH . E 3 HOH A 116 345 213 HOH HOH . E 3 HOH A 117 346 218 HOH HOH . E 3 HOH A 118 347 220 HOH HOH . E 3 HOH A 119 348 221 HOH HOH . E 3 HOH A 120 349 223 HOH HOH . E 3 HOH A 121 350 224 HOH HOH . E 3 HOH A 122 351 228 HOH HOH . E 3 HOH A 123 352 170 HOH HOH . F 3 HOH B 1 230 230 HOH HOH . F 3 HOH B 2 231 1 HOH HOH . F 3 HOH B 3 232 2 HOH HOH . F 3 HOH B 4 233 3 HOH HOH . F 3 HOH B 5 234 234 HOH HOH . F 3 HOH B 6 235 10 HOH HOH . F 3 HOH B 7 236 236 HOH HOH . F 3 HOH B 8 237 237 HOH HOH . F 3 HOH B 9 238 238 HOH HOH . F 3 HOH B 10 239 12 HOH HOH . F 3 HOH B 11 240 13 HOH HOH . F 3 HOH B 12 241 241 HOH HOH . F 3 HOH B 13 242 242 HOH HOH . F 3 HOH B 14 243 14 HOH HOH . F 3 HOH B 15 244 15 HOH HOH . F 3 HOH B 16 245 245 HOH HOH . F 3 HOH B 17 246 17 HOH HOH . F 3 HOH B 18 247 247 HOH HOH . F 3 HOH B 19 248 19 HOH HOH . F 3 HOH B 20 249 20 HOH HOH . F 3 HOH B 21 250 250 HOH HOH . F 3 HOH B 22 251 251 HOH HOH . F 3 HOH B 23 252 252 HOH HOH . F 3 HOH B 24 253 253 HOH HOH . F 3 HOH B 25 254 22 HOH HOH . F 3 HOH B 26 255 255 HOH HOH . F 3 HOH B 27 256 24 HOH HOH . F 3 HOH B 28 257 25 HOH HOH . F 3 HOH B 29 258 29 HOH HOH . F 3 HOH B 30 259 32 HOH HOH . F 3 HOH B 31 260 36 HOH HOH . F 3 HOH B 32 261 37 HOH HOH . F 3 HOH B 33 262 39 HOH HOH . F 3 HOH B 34 263 40 HOH HOH . F 3 HOH B 35 264 41 HOH HOH . F 3 HOH B 36 265 44 HOH HOH . F 3 HOH B 37 266 49 HOH HOH . F 3 HOH B 38 267 50 HOH HOH . F 3 HOH B 39 268 51 HOH HOH . F 3 HOH B 40 269 55 HOH HOH . F 3 HOH B 41 270 56 HOH HOH . F 3 HOH B 42 271 58 HOH HOH . F 3 HOH B 43 272 60 HOH HOH . F 3 HOH B 44 273 61 HOH HOH . F 3 HOH B 45 274 66 HOH HOH . F 3 HOH B 46 275 67 HOH HOH . F 3 HOH B 47 276 69 HOH HOH . F 3 HOH B 48 277 70 HOH HOH . F 3 HOH B 49 278 73 HOH HOH . F 3 HOH B 50 279 75 HOH HOH . F 3 HOH B 51 280 78 HOH HOH . F 3 HOH B 52 281 79 HOH HOH . F 3 HOH B 53 282 81 HOH HOH . F 3 HOH B 54 283 84 HOH HOH . F 3 HOH B 55 284 87 HOH HOH . F 3 HOH B 56 285 89 HOH HOH . F 3 HOH B 57 286 93 HOH HOH . F 3 HOH B 58 287 95 HOH HOH . F 3 HOH B 59 288 96 HOH HOH . F 3 HOH B 60 289 97 HOH HOH . F 3 HOH B 61 290 102 HOH HOH . F 3 HOH B 62 291 103 HOH HOH . F 3 HOH B 63 292 106 HOH HOH . F 3 HOH B 64 293 108 HOH HOH . F 3 HOH B 65 294 112 HOH HOH . F 3 HOH B 66 295 114 HOH HOH . F 3 HOH B 67 296 117 HOH HOH . F 3 HOH B 68 297 118 HOH HOH . F 3 HOH B 69 298 119 HOH HOH . F 3 HOH B 70 299 120 HOH HOH . F 3 HOH B 71 300 121 HOH HOH . F 3 HOH B 72 301 122 HOH HOH . F 3 HOH B 73 302 124 HOH HOH . F 3 HOH B 74 303 125 HOH HOH . F 3 HOH B 75 304 129 HOH HOH . F 3 HOH B 76 305 132 HOH HOH . F 3 HOH B 77 306 133 HOH HOH . F 3 HOH B 78 307 137 HOH HOH . F 3 HOH B 79 308 138 HOH HOH . F 3 HOH B 80 309 139 HOH HOH . F 3 HOH B 81 310 141 HOH HOH . F 3 HOH B 82 311 142 HOH HOH . F 3 HOH B 83 312 145 HOH HOH . F 3 HOH B 84 313 146 HOH HOH . F 3 HOH B 85 314 149 HOH HOH . F 3 HOH B 86 315 150 HOH HOH . F 3 HOH B 87 316 153 HOH HOH . F 3 HOH B 88 317 154 HOH HOH . F 3 HOH B 89 318 155 HOH HOH . F 3 HOH B 90 319 160 HOH HOH . F 3 HOH B 91 320 163 HOH HOH . F 3 HOH B 92 321 165 HOH HOH . F 3 HOH B 93 322 166 HOH HOH . F 3 HOH B 94 323 167 HOH HOH . F 3 HOH B 95 324 169 HOH HOH . F 3 HOH B 96 326 171 HOH HOH . F 3 HOH B 97 327 174 HOH HOH . F 3 HOH B 98 328 175 HOH HOH . F 3 HOH B 99 329 182 HOH HOH . F 3 HOH B 100 330 183 HOH HOH . F 3 HOH B 101 331 184 HOH HOH . F 3 HOH B 102 332 186 HOH HOH . F 3 HOH B 103 333 187 HOH HOH . F 3 HOH B 104 334 188 HOH HOH . F 3 HOH B 105 335 189 HOH HOH . F 3 HOH B 106 336 190 HOH HOH . F 3 HOH B 107 337 191 HOH HOH . F 3 HOH B 108 338 192 HOH HOH . F 3 HOH B 109 339 193 HOH HOH . F 3 HOH B 110 340 195 HOH HOH . F 3 HOH B 111 341 196 HOH HOH . F 3 HOH B 112 342 199 HOH HOH . F 3 HOH B 113 343 200 HOH HOH . F 3 HOH B 114 344 201 HOH HOH . F 3 HOH B 115 345 202 HOH HOH . F 3 HOH B 116 346 203 HOH HOH . F 3 HOH B 117 347 204 HOH HOH . F 3 HOH B 118 348 206 HOH HOH . F 3 HOH B 119 349 208 HOH HOH . F 3 HOH B 120 350 210 HOH HOH . F 3 HOH B 121 351 211 HOH HOH . F 3 HOH B 122 352 214 HOH HOH . F 3 HOH B 123 353 215 HOH HOH . F 3 HOH B 124 354 216 HOH HOH . F 3 HOH B 125 355 217 HOH HOH . F 3 HOH B 126 356 219 HOH HOH . F 3 HOH B 127 357 222 HOH HOH . F 3 HOH B 128 358 225 HOH HOH . F 3 HOH B 129 359 226 HOH HOH . F 3 HOH B 130 360 227 HOH HOH . F 3 HOH B 131 361 229 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 P P BMP . . . D 2 44.429 -21.166 21.609 1 16.02 ? P BMP 229 B 1 HETATM 2 O OP1 BMP . . . D 2 43.225 -21.857 22.309 1 15.88 ? OP1 BMP 229 B 1 HETATM 3 O OP2 BMP . . . D 2 45.246 -20.289 22.593 1 16.51 ? OP2 BMP 229 B 1 HETATM 4 O OP3 BMP . . . D 2 45.312 -22.179 20.89 1 14.26 ? OP3 BMP 229 B 1 HETATM 5 O O5' BMP . . . D 2 43.892 -20.149 20.546 1 16.09 ? O5' BMP 229 B 1 HETATM 6 C C5' BMP . . . D 2 42.76 -20.372 19.817 1 15.4 ? C5' BMP 229 B 1 HETATM 7 C C4' BMP . . . D 2 42.476 -19.227 18.869 1 13.63 ? C4' BMP 229 B 1 HETATM 8 O O4' BMP . . . D 2 41.52 -19.479 17.768 1 15.48 ? O4' BMP 229 B 1 HETATM 9 C C3' BMP . . . D 2 42.085 -17.867 19.405 1 13.13 ? C3' BMP 229 B 1 HETATM 10 O O3' BMP . . . D 2 42.564 -16.73 18.803 1 15.55 ? O3' BMP 229 B 1 HETATM 11 C C2' BMP . . . D 2 40.612 -17.909 19.402 1 16.11 ? C2' BMP 229 B 1 HETATM 12 O O2' BMP . . . D 2 39.878 -16.736 19.473 1 14.71 ? O2' BMP 229 B 1 HETATM 13 C C1' BMP . . . D 2 40.292 -18.822 18.242 1 13.14 ? C1' BMP 229 B 1 HETATM 14 N N1 BMP . . . D 2 39.168 -19.619 17.84 1 12.92 ? N1 BMP 229 B 1 HETATM 15 C C2 BMP . . . D 2 38.88 -20.594 18.913 1 15.15 ? C2 BMP 229 B 1 HETATM 16 O O2 BMP . . . D 2 39.786 -20.888 19.859 1 15.75 ? O2 BMP 229 B 1 HETATM 17 N N3 BMP . . . D 2 37.742 -21.562 18.667 1 15 ? N3 BMP 229 B 1 HETATM 18 C C4 BMP . . . D 2 36.798 -21.205 17.521 1 16.87 ? C4 BMP 229 B 1 HETATM 19 O O4 BMP . . . D 2 35.827 -22.11 17.312 1 15.26 ? O4 BMP 229 B 1 HETATM 20 C C5 BMP . . . D 2 37.215 -20.227 16.451 1 13.3 ? C5 BMP 229 B 1 HETATM 21 C C6 BMP . . . D 2 38.407 -19.403 16.674 1 12.9 ? C6 BMP 229 B 1 HETATM 22 O O1 BMP . . . D 2 38.835 -18.514 15.723 1 15.94 ? O1 BMP 229 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #