data_3LTP # _model_server_result.job_id QO61nD-87TrqYE0jXLTYBA _model_server_result.datetime_utc '2024-10-17 11:25:49' _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 3ltp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":229}' # _entry.id 3LTP # _exptl.entry_id 3LTP _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 115.46 _cell.angle_gamma 90 _cell.entry_id 3LTP _cell.length_a 59.772 _cell.length_b 64.07 _cell.length_c 61.639 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LTP _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 _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 3LTP _atom_sites.fract_transf_matrix[1][1] 0.01673 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007965 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015608 _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] 0.017968 _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 10 HOH HOH . E 3 HOH A 2 231 231 HOH HOH . E 3 HOH A 3 232 14 HOH HOH . E 3 HOH A 4 233 18 HOH HOH . E 3 HOH A 5 234 19 HOH HOH . E 3 HOH A 6 235 20 HOH HOH . E 3 HOH A 7 236 236 HOH HOH . E 3 HOH A 8 237 21 HOH HOH . E 3 HOH A 9 238 238 HOH HOH . E 3 HOH A 10 239 239 HOH HOH . E 3 HOH A 11 240 22 HOH HOH . E 3 HOH A 12 241 241 HOH HOH . E 3 HOH A 13 242 24 HOH HOH . E 3 HOH A 14 243 28 HOH HOH . E 3 HOH A 15 244 244 HOH HOH . E 3 HOH A 16 245 33 HOH HOH . E 3 HOH A 17 246 246 HOH HOH . E 3 HOH A 18 247 37 HOH HOH . E 3 HOH A 19 248 39 HOH HOH . E 3 HOH A 20 249 249 HOH HOH . E 3 HOH A 21 250 40 HOH HOH . E 3 HOH A 22 251 251 HOH HOH . E 3 HOH A 23 252 252 HOH HOH . E 3 HOH A 24 253 42 HOH HOH . E 3 HOH A 25 254 254 HOH HOH . E 3 HOH A 26 255 43 HOH HOH . E 3 HOH A 27 256 45 HOH HOH . E 3 HOH A 28 257 257 HOH HOH . E 3 HOH A 29 258 46 HOH HOH . E 3 HOH A 30 259 47 HOH HOH . E 3 HOH A 31 260 260 HOH HOH . E 3 HOH A 32 261 49 HOH HOH . E 3 HOH A 33 262 262 HOH HOH . E 3 HOH A 34 263 51 HOH HOH . E 3 HOH A 35 264 52 HOH HOH . E 3 HOH A 36 265 53 HOH HOH . E 3 HOH A 37 266 266 HOH HOH . E 3 HOH A 38 267 58 HOH HOH . E 3 HOH A 39 268 268 HOH HOH . E 3 HOH A 40 269 61 HOH HOH . E 3 HOH A 41 270 62 HOH HOH . E 3 HOH A 42 271 271 HOH HOH . E 3 HOH A 43 272 272 HOH HOH . E 3 HOH A 44 273 273 HOH HOH . E 3 HOH A 45 274 274 HOH HOH . E 3 HOH A 46 275 65 HOH HOH . E 3 HOH A 47 276 276 HOH HOH . E 3 HOH A 48 277 66 HOH HOH . E 3 HOH A 49 278 73 HOH HOH . E 3 HOH A 50 279 74 HOH HOH . E 3 HOH A 51 281 78 HOH HOH . E 3 HOH A 52 282 282 HOH HOH . E 3 HOH A 53 283 80 HOH HOH . E 3 HOH A 54 284 81 HOH HOH . E 3 HOH A 55 285 83 HOH HOH . E 3 HOH A 56 286 286 HOH HOH . E 3 HOH A 57 287 287 HOH HOH . E 3 HOH A 58 288 288 HOH HOH . E 3 HOH A 59 289 84 HOH HOH . E 3 HOH A 60 290 86 HOH HOH . E 3 HOH A 61 291 291 HOH HOH . E 3 HOH A 62 292 292 HOH HOH . E 3 HOH A 63 293 87 HOH HOH . E 3 HOH A 64 294 294 HOH HOH . E 3 HOH A 65 295 295 HOH HOH . E 3 HOH A 66 296 296 HOH HOH . E 3 HOH A 67 297 90 HOH HOH . E 3 HOH A 68 298 93 HOH HOH . E 3 HOH A 69 299 94 HOH HOH . E 3 HOH A 70 300 96 HOH HOH . E 3 HOH A 71 301 97 HOH HOH . E 3 HOH A 72 302 100 HOH HOH . E 3 HOH A 73 303 101 HOH HOH . E 3 HOH A 74 304 104 HOH HOH . E 3 HOH A 75 305 105 HOH HOH . E 3 HOH A 76 306 111 HOH HOH . E 3 HOH A 77 307 112 HOH HOH . E 3 HOH A 78 308 113 HOH HOH . E 3 HOH A 79 309 114 HOH HOH . E 3 HOH A 80 310 116 HOH HOH . E 3 HOH A 81 311 118 HOH HOH . E 3 HOH A 82 312 119 HOH HOH . E 3 HOH A 83 313 120 HOH HOH . E 3 HOH A 84 314 121 HOH HOH . E 3 HOH A 85 315 122 HOH HOH . E 3 HOH A 86 316 123 HOH HOH . E 3 HOH A 87 317 127 HOH HOH . E 3 HOH A 88 318 129 HOH HOH . E 3 HOH A 89 319 131 HOH HOH . E 3 HOH A 90 320 135 HOH HOH . E 3 HOH A 91 321 136 HOH HOH . E 3 HOH A 92 322 138 HOH HOH . E 3 HOH A 93 323 139 HOH HOH . E 3 HOH A 94 324 141 HOH HOH . E 3 HOH A 95 325 144 HOH HOH . E 3 HOH A 96 326 148 HOH HOH . E 3 HOH A 97 327 150 HOH HOH . E 3 HOH A 98 328 152 HOH HOH . E 3 HOH A 99 329 154 HOH HOH . E 3 HOH A 100 330 157 HOH HOH . E 3 HOH A 101 331 158 HOH HOH . E 3 HOH A 102 332 161 HOH HOH . E 3 HOH A 103 333 163 HOH HOH . E 3 HOH A 104 334 166 HOH HOH . E 3 HOH A 105 335 169 HOH HOH . E 3 HOH A 106 336 171 HOH HOH . E 3 HOH A 107 337 178 HOH HOH . E 3 HOH A 108 338 179 HOH HOH . E 3 HOH A 109 339 181 HOH HOH . E 3 HOH A 110 340 185 HOH HOH . E 3 HOH A 111 341 186 HOH HOH . E 3 HOH A 112 342 187 HOH HOH . E 3 HOH A 113 343 188 HOH HOH . E 3 HOH A 114 344 189 HOH HOH . E 3 HOH A 115 345 190 HOH HOH . E 3 HOH A 116 346 192 HOH HOH . E 3 HOH A 117 347 193 HOH HOH . E 3 HOH A 118 349 199 HOH HOH . E 3 HOH A 119 350 201 HOH HOH . E 3 HOH A 120 351 202 HOH HOH . E 3 HOH A 121 352 208 HOH HOH . E 3 HOH A 122 353 209 HOH HOH . E 3 HOH A 123 354 214 HOH HOH . E 3 HOH A 124 355 215 HOH HOH . E 3 HOH A 125 356 217 HOH HOH . E 3 HOH A 126 357 219 HOH HOH . E 3 HOH A 127 358 224 HOH HOH . E 3 HOH A 128 359 228 HOH HOH . E 3 HOH A 129 360 229 HOH HOH . F 3 HOH B 1 230 230 HOH HOH . F 3 HOH B 2 231 7 HOH HOH . F 3 HOH B 3 232 8 HOH HOH . F 3 HOH B 4 233 233 HOH HOH . F 3 HOH B 5 234 234 HOH HOH . F 3 HOH B 6 235 235 HOH HOH . F 3 HOH B 7 236 12 HOH HOH . F 3 HOH B 8 237 237 HOH HOH . F 3 HOH B 9 238 13 HOH HOH . F 3 HOH B 10 239 15 HOH HOH . F 3 HOH B 11 240 240 HOH HOH . F 3 HOH B 12 241 17 HOH HOH . F 3 HOH B 13 242 242 HOH HOH . F 3 HOH B 14 243 23 HOH HOH . F 3 HOH B 15 244 27 HOH HOH . F 3 HOH B 16 245 245 HOH HOH . F 3 HOH B 17 246 29 HOH HOH . F 3 HOH B 18 247 247 HOH HOH . F 3 HOH B 19 248 248 HOH HOH . F 3 HOH B 20 249 30 HOH HOH . F 3 HOH B 21 250 250 HOH HOH . F 3 HOH B 22 251 32 HOH HOH . F 3 HOH B 23 252 34 HOH HOH . F 3 HOH B 24 253 253 HOH HOH . F 3 HOH B 25 254 35 HOH HOH . F 3 HOH B 26 255 255 HOH HOH . F 3 HOH B 27 256 36 HOH HOH . F 3 HOH B 28 257 38 HOH HOH . F 3 HOH B 29 258 41 HOH HOH . F 3 HOH B 30 259 259 HOH HOH . F 3 HOH B 31 260 44 HOH HOH . F 3 HOH B 32 261 261 HOH HOH . F 3 HOH B 33 262 48 HOH HOH . F 3 HOH B 34 263 263 HOH HOH . F 3 HOH B 35 264 264 HOH HOH . F 3 HOH B 36 265 50 HOH HOH . F 3 HOH B 37 266 54 HOH HOH . F 3 HOH B 38 267 267 HOH HOH . F 3 HOH B 39 268 55 HOH HOH . F 3 HOH B 40 269 269 HOH HOH . F 3 HOH B 41 270 270 HOH HOH . F 3 HOH B 42 271 56 HOH HOH . F 3 HOH B 43 272 57 HOH HOH . F 3 HOH B 44 273 59 HOH HOH . F 3 HOH B 45 274 60 HOH HOH . F 3 HOH B 46 275 275 HOH HOH . F 3 HOH B 47 276 63 HOH HOH . F 3 HOH B 48 277 277 HOH HOH . F 3 HOH B 49 278 278 HOH HOH . F 3 HOH B 50 279 279 HOH HOH . F 3 HOH B 51 280 280 HOH HOH . F 3 HOH B 52 281 281 HOH HOH . F 3 HOH B 53 282 67 HOH HOH . F 3 HOH B 54 283 68 HOH HOH . F 3 HOH B 55 284 284 HOH HOH . F 3 HOH B 56 285 285 HOH HOH . F 3 HOH B 57 286 69 HOH HOH . F 3 HOH B 58 287 70 HOH HOH . F 3 HOH B 59 288 71 HOH HOH . F 3 HOH B 60 289 289 HOH HOH . F 3 HOH B 61 290 290 HOH HOH . F 3 HOH B 62 291 72 HOH HOH . F 3 HOH B 63 292 75 HOH HOH . F 3 HOH B 64 293 293 HOH HOH . F 3 HOH B 65 294 76 HOH HOH . F 3 HOH B 66 295 77 HOH HOH . F 3 HOH B 67 296 79 HOH HOH . F 3 HOH B 68 297 297 HOH HOH . F 3 HOH B 69 298 82 HOH HOH . F 3 HOH B 70 299 85 HOH HOH . F 3 HOH B 71 300 88 HOH HOH . F 3 HOH B 72 301 89 HOH HOH . F 3 HOH B 73 302 91 HOH HOH . F 3 HOH B 74 303 92 HOH HOH . F 3 HOH B 75 304 95 HOH HOH . F 3 HOH B 76 305 102 HOH HOH . F 3 HOH B 77 306 103 HOH HOH . F 3 HOH B 78 307 106 HOH HOH . F 3 HOH B 79 308 107 HOH HOH . F 3 HOH B 80 309 108 HOH HOH . F 3 HOH B 81 310 109 HOH HOH . F 3 HOH B 82 311 110 HOH HOH . F 3 HOH B 83 312 115 HOH HOH . F 3 HOH B 84 313 117 HOH HOH . F 3 HOH B 85 314 124 HOH HOH . F 3 HOH B 86 315 125 HOH HOH . F 3 HOH B 87 316 126 HOH HOH . F 3 HOH B 88 317 128 HOH HOH . F 3 HOH B 89 318 130 HOH HOH . F 3 HOH B 90 319 132 HOH HOH . F 3 HOH B 91 320 133 HOH HOH . F 3 HOH B 92 321 134 HOH HOH . F 3 HOH B 93 322 137 HOH HOH . F 3 HOH B 94 323 140 HOH HOH . F 3 HOH B 95 324 142 HOH HOH . F 3 HOH B 96 325 143 HOH HOH . F 3 HOH B 97 326 145 HOH HOH . F 3 HOH B 98 327 146 HOH HOH . F 3 HOH B 99 328 147 HOH HOH . F 3 HOH B 100 329 151 HOH HOH . F 3 HOH B 101 330 153 HOH HOH . F 3 HOH B 102 331 155 HOH HOH . F 3 HOH B 103 332 156 HOH HOH . F 3 HOH B 104 333 159 HOH HOH . F 3 HOH B 105 334 160 HOH HOH . F 3 HOH B 106 335 162 HOH HOH . F 3 HOH B 107 336 165 HOH HOH . F 3 HOH B 108 337 167 HOH HOH . F 3 HOH B 109 338 168 HOH HOH . F 3 HOH B 110 339 170 HOH HOH . F 3 HOH B 111 340 172 HOH HOH . F 3 HOH B 112 341 173 HOH HOH . F 3 HOH B 113 342 174 HOH HOH . F 3 HOH B 114 343 175 HOH HOH . F 3 HOH B 115 344 176 HOH HOH . F 3 HOH B 116 345 177 HOH HOH . F 3 HOH B 117 346 180 HOH HOH . F 3 HOH B 118 347 182 HOH HOH . F 3 HOH B 119 348 197 HOH HOH . F 3 HOH B 120 349 184 HOH HOH . F 3 HOH B 121 350 191 HOH HOH . F 3 HOH B 122 351 194 HOH HOH . F 3 HOH B 123 352 195 HOH HOH . F 3 HOH B 124 353 196 HOH HOH . F 3 HOH B 125 354 198 HOH HOH . F 3 HOH B 126 355 200 HOH HOH . F 3 HOH B 127 356 205 HOH HOH . F 3 HOH B 128 357 207 HOH HOH . F 3 HOH B 129 358 210 HOH HOH . F 3 HOH B 130 359 211 HOH HOH . F 3 HOH B 131 360 212 HOH HOH . F 3 HOH B 132 361 213 HOH HOH . F 3 HOH B 133 362 216 HOH HOH . F 3 HOH B 134 363 218 HOH HOH . F 3 HOH B 135 364 220 HOH HOH . F 3 HOH B 136 365 221 HOH HOH . F 3 HOH B 137 366 222 HOH HOH . F 3 HOH B 138 367 225 HOH HOH . F 3 HOH B 139 368 226 HOH HOH . F 3 HOH B 140 369 227 HOH HOH . F 3 HOH B 141 370 64 HOH HOH . F 3 HOH B 142 371 183 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 . . . C 2 25.041 -2.432 8.425 1 8.74 ? P BMP 229 A 1 HETATM 2 O OP1 BMP . . . C 2 24.317 -3.252 7.4 1 8.97 ? OP1 BMP 229 A 1 HETATM 3 O OP2 BMP . . . C 2 25.78 -3.307 9.371 1 9.58 ? OP2 BMP 229 A 1 HETATM 4 O OP3 BMP . . . C 2 26.094 -1.401 7.795 1 9.4 ? OP3 BMP 229 A 1 HETATM 5 O O5' BMP . . . C 2 24.058 -1.573 9.336 1 7.73 ? O5' BMP 229 A 1 HETATM 6 C C5' BMP . . . C 2 22.913 -0.917 8.803 1 9.34 ? C5' BMP 229 A 1 HETATM 7 C C4' BMP . . . C 2 22.227 -0.21 9.953 1 7.72 ? C4' BMP 229 A 1 HETATM 8 O O4' BMP . . . C 2 21.163 0.59 9.417 1 7.63 ? O4' BMP 229 A 1 HETATM 9 C C3' BMP . . . C 2 21.564 -1.064 11.025 1 7.38 ? C3' BMP 229 A 1 HETATM 10 O O3' BMP . . . C 2 21.625 -0.449 12.325 1 8.17 ? O3' BMP 229 A 1 HETATM 11 C C2' BMP . . . C 2 20.14 -1.194 10.536 1 7.72 ? C2' BMP 229 A 1 HETATM 12 O O2' BMP . . . C 2 19.208 -1.51 11.58 1 8.27 ? O2' BMP 229 A 1 HETATM 13 C C1' BMP . . . C 2 19.914 0.151 9.863 1 6.21 ? C1' BMP 229 A 1 HETATM 14 N N1 BMP . . . C 2 18.966 0.217 8.719 1 7.4 ? N1 BMP 229 A 1 HETATM 15 C C2 BMP . . . C 2 19.13 -0.65 7.586 1 7.41 ? C2 BMP 229 A 1 HETATM 16 O O2 BMP . . . C 2 20.054 -1.44 7.507 1 7.7 ? O2 BMP 229 A 1 HETATM 17 N N3 BMP . . . C 2 18.173 -0.51 6.615 1 7.21 ? N3 BMP 229 A 1 HETATM 18 C C4 BMP . . . C 2 17.102 0.403 6.604 1 8.26 ? C4 BMP 229 A 1 HETATM 19 O O4 BMP . . . C 2 16.397 0.422 5.622 1 8.96 ? O4 BMP 229 A 1 HETATM 20 C C5 BMP . . . C 2 16.979 1.227 7.79 1 7.49 ? C5 BMP 229 A 1 HETATM 21 C C6 BMP . . . C 2 17.914 1.181 8.761 1 7.08 ? C6 BMP 229 A 1 HETATM 22 O O1 BMP . . . C 2 17.914 1.984 9.732 1 8.29 ? O1 BMP 229 A 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #