0.006684 0.000000 0.000000 0.000000 0.006684 0.000000 0.000000 0.000000 0.006684 0.00000 0.00000 0.00000 Armstrong, S.R. Cook, W.J. Short, S.A. Ealick, S.E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 48 90.00 90.00 90.00 149.600 149.600 149.600 C10 H14 N2 O5 242.229 2'-deoxy-1-methyl-pseudouridine 5-METHYL-2'-DEOXYPSEUDOURIDINE DNA linking C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N O N 2 N C N 3 R C N 4 N O N 5 R C N 6 N C N 7 N C N 8 N C N 9 N O N 10 N N N 11 N C N 12 N O N 13 N N N 14 N C N 15 S C N 16 N O N 17 N C N 18 N H N 19 N H N 20 N H N 21 N H N 22 N H N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N N N 33 S C N 34 N C N 35 N O N 36 N C N 37 N O N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N N N 46 S C N 47 N C N 48 N O N 49 N C N 50 N C N 51 N C N 52 N N N 53 N C N 54 N N N 55 N N N 56 N O N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N N N 73 S C N 74 N C N 75 N O N 76 N C N 77 N C N 78 N O N 79 N N N 80 N O N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N N N 90 S C N 91 N C N 92 N O N 93 N C N 94 N C N 95 N O N 96 N O N 97 N O N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N N N 106 S C N 107 N C N 108 N O N 109 N C N 110 N C N 111 N C N 112 N O N 113 N N N 114 N O N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N N N 126 S C N 127 N C N 128 N O N 129 N C N 130 N C N 131 N C N 132 N O N 133 N O N 134 N O N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N N N 145 N C N 146 N C N 147 N O N 148 N O N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N N N 155 S C N 156 N C N 157 N O N 158 N C Y 159 N C Y 160 N N Y 161 N C Y 162 N C Y 163 N N N 164 N O N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N O N 176 N H N 177 N H N 178 N N N 179 S C N 180 N C N 181 N O N 182 S C N 183 N C N 184 N C N 185 N C N 186 N O N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N N N 201 S C N 202 N C N 203 N O N 204 N C N 205 N C N 206 N C N 207 N C N 208 N O N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N N N 223 S C N 224 N C N 225 N O N 226 N C N 227 N C N 228 N C N 229 N C N 230 N N N 231 N O N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N N N 248 S C N 249 N C N 250 N O N 251 N C N 252 N C N 253 N S N 254 N C N 255 N O N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N N N 268 S C N 269 N C N 270 N O N 271 N C Y 272 N C Y 273 N C Y 274 N C Y 275 N C Y 276 N C Y 277 N C N 278 N O N 279 N H N 280 N H N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N N N 291 S C N 292 N C N 293 N O N 294 N C N 295 N C N 296 N C N 297 N O N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N H N 305 N H N 306 N H N 307 N N N 308 S C N 309 N C N 310 N O N 311 N C N 312 N O N 313 N O N 314 N H N 315 N H N 316 N H N 317 N H N 318 N H N 319 N H N 320 N H N 321 N N N 322 S C N 323 N C N 324 N O N 325 R C N 326 N O N 327 N C N 328 N O N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N N N 339 S C N 340 N C N 341 N O N 342 N C Y 343 N C Y 344 N C Y 345 N C Y 346 N N Y 347 N C Y 348 N C Y 349 N C Y 350 N C Y 351 N C N 352 N O N 353 N H N 354 N H N 355 N H N 356 N H N 357 N H N 358 N H N 359 N H N 360 N H N 361 N H N 362 N H N 363 N H N 364 N H N 365 N N N 366 S C N 367 N C N 368 N O N 369 N C Y 370 N C Y 371 N C Y 372 N C Y 373 N C Y 374 N C Y 375 N C N 376 N O N 377 N O N 378 N H N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N N N 390 S C N 391 N C N 392 N O N 393 N C N 394 N C N 395 N C N 396 N O N 397 N H N 398 N H N 399 N H N 400 N H N 401 N H N 402 N H N 403 N H N 404 N H N 405 N H N 406 N H N 407 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N doub N 14 N sing N 15 N sing N 16 N sing N 17 N doub N 18 N sing N 19 N sing N 20 N sing N 21 N doub N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N doub N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N doub N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N doub N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N doub N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N doub N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N doub N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N doub N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N doub N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N doub N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N doub N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N doub N 155 N sing N 156 N sing N 157 N sing N 158 N sing Y 159 N sing Y 160 N doub Y 161 N doub N 162 N sing Y 163 N sing N 164 N sing Y 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N doub N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N doub N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N doub N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N doub N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N doub N 263 N sing N 264 N sing N 265 N sing N 266 N sing Y 267 N doub Y 268 N sing Y 269 N sing N 270 N sing Y 271 N doub N 272 N sing Y 273 N doub N 274 N sing Y 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N doub N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N doub N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N doub N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N doub N 332 N sing N 333 N sing N 334 N sing N 335 N sing Y 336 N doub Y 337 N sing Y 338 N sing N 339 N sing Y 340 N doub Y 341 N sing Y 342 N sing N 343 N sing Y 344 N sing Y 345 N doub N 346 N sing Y 347 N doub N 348 N sing Y 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N doub N 360 N sing N 361 N sing N 362 N sing N 363 N sing Y 364 N doub Y 365 N sing Y 366 N sing N 367 N sing Y 368 N doub N 369 N sing Y 370 N doub N 371 N sing Y 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N doub N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N sing N 394 N sing UK Structure STRUE6 2005 0969-2126 4 97 107 10.1016/S0969-2126(96)00013-5 8805514 Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site. 1996 10.2210/pdb1f8y/pdb pdb_00001f8y 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 296 1 AREA DETECTOR 1992-01-01 SDMS SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 18098.354 NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE 2.4.2.6 2 nat polymer 242.229 2'-deoxy-1-methyl-pseudouridine 2 syn non-polymer 18.015 water 76 nat water no no MPKKTIYFGAGWFTDRQNKAYKEAMEALKENPTIDLENSYVPLDNQYKGIRVDEHPEYLHDKVWATATYNNDLNGIKTND IMLGVYIPDEEDVGLGMELGYALSQGKYVLLVIPDEDYGKPINLMSWGVSDNVIKMSQLKDFNFNKPRFDFYEGAVY MPKKTIYFGAGWFTDRQNKAYKEAMEALKENPTIDLENSYVPLDNQYKGIRVDEHPEYLHDKVWATATYNNDLNGIKTND IMLGVYIPDEEDVGLGMELGYALSQGKYVLLVIPDEDYGKPINLMSWGVSDNVIKMSQLKDFNFNKPRFDFYEGAVY A,B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Lactobacillus sample 28039 Lactobacillus leichmannii 1 3.85 68.07 VAPOR DIFFUSION, HANGING DROP 5.4 Ammonium Sulfate, Citrate Buffer, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K 296 chem_comp chem_comp_atom chem_comp_bond database_2 entity pdbx_entity_nonpoly struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Structure summary 1 0 2000-08-09 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-02-07 _chem_comp.name _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _entity.pdbx_description _pdbx_entity_nonpoly.name _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 1F8X contains the same protein in the uncomplexed form. RCSB Y RCSB 2000-07-05 REL 5MD 2'-deoxy-1-methyl-pseudouridine HOH water 5MD 1 2 5MD 5MD 158 A 5MD 2 2 5MD 5MD 2 B HOH 801 3 HOH HOH 801 A HOH 803 3 HOH HOH 803 A HOH 804 3 HOH HOH 804 A HOH 806 3 HOH HOH 806 A HOH 807 3 HOH HOH 807 A HOH 808 3 HOH HOH 808 A HOH 809 3 HOH HOH 809 A HOH 810 3 HOH HOH 810 A HOH 811 3 HOH HOH 811 A HOH 812 3 HOH HOH 812 A HOH 813 3 HOH HOH 813 A HOH 814 3 HOH HOH 814 A HOH 816 3 HOH HOH 816 A HOH 817 3 HOH HOH 817 A HOH 818 3 HOH HOH 818 A HOH 819 3 HOH HOH 819 A HOH 820 3 HOH HOH 820 A HOH 821 3 HOH HOH 821 A HOH 822 3 HOH HOH 822 A HOH 823 3 HOH HOH 823 A HOH 824 3 HOH HOH 824 A HOH 825 3 HOH HOH 825 A HOH 827 3 HOH HOH 827 A HOH 836 3 HOH HOH 836 A HOH 839 3 HOH HOH 839 A HOH 841 3 HOH HOH 841 A HOH 842 3 HOH HOH 842 A HOH 843 3 HOH HOH 843 A HOH 844 3 HOH HOH 844 A HOH 848 3 HOH HOH 848 A HOH 849 3 HOH HOH 849 A HOH 850 3 HOH HOH 850 A HOH 852 3 HOH HOH 852 A HOH 853 3 HOH HOH 853 A HOH 855 3 HOH HOH 855 A HOH 856 3 HOH HOH 856 A HOH 857 3 HOH HOH 857 A HOH 858 3 HOH HOH 858 A HOH 859 3 HOH HOH 859 A HOH 860 3 HOH HOH 860 A HOH 867 3 HOH HOH 867 A HOH 868 3 HOH HOH 868 A HOH 869 3 HOH HOH 869 A HOH 870 3 HOH HOH 870 A HOH 874 3 HOH HOH 874 A HOH 875 3 HOH HOH 875 A HOH 876 3 HOH HOH 876 A HOH 802 3 HOH HOH 802 B HOH 805 3 HOH HOH 805 B HOH 815 3 HOH HOH 815 B HOH 826 3 HOH HOH 826 B HOH 828 3 HOH HOH 828 B HOH 829 3 HOH HOH 829 B HOH 830 3 HOH HOH 830 B HOH 831 3 HOH HOH 831 B HOH 832 3 HOH HOH 832 B HOH 833 3 HOH HOH 833 B HOH 834 3 HOH HOH 834 B HOH 835 3 HOH HOH 835 B HOH 837 3 HOH HOH 837 B HOH 838 3 HOH HOH 838 B HOH 840 3 HOH HOH 840 B HOH 845 3 HOH HOH 845 B HOH 846 3 HOH HOH 846 B HOH 847 3 HOH HOH 847 B HOH 851 3 HOH HOH 851 B HOH 854 3 HOH HOH 854 B HOH 861 3 HOH HOH 861 B HOH 862 3 HOH HOH 862 B HOH 863 3 HOH HOH 863 B HOH 864 3 HOH HOH 864 B HOH 865 3 HOH HOH 865 B HOH 866 3 HOH HOH 866 B HOH 871 3 HOH HOH 871 B HOH 872 3 HOH HOH 872 B HOH 873 3 HOH HOH 873 B n 1 1 A PRO 2 n 2 PRO 2 A LYS 3 n 3 LYS 3 A LYS 4 n 4 LYS 4 A THR 5 n 5 THR 5 A ILE 6 n 6 ILE 6 A TYR 7 n 7 TYR 7 A PHE 8 n 8 PHE 8 A GLY 9 n 9 GLY 9 A ALA 10 n 10 ALA 10 A GLY 11 n 11 GLY 11 A TRP 12 n 12 TRP 12 A PHE 13 n 13 PHE 13 A THR 14 n 14 THR 14 A ASP 15 n 15 ASP 15 A ARG 16 n 16 ARG 16 A GLN 17 n 17 GLN 17 A ASN 18 n 18 ASN 18 A LYS 19 n 19 LYS 19 A ALA 20 n 20 ALA 20 A TYR 21 n 21 TYR 21 A LYS 22 n 22 LYS 22 A GLU 23 n 23 GLU 23 A ALA 24 n 24 ALA 24 A MET 25 n 25 MET 25 A GLU 26 n 26 GLU 26 A ALA 27 n 27 ALA 27 A LEU 28 n 28 LEU 28 A LYS 29 n 29 LYS 29 A GLU 30 n 30 GLU 30 A ASN 31 n 31 ASN 31 A PRO 32 n 32 PRO 32 A THR 33 n 33 THR 33 A ILE 34 n 34 ILE 34 A ASP 35 n 35 ASP 35 A LEU 36 n 36 LEU 36 A GLU 37 n 37 GLU 37 A ASN 38 n 38 ASN 38 A SER 39 n 39 SER 39 A TYR 40 n 40 TYR 40 A VAL 41 n 41 VAL 41 A PRO 42 n 42 PRO 42 A LEU 43 n 43 LEU 43 A ASP 44 n 44 ASP 44 A ASN 45 n 45 ASN 45 A GLN 46 n 46 GLN 46 A TYR 47 n 47 TYR 47 A LYS 48 n 48 LYS 48 A GLY 49 n 49 GLY 49 A ILE 50 n 50 ILE 50 A ARG 51 n 51 ARG 51 A VAL 52 n 52 VAL 52 A ASP 53 n 53 ASP 53 A GLU 54 n 54 GLU 54 A HIS 55 n 55 HIS 55 A PRO 56 n 56 PRO 56 A GLU 57 n 57 GLU 57 A TYR 58 n 58 TYR 58 A LEU 59 n 59 LEU 59 A HIS 60 n 60 HIS 60 A ASP 61 n 61 ASP 61 A LYS 62 n 62 LYS 62 A VAL 63 n 63 VAL 63 A TRP 64 n 64 TRP 64 A ALA 65 n 65 ALA 65 A THR 66 n 66 THR 66 A ALA 67 n 67 ALA 67 A THR 68 n 68 THR 68 A TYR 69 n 69 TYR 69 A ASN 70 n 70 ASN 70 A ASN 71 n 71 ASN 71 A ASP 72 n 72 ASP 72 A LEU 73 n 73 LEU 73 A ASN 74 n 74 ASN 74 A GLY 75 n 75 GLY 75 A ILE 76 n 76 ILE 76 A LYS 77 n 77 LYS 77 A THR 78 n 78 THR 78 A ASN 79 n 79 ASN 79 A ASP 80 n 80 ASP 80 A ILE 81 n 81 ILE 81 A MET 82 n 82 MET 82 A LEU 83 n 83 LEU 83 A GLY 84 n 84 GLY 84 A VAL 85 n 85 VAL 85 A TYR 86 n 86 TYR 86 A ILE 87 n 87 ILE 87 A PRO 88 n 88 PRO 88 A ASP 89 n 89 ASP 89 A GLU 90 n 90 GLU 90 A GLU 91 n 91 GLU 91 A ASP 92 n 92 ASP 92 A VAL 93 n 93 VAL 93 A GLY 94 n 94 GLY 94 A LEU 95 n 95 LEU 95 A GLY 96 n 96 GLY 96 A MET 97 n 97 MET 97 A GLU 98 n 98 GLU 98 A LEU 99 n 99 LEU 99 A GLY 100 n 100 GLY 100 A TYR 101 n 101 TYR 101 A ALA 102 n 102 ALA 102 A LEU 103 n 103 LEU 103 A SER 104 n 104 SER 104 A GLN 105 n 105 GLN 105 A GLY 106 n 106 GLY 106 A LYS 107 n 107 LYS 107 A TYR 108 n 108 TYR 108 A VAL 109 n 109 VAL 109 A LEU 110 n 110 LEU 110 A LEU 111 n 111 LEU 111 A VAL 112 n 112 VAL 112 A ILE 113 n 113 ILE 113 A PRO 114 n 114 PRO 114 A ASP 115 n 115 ASP 115 A GLU 116 n 116 GLU 116 A ASP 117 n 117 ASP 117 A TYR 118 n 118 TYR 118 A GLY 119 n 119 GLY 119 A LYS 120 n 120 LYS 120 A PRO 121 n 121 PRO 121 A ILE 122 n 122 ILE 122 A ASN 123 n 123 ASN 123 A LEU 124 n 124 LEU 124 A MET 125 n 125 MET 125 A SER 126 n 126 SER 126 A TRP 127 n 127 TRP 127 A GLY 128 n 128 GLY 128 A VAL 129 n 129 VAL 129 A SER 130 n 130 SER 130 A ASP 131 n 131 ASP 131 A ASN 132 n 132 ASN 132 A VAL 133 n 133 VAL 133 A ILE 134 n 134 ILE 134 A LYS 135 n 135 LYS 135 A MET 136 n 136 MET 136 A SER 137 n 137 SER 137 A GLN 138 n 138 GLN 138 A LEU 139 n 139 LEU 139 A LYS 140 n 140 LYS 140 A ASP 141 n 141 ASP 141 A PHE 142 n 142 PHE 142 A ASN 143 n 143 ASN 143 A PHE 144 n 144 PHE 144 A ASN 145 n 145 ASN 145 A LYS 146 n 146 LYS 146 A PRO 147 n 147 PRO 147 A ARG 148 n 148 ARG 148 A PHE 149 n 149 PHE 149 A ASP 150 n 150 ASP 150 A PHE 151 n 151 PHE 151 A TYR 152 n 152 TYR 152 A GLU 153 n 153 GLU 153 A GLY 154 n 154 GLY 154 A ALA 155 n 155 ALA 155 A VAL 156 n 156 VAL 156 A TYR 157 n 157 TYR 157 A n 1 201 B PRO 202 n 2 PRO 202 B LYS 203 n 3 LYS 203 B LYS 204 n 4 LYS 204 B THR 205 n 5 THR 205 B ILE 206 n 6 ILE 206 B TYR 207 n 7 TYR 207 B PHE 208 n 8 PHE 208 B GLY 209 n 9 GLY 209 B ALA 210 n 10 ALA 210 B GLY 211 n 11 GLY 211 B TRP 212 n 12 TRP 212 B PHE 213 n 13 PHE 213 B THR 214 n 14 THR 214 B ASP 215 n 15 ASP 215 B ARG 216 n 16 ARG 216 B GLN 217 n 17 GLN 217 B ASN 218 n 18 ASN 218 B LYS 219 n 19 LYS 219 B ALA 220 n 20 ALA 220 B TYR 221 n 21 TYR 221 B LYS 222 n 22 LYS 222 B GLU 223 n 23 GLU 223 B ALA 224 n 24 ALA 224 B MET 225 n 25 MET 225 B GLU 226 n 26 GLU 226 B ALA 227 n 27 ALA 227 B LEU 228 n 28 LEU 228 B LYS 229 n 29 LYS 229 B GLU 230 n 30 GLU 230 B ASN 231 n 31 ASN 231 B PRO 232 n 32 PRO 232 B THR 233 n 33 THR 233 B ILE 234 n 34 ILE 234 B ASP 235 n 35 ASP 235 B LEU 236 n 36 LEU 236 B GLU 237 n 37 GLU 237 B ASN 238 n 38 ASN 238 B SER 239 n 39 SER 239 B TYR 240 n 40 TYR 240 B VAL 241 n 41 VAL 241 B PRO 242 n 42 PRO 242 B LEU 243 n 43 LEU 243 B ASP 244 n 44 ASP 244 B ASN 245 n 45 ASN 245 B GLN 246 n 46 GLN 246 B TYR 247 n 47 TYR 247 B LYS 248 n 48 LYS 248 B GLY 249 n 49 GLY 249 B ILE 250 n 50 ILE 250 B ARG 251 n 51 ARG 251 B VAL 252 n 52 VAL 252 B ASP 253 n 53 ASP 253 B GLU 254 n 54 GLU 254 B HIS 255 n 55 HIS 255 B PRO 256 n 56 PRO 256 B GLU 257 n 57 GLU 257 B TYR 258 n 58 TYR 258 B LEU 259 n 59 LEU 259 B HIS 260 n 60 HIS 260 B ASP 261 n 61 ASP 261 B LYS 262 n 62 LYS 262 B VAL 263 n 63 VAL 263 B TRP 264 n 64 TRP 264 B ALA 265 n 65 ALA 265 B THR 266 n 66 THR 266 B ALA 267 n 67 ALA 267 B THR 268 n 68 THR 268 B TYR 269 n 69 TYR 269 B ASN 270 n 70 ASN 270 B ASN 271 n 71 ASN 271 B ASP 272 n 72 ASP 272 B LEU 273 n 73 LEU 273 B ASN 274 n 74 ASN 274 B GLY 275 n 75 GLY 275 B ILE 276 n 76 ILE 276 B LYS 277 n 77 LYS 277 B THR 278 n 78 THR 278 B ASN 279 n 79 ASN 279 B ASP 280 n 80 ASP 280 B ILE 281 n 81 ILE 281 B MET 282 n 82 MET 282 B LEU 283 n 83 LEU 283 B GLY 284 n 84 GLY 284 B VAL 285 n 85 VAL 285 B TYR 286 n 86 TYR 286 B ILE 287 n 87 ILE 287 B PRO 288 n 88 PRO 288 B ASP 289 n 89 ASP 289 B GLU 290 n 90 GLU 290 B GLU 291 n 91 GLU 291 B ASP 292 n 92 ASP 292 B VAL 293 n 93 VAL 293 B GLY 294 n 94 GLY 294 B LEU 295 n 95 LEU 295 B GLY 296 n 96 GLY 296 B MET 297 n 97 MET 297 B GLU 298 n 98 GLU 298 B LEU 299 n 99 LEU 299 B GLY 300 n 100 GLY 300 B TYR 301 n 101 TYR 301 B ALA 302 n 102 ALA 302 B LEU 303 n 103 LEU 303 B SER 304 n 104 SER 304 B GLN 305 n 105 GLN 305 B GLY 306 n 106 GLY 306 B LYS 307 n 107 LYS 307 B TYR 308 n 108 TYR 308 B VAL 309 n 109 VAL 309 B LEU 310 n 110 LEU 310 B LEU 311 n 111 LEU 311 B VAL 312 n 112 VAL 312 B ILE 313 n 113 ILE 313 B PRO 314 n 114 PRO 314 B ASP 315 n 115 ASP 315 B GLU 316 n 116 GLU 316 B ASP 317 n 117 ASP 317 B TYR 318 n 118 TYR 318 B GLY 319 n 119 GLY 319 B LYS 320 n 120 LYS 320 B PRO 321 n 121 PRO 321 B ILE 322 n 122 ILE 322 B ASN 323 n 123 ASN 323 B LEU 324 n 124 LEU 324 B MET 325 n 125 MET 325 B SER 326 n 126 SER 326 B TRP 327 n 127 TRP 327 B GLY 328 n 128 GLY 328 B VAL 329 n 129 VAL 329 B SER 330 n 130 SER 330 B ASP 331 n 131 ASP 331 B ASN 332 n 132 ASN 332 B VAL 333 n 133 VAL 333 B ILE 334 n 134 ILE 334 B LYS 335 n 135 LYS 335 B MET 336 n 136 MET 336 B SER 337 n 137 SER 337 B GLN 338 n 138 GLN 338 B LEU 339 n 139 LEU 339 B LYS 340 n 140 LYS 340 B ASP 341 n 141 ASP 341 B PHE 342 n 142 PHE 342 B ASN 343 n 143 ASN 343 B PHE 344 n 144 PHE 344 B ASN 345 n 145 ASN 345 B LYS 346 n 146 LYS 346 B PRO 347 n 147 PRO 347 B ARG 348 n 148 ARG 348 B PHE 349 n 149 PHE 349 B ASP 350 n 150 ASP 350 B PHE 351 n 151 PHE 351 B TYR 352 n 152 TYR 352 B GLU 353 n 153 GLU 353 B GLY 354 n 154 GLY 354 B ALA 355 n 155 ALA 355 B VAL 356 n 156 VAL 356 B TYR 357 n 157 TYR 357 B author_defined_assembly 6 hexameric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 6_555 z+1/2,-x+1/2,-y crystal symmetry operation 74.8000000000 74.8000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 1.0000000000 0.0000000000 0.0000000000 12_554 -y+1/2,-z,x-1/2 crystal symmetry operation 74.8000000000 0.0000000000 -74.8000000000 A N TYR 7 A N TYR 7 A O ILE 81 A O ILE 81 A N MET 82 A N MET 82 A O TYR 108 A O TYR 108 A N LEU 111 A N LEU 111 A O ASN 132 A O ASN 132 B N TYR 207 B N TYR 7 B O ILE 281 B O ILE 81 B N MET 282 B N MET 82 B O TYR 308 B O TYR 108 B N LEU 311 B N LEU 111 B O ASN 332 B O ASN 132 1 A MET 1 A MET 1 1 Y 1 B MET 201 B MET 1 1 Y 1 A TRP 12 -146.41 40.46 1 B TRP 212 -152.05 33.87 1 B HIS 255 -155.65 72.19 1 B PRO 256 -52.98 -7.26 1 B ASN 332 -173.70 147.27 0.218 0.16 0.16 2.40 5.00 1792 17921 17921 RANDOM 1 2.000 0 Engh & Huber 2.40 5.00 76 2646 34 0 2536 .008 1.56 2.4 100 1F8Y 21897 21897 0 0 0.075 1 4.6 93 model building X-PLOR refinement X-PLOR data reduction SDMS data scaling SDMS phasing X-PLOR CRYSTAL STRUCTURE ANALYSIS OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE COMPLEXED WITH 5-METHYL-2'-DEOXYPSEUDOURIDINE 1 N N 1 N N 2 N N 2 N N 3 N N 3 N N The biological assembly is a hexamer. Each pair of monomers is related by a noncrystallographic twofold symmetry axis. A THR 14 A THR 14 HELX_P A ASN 31 A ASN 31 1 1 18 A VAL 41 A VAL 41 HELX_P A ASN 45 A ASN 45 5 2 5 A GLN 46 A GLN 46 HELX_P A ILE 50 A ILE 50 5 3 5 A HIS 55 A HIS 55 HELX_P A HIS 60 A HIS 60 5 4 6 A ASP 61 A ASP 61 HELX_P A THR 78 A THR 78 1 5 18 A ILE 87 A ILE 87 HELX_P A GLU 91 A GLU 91 5 6 5 A ASP 92 A ASP 92 HELX_P A GLN 105 A GLN 105 1 7 14 A PRO 114 A PRO 114 HELX_P A TYR 118 A TYR 118 5 8 5 A ASN 123 A ASN 123 HELX_P A SER 130 A SER 130 1 9 8 A SER 137 A SER 137 HELX_P A LEU 139 A LEU 139 5 10 3 B THR 214 B THR 14 HELX_P B ASN 231 B ASN 31 1 11 18 B VAL 241 B VAL 41 HELX_P B ASN 245 B ASN 45 5 12 5 B GLN 246 B GLN 46 HELX_P B ILE 250 B ILE 50 5 13 5 B ARG 251 B ARG 51 HELX_P B HIS 255 B HIS 55 5 14 5 B HIS 255 B HIS 55 HELX_P B HIS 260 B HIS 60 5 15 6 B ASP 261 B ASP 61 HELX_P B THR 278 B THR 78 1 16 18 B ASP 292 B ASP 92 HELX_P B GLN 305 B GLN 105 1 17 14 B ASN 323 B ASN 123 HELX_P B SER 330 B SER 130 1 18 8 B SER 337 B SER 137 HELX_P B LEU 339 B LEU 139 5 19 3 TRANSFERASE active site, alpha/beta protein, biocatalyst, nucleoside, TRANSFERASE NTD_LACLE UNP 1 1 Q9R5V5 MPKKTIYFGAGWFTDRQNKAYKEAMEALKENPTIDLENSYVPLDNQYKGIRVDEHPEYLHDKVWATATYNNDLNGIKTND IMLGVYIPDEEDVGLGMELGYALSQGKYVLLVIPDEDYGKPINLMSWGVSDNVIKMSQLKDFNFNKPRFDFYEGAVY 1 157 1F8Y 1 157 Q9R5V5 A 1 1 157 1 157 1F8Y 201 357 Q9R5V5 B 1 1 157 4 4 parallel parallel parallel parallel parallel parallel A ILE 6 A ILE 6 A GLY 9 A GLY 9 A ILE 81 A ILE 81 A VAL 85 A VAL 85 A TYR 108 A TYR 108 A ILE 113 A ILE 113 A ASN 132 A ASN 132 A LYS 135 A LYS 135 B ILE 206 B ILE 6 B GLY 209 B GLY 9 B ILE 281 B ILE 81 B VAL 285 B VAL 85 B TYR 308 B TYR 108 B ILE 313 B ILE 113 B ASN 332 B ASN 132 B LYS 335 B LYS 135 BINDING SITE FOR RESIDUE 5MD A 158 A 5MD 158 Software 12 BINDING SITE FOR RESIDUE 5MD B 2 B 5MD 2 Software 11 A TYR 7 A TYR 7 12 1_555 A GLY 9 A GLY 9 12 1_555 A ALA 10 A ALA 10 12 1_555 A TRP 12 A TRP 12 12 1_555 A PHE 13 A PHE 13 12 1_555 A GLN 46 A GLN 46 12 1_555 A ASP 72 A ASP 72 12 1_555 A ASP 92 A ASP 92 12 1_555 A GLY 94 A GLY 94 12 1_555 A GLU 98 A GLU 98 12 1_555 B ASN 323 B ASN 123 12 1_555 B TYR 357 B TYR 157 12 1_555 A ASN 123 A ASN 123 11 1_555 A MET 125 A MET 125 11 1_555 A TYR 157 A TYR 157 11 1_555 B TYR 207 B TYR 7 11 1_555 B GLY 209 B GLY 9 11 1_555 B TRP 212 B TRP 12 11 1_555 B PRO 242 B PRO 42 11 1_555 B GLN 246 B GLN 46 11 1_555 B ASP 272 B ASP 72 11 1_555 B ASP 292 B ASP 92 11 1_555 B GLU 298 B GLU 98 11 1_555 199 I 21 3