1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Lescrnier, E. Esnouf, R. Heus, H.A. Hilbers, C.W. Herdewijn, P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C11 H16 N5 O6 P 345.248 n 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(ADENIN-9-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL DNA linking C10 H16 N3 O7 P 321.224 n 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(CYTOSIN-1-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL DNA linking C11 H16 N5 O7 P 361.248 n 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(GUANIN-9-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL DNA linking C11 H17 N2 O8 P 336.235 n 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(THYMIN-1-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL DNA linking C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C3 H9 O5 P 156.074 PHOSPHORIC ACID MONO-(3-HYDROXY-PROPYL) ESTER non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N P N 2 N O N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 S C N 13 N C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C 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 H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N P N 41 N O N 42 N O N 43 N O N 44 N O N 45 N C N 46 R C N 47 N O N 48 S C N 49 N O N 50 N C N 51 S C N 52 N C N 53 N N N 54 N C N 55 N O N 56 N N N 57 N C N 58 N N N 59 N C N 60 N C 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 H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N P N 78 N O N 79 N O N 80 N O N 81 N O N 82 N C N 83 R C N 84 N O N 85 S C N 86 N O N 87 N C N 88 S C N 89 N C Y 90 N N Y 91 N C Y 92 N N Y 93 N C N 94 N C N 95 N O N 96 N N N 97 N C N 98 N N N 99 N N Y 100 N C N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N P N 118 N O N 119 N O N 120 N O N 121 N O N 122 N C N 123 R C N 124 N O N 125 S C N 126 N O N 127 N C N 128 S C N 129 N C N 130 N N N 131 N C N 132 N O N 133 N N N 134 N C N 135 N O N 136 N C N 137 N C N 138 N C N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N O N 157 N P N 158 N O N 159 N O N 160 N O N 161 N C N 162 R C N 163 N O N 164 S C N 165 N O N 166 R C N 167 N O N 168 R C Y 169 N N Y 170 N C Y 171 N N Y 172 N C Y 173 N C N 174 N N Y 175 N N Y 176 N C Y 177 N N Y 178 N C N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H 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 O N 194 N P N 195 N O N 196 N O N 197 N O N 198 N C N 199 R C N 200 N O N 201 S C N 202 N O N 203 R C N 204 N O N 205 R C N 206 N N N 207 N C N 208 N O N 209 N N N 210 N C N 211 N N N 212 N C N 213 N C 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 H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N O N 229 N P N 230 N O N 231 N O N 232 N O N 233 N C N 234 R C N 235 N O N 236 S C N 237 N O N 238 R C N 239 N O N 240 R C Y 241 N N Y 242 N C Y 243 N N Y 244 N C N 245 N C N 246 N O N 247 N N N 248 N C N 249 N N N 250 N N Y 251 N C N 252 N H N 253 N H N 254 N H N 255 N H 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 O N 267 N P N 268 N O N 269 N O N 270 N O N 271 N C N 272 N C N 273 N C N 274 N O N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 N H N 281 N H N 282 N H N 283 N H N 284 N O N 285 N P N 286 N O N 287 N O N 288 N O N 289 N C N 290 R C N 291 N O N 292 S C N 293 N O N 294 R C N 295 N O N 296 R C N 297 N N N 298 N C N 299 N O N 300 N N N 301 N C N 302 N O N 303 N C N 304 N C N 305 N H N 306 N H N 307 N H N 308 N H N 309 N H N 310 N H N 311 N H N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 1 N doub 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 sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing Y 27 N sing Y 28 N sing Y 29 N doub N 30 N sing Y 31 N sing Y 32 N sing Y 33 N doub N 34 N sing Y 35 N doub N 36 N sing N 37 N sing Y 38 N sing Y 39 N doub N 40 N sing Y 41 N sing N 42 N doub 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 sing 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 sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N doub N 71 N sing N 72 N doub 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 doub N 81 N sing N 82 N sing 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 sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing 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 Y 106 N sing Y 107 N sing Y 108 N doub N 109 N sing Y 110 N sing N 111 N sing Y 112 N doub N 113 N doub N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N doub N 119 N sing N 120 N sing N 121 N sing N 122 N doub N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing 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 sing 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 sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N doub 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 doub N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N doub N 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 sing 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 Y 186 N sing Y 187 N sing Y 188 N doub N 189 N sing Y 190 N sing Y 191 N sing Y 192 N doub N 193 N sing Y 194 N doub N 195 N sing N 196 N sing Y 197 N sing Y 198 N doub N 199 N sing Y 200 N sing N 201 N sing N 202 N sing N 203 N doub 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 sing 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 doub N 228 N sing N 229 N doub N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N doub N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N doub N 240 N sing N 241 N sing N 242 N sing N 243 N sing 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 Y 261 N sing Y 262 N sing Y 263 N doub N 264 N sing Y 265 N sing N 266 N sing Y 267 N doub N 268 N doub N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N doub N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N doub N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing 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 doub N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing 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 sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N doub N 321 N sing N 322 N sing N 323 N sing N 324 N doub N 325 N sing N 326 N doub N 327 N sing N 328 N sing UK Chem.Biol. CBOLE2 2050 1074-5521 7 719 731 10.1016/S1074-5521(00)00017-X 10980452 Solution structure of a HNA-RNA hybrid. 2000 US J.Am.Chem.Soc. JACSAT 0004 0002-7863 120 5381 5394 10.1021/ja973721f Minor Groove Hydration Contributes to the relative Stability of HNA/RNA Hybrids Compared to HNA/DNA Complexes 1998 10.2210/pdb1ejz/pdb pdb_00001ejz 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 2501.553 RNA (5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3') 1 syn polymer THE SUGAR MOIETIES ARE NOT DEOXYRIBOSE BUT D-ARABINO-HEXITOL 2579.844 DNA (5'-H(*(6HG)P*(6HC)P*(6HG)P*(6HT)P*(6HA)P*(6HG)P*(6HC)P*(6HG))-3') 1 syn polymer 156.074 PHOSPHORIC ACID MONO-(3-HYDROXY-PROPYL) ESTER 1 syn non-polymer no no CGCUACGC CGCUACGC A polyribonucleotide no yes (6HG)(6HC)(6HG)(6HT)(6HA)(6HG)(6HC)(6HG) GCGTAGCG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n 14.355 1 19 A 1 B 16 -1.121 A_C1:6HG16_B 1 -17.109 0.333 -0.020 -0.258 16.687 1 19 A 2 B 15 -1.486 A_G2:6HC15_B 2 -8.362 -0.431 0.282 -0.343 22.729 1 19 A 3 B 14 -0.518 A_C3:6HG14_B 3 -18.939 0.508 -0.332 -0.305 19.044 1 20 A 4 B 13 2.385 A_U4:6HA13_B 4 -21.429 0.113 -0.165 -0.306 13.829 1 20 A 5 B 12 -3.429 A_A5:6HT12_B 5 -17.719 0.129 0.573 -0.326 18.578 1 19 A 6 B 11 -3.957 A_C6:6HG11_B 6 -27.031 0.563 -0.073 -0.364 7.665 1 19 A 7 B 10 0.623 A_G7:6HC10_B 7 -13.548 -0.243 0.194 -0.300 20.666 1 19 A 8 B 9 2.380 A_C8:6HG9_B 8 -20.382 0.873 -0.301 -0.313 2.391 39.144 A A 1 2 19.092 B B 16 15 2.868 12.559 -0.887 -1.325 AA_C1G2:6HC156HG16_BB 1 -4.064 6.178 36.934 -3.227 0.920 3.238 33.996 A A 2 3 -3.268 B B 15 14 3.159 -1.906 0.280 -1.341 AA_G2C3:6HG146HC15_BB 2 3.905 -6.696 33.726 -1.994 0.134 2.774 35.723 A A 3 4 17.499 B B 14 13 3.206 10.578 0.169 -1.047 AA_C3U4:6HA136HG14_BB 3 1.967 -3.253 34.115 -3.139 -0.009 2.918 39.295 A A 4 5 16.456 B B 13 12 3.253 10.925 -0.558 -0.909 AA_U4A5:6HT126HA13_BB 4 -2.374 3.575 37.732 -2.605 0.558 3.183 36.288 A A 5 6 -4.591 B B 12 11 3.152 -2.848 -0.193 -1.251 AA_A5C6:6HG116HT12_BB 5 5.042 -8.127 35.839 -1.620 0.998 2.173 34.448 A A 6 7 27.049 B B 11 10 3.197 15.477 0.502 -1.578 AA_C6G7:6HC106HG11_BB 6 -0.627 1.095 30.864 -4.757 -0.932 2.771 36.061 A A 7 8 3.981 B B 10 9 2.886 2.457 -0.039 -1.288 AA_G7C8:6HG96HC10_BB 7 4.378 -7.093 35.721 -2.384 0.602 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Data collection 1 0 2000-10-23 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 1 4 2024-05-22 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Solution Structure of a Hexitol Nucleic Acid Duplex with Four Consecustive T:T Base Pairs RCSB Y RCSB 2000-03-06 REL PDI PHOSPHORIC ACID MONO-(3-HYDROXY-PROPYL) ESTER structure closest to the average of all refined structures 100 1 2D NOESY DQF-COSY H-P Hetcor TOCSY Watergate NOESY 1D Jump-Return 7 ambient 20 K 7 ambient 5 K Torsion Angles Dynamics and Gentle Molecular Dynamics 1 closest to the average 1.7 mM HNA, 1.7 mM RNA D2O 1.7 mM HNA, 1.7 mM RNA 10% D2O 90% H2O Varian collection VNMR 5.3 Biosym processing Felix 97.0 Biosym data analysis Felix 97.0 A.T. Brunger structure solution X-PLOR 3.518 A.T. Brunger refinement X-PLOR 3.518 500 Varian UNITY 500 Varian UNITYPLUS PDI 17 3 PDI PDI 17 B C 1 n 1 C 1 A G 2 n 2 G 2 A C 3 n 3 C 3 A U 4 n 4 U 4 A A 5 n 5 A 5 A C 6 n 6 C 6 A G 7 n 7 G 7 A C 8 n 8 C 8 A 6HG 9 n 1 6HG 9 B 6HC 10 n 2 6HC 10 B 6HG 11 n 3 6HG 11 B 6HT 12 n 4 6HT 12 B 6HA 13 n 5 6HA 13 B 6HG 14 n 6 6HG 14 B 6HC 15 n 7 6HC 15 B 6HG 16 n 8 6HG 16 B author_defined_assembly 2 dimeric B 6HG 9 B 6HG 1 DG B 6HC 10 B 6HC 2 DC B 6HG 11 B 6HG 3 DG B 6HT 12 B 6HT 4 DT B 6HA 13 B 6HA 5 DA B 6HG 14 B 6HG 6 DG B 6HC 15 B 6HC 7 DC B 6HG 16 B 6HG 8 DG 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 1 4.61 0.50 113.10 117.71 A A A N7 C8 N9 G G G 2 2 2 N 1 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 2 2 2 N 1 3.71 0.50 113.80 117.51 A A A N7 C8 N9 A A A 5 5 5 N 1 4.45 0.50 113.10 117.55 A A A N7 C8 N9 G G G 7 7 7 N 1 -2.58 0.40 106.40 103.82 A A A C8 N9 C4 G G G 7 7 7 N SOLUTION STRUCTURE OF A HNA-RNA HYBRID 1 N N 2 N N 3 N N covale 1.609 both B 6HG 9 B O3' 6HG 1 1_555 B 6HC 10 B P 6HC 2 1_555 covale 1.606 both B 6HC 10 B O3' 6HC 2 1_555 B 6HG 11 B P 6HG 3 1_555 covale 1.608 both B 6HG 11 B O3' 6HG 3 1_555 B 6HT 12 B P 6HT 4 1_555 covale 1.607 both B 6HT 12 B O3' 6HT 4 1_555 B 6HA 13 B P 6HA 5 1_555 covale 1.607 both B 6HA 13 B O3' 6HA 5 1_555 B 6HG 14 B P 6HG 6 1_555 covale 1.612 both B 6HG 14 B O3' 6HG 6 1_555 B 6HC 15 B P 6HC 7 1_555 covale 1.606 both B 6HC 15 B O3' 6HC 7 1_555 B 6HG 16 B P 6HG 8 1_555 covale 1.607 one B 6HG 16 B O3' 6HG 8 1_555 B PDI 17 C P PDI 1_555 hydrog WATSON-CRICK A C 1 A N3 C 1 1_555 B 6HG 16 B N1 6HG 8 1_555 hydrog WATSON-CRICK A C 1 A N4 C 1 1_555 B 6HG 16 B O6 6HG 8 1_555 hydrog WATSON-CRICK A C 1 A O2 C 1 1_555 B 6HG 16 B N2 6HG 8 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 B 6HC 15 B N3 6HC 7 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 B 6HC 15 B O2 6HC 7 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 B 6HC 15 B N4 6HC 7 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 B 6HG 14 B N1 6HG 6 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 B 6HG 14 B O6 6HG 6 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 B 6HG 14 B N2 6HG 6 1_555 hydrog WATSON-CRICK A U 4 A N3 U 4 1_555 B 6HA 13 B N1 6HA 5 1_555 hydrog WATSON-CRICK A U 4 A O4 U 4 1_555 B 6HA 13 B N6 6HA 5 1_555 hydrog WATSON-CRICK A A 5 A N1 A 5 1_555 B 6HT 12 B N3 6HT 4 1_555 hydrog WATSON-CRICK A A 5 A N6 A 5 1_555 B 6HT 12 B O4 6HT 4 1_555 hydrog WATSON-CRICK A C 6 A N3 C 6 1_555 B 6HG 11 B N1 6HG 3 1_555 hydrog WATSON-CRICK A C 6 A N4 C 6 1_555 B 6HG 11 B O6 6HG 3 1_555 hydrog WATSON-CRICK A C 6 A O2 C 6 1_555 B 6HG 11 B N2 6HG 3 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B 6HC 10 B N3 6HC 2 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B 6HC 10 B O2 6HC 2 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B 6HC 10 B N4 6HC 2 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 B 6HG 9 B N1 6HG 1 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 B 6HG 9 B O6 6HG 1 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 B 6HG 9 B N2 6HG 1 1_555 RNA HNA-RNA complex, double helix, A-type conformation, RNA 1EJZ PDB 1 1EJZ 1EJZ PDB 2 1EJZ 1 8 1EJZ 1 8 1EJZ A 1 1 8 9 16 1EJZ 9 16 1EJZ B 2 1 8 BINDING SITE FOR RESIDUE PDI B 17 B PDI 17 Software 1 B 6HG 16 B 6HG 8 1 1_555 1 P 1