1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Brown, S.C. Veal, J.M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C11 H16 N7 O3 1 294.290 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE peptide-like C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H16 N5 O4 1 270.265 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE peptide-like C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C11 H16 N7 O4 1 310.289 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE peptide-like C11 H17 N4 O5 1 285.276 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE peptide-like C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N O N 2 N P 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 R C N 12 N O N 13 R 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 C N 39 N C N 40 N O N 41 N C N 42 N C N 43 N O N 44 N O N 45 N N N 46 N C N 47 N C N 48 N N Y 49 N N Y 50 N C Y 51 N N Y 52 N C Y 53 N C N 54 N N Y 55 N N Y 56 N C Y 57 N N Y 58 N C 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 H N 73 N H N 74 N H N 75 N O N 76 N P N 77 N O N 78 N O N 79 N O N 80 N C N 81 R C N 82 N O N 83 S C N 84 N O N 85 R C N 86 N O N 87 R C N 88 N N N 89 N C N 90 N O N 91 N N N 92 N C N 93 N N N 94 N C N 95 N C N 96 N H N 97 N H 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 H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N C N 111 N C N 112 N O N 113 N C N 114 N C N 115 N O N 116 N O N 117 N N N 118 N C N 119 N C N 120 N N N 121 N N N 122 N C N 123 N N N 124 N C N 125 N C N 126 N C N 127 N O N 128 N N N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H 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 H N 145 N O N 146 N P N 147 N O N 148 N O N 149 N O N 150 N C N 151 R C N 152 N O N 153 S C N 154 N O N 155 R C N 156 N O N 157 R C Y 158 N N Y 159 N C Y 160 N N Y 161 N C N 162 N C N 163 N O N 164 N N N 165 N C N 166 N N N 167 N N Y 168 N C 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 H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N C N 184 N C N 185 N O N 186 N C N 187 N C N 188 N O N 189 N O N 190 N N N 191 N C N 192 N C N 193 N N Y 194 N N Y 195 N C Y 196 N N Y 197 N C N 198 N C N 199 N O N 200 N N N 201 N C N 202 N N N 203 N N Y 204 N C N 205 N H N 206 N H N 207 N H N 208 N H 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 C N 222 N C N 223 N O N 224 N C N 225 N C N 226 N O N 227 N O N 228 N N N 229 N C N 230 N C N 231 N N N 232 N N N 233 N C N 234 N C N 235 N O N 236 N N N 237 N C N 238 N O N 239 N C N 240 N C 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 H N 248 N H N 249 N H N 250 N H N 251 N H 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 O N 259 N P N 260 N O N 261 N O N 262 N O N 263 N C N 264 R C N 265 N O N 266 S C N 267 N O N 268 R C N 269 N O N 270 R C N 271 N N N 272 N C N 273 N O N 274 N N N 275 N C N 276 N O N 277 N C N 278 N C 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 H N 291 N H N 1 N sing N 2 N sing N 3 N doub 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 Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N doub N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub 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 Y 63 N sing Y 64 N sing Y 65 N doub N 66 N sing Y 67 N sing Y 68 N sing Y 69 N doub N 70 N sing Y 71 N doub N 72 N sing N 73 N sing Y 74 N sing Y 75 N doub N 76 N sing Y 77 N sing 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 doub N 105 N sing N 106 N doub N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N doub N 112 N sing N 113 N sing 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 sing N 123 N sing N 124 N doub 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 doub N 141 N doub N 142 N sing N 143 N sing N 144 N doub N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N doub N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing 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 sing 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 Y 173 N sing Y 174 N sing Y 175 N doub N 176 N sing Y 177 N sing N 178 N sing Y 179 N doub N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N doub 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 doub N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N doub 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 Y 212 N sing Y 213 N sing Y 214 N doub N 215 N sing Y 216 N sing N 217 N sing Y 218 N doub N 219 N doub N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N doub 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 doub N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N doub N 239 N sing 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 doub N 254 N sing N 255 N doub N 256 N sing N 257 N sing N 258 N sing N 259 N doub N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N doub N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 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 sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N doub N 292 N sing N 293 N sing N 294 N sing N 295 N doub N 296 N sing N 297 N doub N 298 N sing N 299 N sing US Science SCIEAS 0038 0036-8075 265 777 780 7519361 NMR solution structure of a peptide nucleic acid complexed with RNA. 1994 10.2210/pdb176d/pdb pdb_0000176d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1634.599 DNA (5'-D(*GPN*APN*APN*CPN*TPN*CPN)-3') 1 syn polymer 1892.173 RNA (5'-R(P*GP*AP*GP*UP*UP*C)-3') 1 syn polymer PEPTIDE NUCLEIC ACID RIBONUCLEIC ACID no yes (GPN)(APN)(APN)(CPN)(TPN)(CPN) XXXXXX A peptide nucleic acid no no GAGUUC GAGUUC B polyribonucleotide n n n n n n n n n n n n -5.733 1 19 A 1 B 12 4.380 A_GPN1:C12_B 1 -7.082 -0.951 -0.311 -0.092 5.822 1 20 A 2 B 11 2.083 A_APN2:U11_B 2 -14.313 -0.058 -0.068 0.024 1.691 1 20 A 3 B 10 4.967 A_APN3:U10_B 3 -18.606 -0.479 0.162 0.043 7.994 1 19 A 4 B 9 0.808 A_CPN4:G9_B 4 -19.789 -0.184 -0.014 -0.004 6.889 1 20 A 5 B 8 -2.880 A_TPN5:A8_B 5 -19.138 0.467 0.553 -0.247 -21.945 1 19 A 6 B 7 -1.964 A_CPN6:G7_B 6 -8.741 0.952 1.355 -0.307 2.858 28.174 A A 1 2 10.420 B B 12 11 3.220 5.041 0.470 -1.523 AA_GPN1APN2:U11C12_BB 1 -2.162 4.468 27.645 -4.235 -1.440 2.281 29.042 A A 2 3 20.994 B B 11 10 3.294 10.272 0.231 -2.137 AA_APN2APN3:U10U11_BB 2 -4.117 8.413 26.893 -6.263 -1.263 3.255 29.695 A A 3 4 -4.087 B B 10 9 3.152 -2.093 -0.162 -1.572 AA_APN3CPN4:G9U10_BB 3 -0.694 1.355 29.615 -2.635 0.173 3.085 32.698 A A 4 5 9.238 B B 9 8 3.316 5.170 0.538 -0.734 AA_CPN4TPN5:A8G9_BB 4 -3.658 6.537 32.096 -2.186 -1.581 3.783 35.559 A A 5 6 3.278 B B 8 7 3.983 1.999 0.779 -2.170 AA_TPN5CPN6:G7A8_BB 5 -2.976 4.881 35.384 -3.900 -1.793 atom_site chem_comp_atom chem_comp_bond database_2 entity pdbx_database_status struct_conn repository Initial release Version format compliance Non-polymer description Version format compliance Atomic model Data collection Database references Derived calculations Other Structure summary 1 0 1994-11-01 1 1 2008-03-24 1 2 2011-07-13 2 0 2023-11-15 _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.label_atom_id _database_2.pdbx_DOI _database_2.pdbx_database_accession _entity.formula_weight _pdbx_database_status.process_site _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr2_label_atom_id Y BNL 1994-05-17 REL CHEMICALLY SYNTHESIZED sample CHEMICALLY SYNTHESIZED sample 10 NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 3930 NUMBER OF SOLVENT ATOMS 0 DISTANCE GEOMETRY, SIMULATED ANNEALING BRUNGER refinement X-PLOR 3.10 GPN 1 n 1 GPN 1 A APN 2 n 2 APN 2 A APN 3 n 3 APN 3 A CPN 4 n 4 CPN 4 A TPN 5 n 5 TPN 5 A CPN 6 n 6 CPN 6 A G 7 n 1 G 7 B A 8 n 2 A 8 B G 9 n 3 G 9 B U 10 n 4 U 10 B U 11 n 5 U 11 B C 12 n 6 C 12 B author_defined_assembly 2 dimeric A GPN 1 A GPN 1 DG A APN 2 A APN 2 DA A APN 3 A APN 3 DA A CPN 4 A CPN 4 DC A TPN 5 A TPN 5 DT A CPN 6 A CPN 6 DC 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 B A 8 0.065 SIDE CHAIN 1 B U 10 0.059 SIDE CHAIN 2 B U 10 0.070 SIDE CHAIN 3 B A 8 0.080 SIDE CHAIN 3 B U 10 0.074 SIDE CHAIN 4 B A 8 0.065 SIDE CHAIN 4 B U 11 0.103 SIDE CHAIN 5 B A 8 0.102 SIDE CHAIN 5 B U 10 0.083 SIDE CHAIN 5 B C 12 0.074 SIDE CHAIN 6 B G 7 0.080 SIDE CHAIN 6 B A 8 0.113 SIDE CHAIN 6 B U 10 0.059 SIDE CHAIN 7 B G 7 0.127 SIDE CHAIN 7 B A 8 0.095 SIDE CHAIN 7 B G 9 0.072 SIDE CHAIN 7 B U 10 0.089 SIDE CHAIN 7 B C 12 0.092 SIDE CHAIN 8 B A 8 0.095 SIDE CHAIN 8 B U 10 0.076 SIDE CHAIN 9 B G 9 0.062 SIDE CHAIN 9 B U 10 0.077 SIDE CHAIN 9 B C 12 0.077 SIDE CHAIN 10 B A 8 0.075 SIDE CHAIN 10 B U 10 0.067 SIDE CHAIN 1 5.47 0.70 108.50 113.97 B B B O4' C1' N1 U U U 10 10 10 N 1 4.65 0.70 108.50 113.15 B B B O4' C1' N1 U U U 11 11 11 N 2 5.44 0.90 109.80 115.24 B B B C5' C4' O4' G G G 7 7 7 N 2 4.66 0.70 108.50 113.16 B B B O4' C1' N9 G G G 9 9 9 N 2 5.21 0.70 108.50 113.71 B B B O4' C1' N1 U U U 10 10 10 N 2 4.47 0.70 108.50 112.97 B B B O4' C1' N1 U U U 11 11 11 N 3 4.71 0.70 108.50 113.21 B B B O4' C1' N1 U U U 10 10 10 N 3 4.92 0.70 108.50 113.42 B B B O4' C1' N1 U U U 11 11 11 N 4 4.69 0.70 108.50 113.19 B B B O4' C1' N1 U U U 10 10 10 N 4 5.08 0.70 108.50 113.58 B B B O4' C1' N1 U U U 11 11 11 N 5 4.65 0.70 108.50 113.15 B B B O4' C1' N1 U U U 10 10 10 N 5 4.32 0.70 108.50 112.82 B B B O4' C1' N1 U U U 11 11 11 N 6 4.98 0.70 108.50 113.48 B B B O4' C1' N1 U U U 10 10 10 N 6 4.39 0.70 108.50 112.89 B B B O4' C1' N1 U U U 11 11 11 N 7 5.06 0.70 108.50 113.56 B B B O4' C1' N1 U U U 10 10 10 N 7 4.86 0.70 108.50 113.36 B B B O4' C1' N1 U U U 11 11 11 N 8 5.04 0.70 108.50 113.54 B B B O4' C1' N1 U U U 10 10 10 N 8 4.70 0.70 108.50 113.20 B B B O4' C1' N1 U U U 11 11 11 N 9 5.46 0.70 108.50 113.96 B B B O4' C1' N1 U U U 10 10 10 N 9 4.47 0.70 108.50 112.97 B B B O4' C1' N1 U U U 11 11 11 N 10 4.70 0.70 108.50 113.20 B B B O4' C1' N1 U U U 10 10 10 N 10 4.99 0.70 108.50 113.49 B B B O4' C1' N1 U U U 11 11 11 N model building X-PLOR refinement X-PLOR phasing X-PLOR NMR SOLUTION STRUCTURE OF A PEPTIDE NUCLEIC ACID COMPLEXED WITH RNA 1 N N 2 N N covale 1.339 both A GPN 1 A C GPN 1 1_555 A APN 2 A N APN 2 1_555 covale 1.337 both A APN 2 A C APN 2 1_555 A APN 3 A N APN 3 1_555 covale 1.336 both A APN 3 A C APN 3 1_555 A CPN 4 A N CPN 4 1_555 covale 1.340 both A CPN 4 A C CPN 4 1_555 A TPN 5 A N TPN 5 1_555 covale 1.337 both A TPN 5 A C TPN 5 1_555 A CPN 6 A N CPN 6 1_555 hydrog WATSON-CRICK A GPN 1 A N1 GPN 1 1_555 B C 12 B N3 C 6 1_555 hydrog WATSON-CRICK A GPN 1 A N2 GPN 1 1_555 B C 12 B O2 C 6 1_555 hydrog WATSON-CRICK A GPN 1 A O6 GPN 1 1_555 B C 12 B N4 C 6 1_555 hydrog WATSON-CRICK A APN 2 A N1 APN 2 1_555 B U 11 B N3 U 5 1_555 hydrog WATSON-CRICK A APN 2 A N6 APN 2 1_555 B U 11 B O4 U 5 1_555 hydrog WATSON-CRICK A APN 3 A N1 APN 3 1_555 B U 10 B N3 U 4 1_555 hydrog WATSON-CRICK A APN 3 A N6 APN 3 1_555 B U 10 B O4 U 4 1_555 hydrog WATSON-CRICK A CPN 4 A N3 CPN 4 1_555 B G 9 B N1 G 3 1_555 hydrog WATSON-CRICK A CPN 4 A N4 CPN 4 1_555 B G 9 B O6 G 3 1_555 hydrog WATSON-CRICK A CPN 4 A O2 CPN 4 1_555 B G 9 B N2 G 3 1_555 hydrog WATSON-CRICK A TPN 5 A N3 TPN 5 1_555 B A 8 B N1 A 2 1_555 hydrog WATSON-CRICK A TPN 5 A O4 TPN 5 1_555 B A 8 B N6 A 2 1_555 hydrog WATSON-CRICK A CPN 6 A N3 CPN 6 1_555 B G 7 B N1 G 1 1_555 hydrog WATSON-CRICK A CPN 6 A N4 CPN 6 1_555 B G 7 B O6 G 1 1_555 hydrog WATSON-CRICK A CPN 6 A O2 CPN 6 1_555 B G 7 B N2 G 1 1_555 PEPTIDE NUCLEIC ACID/RNA RNA, PNA, DOUBLE HELIX, PEPTIDE NUCLEIC ACID-RNA COMPLEX 176D PDB 1 176D 176D PDB 2 176D 1 6 176D 1 6 176D A 1 1 6 7 12 176D 7 12 176D B 2 1 6 1 P 1