1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Davidson, A. Leeper, T.C. Varani, G. 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 C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C5 H9 N O2 115.130 D-PROLINE D-peptide linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking C5 H11 N O2 117.146 y VALINE L-peptide 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 N N 39 S C N 40 N C N 41 N O N 42 N C N 43 N C N 44 N C N 45 N N N 46 N C N 47 N N N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H 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 O N 66 N P N 67 N O N 68 N O N 69 N O N 70 N C N 71 R C N 72 N O N 73 S C N 74 N O N 75 R C N 76 N O N 77 R C N 78 N N N 79 N C N 80 N O N 81 N N N 82 N C N 83 N N N 84 N C N 85 N C N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N N N 101 R C N 102 N C N 103 N C N 104 N C N 105 N C N 106 N O N 107 N O 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 O N 118 N P 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 R C N 128 N O N 129 R C Y 130 N N Y 131 N C Y 132 N N Y 133 N C N 134 N C N 135 N O N 136 N N N 137 N C N 138 N N N 139 N N Y 140 N C 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 N N 156 N C N 157 N C N 158 N O N 159 N O N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N N N 166 S C N 167 N C N 168 N O N 169 S C N 170 N C N 171 N C N 172 N C N 173 N O 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 H N 184 N H N 185 N H N 186 N H N 187 N N N 188 S C N 189 N C N 190 N O N 191 N C N 192 N C N 193 N C N 194 N C N 195 N N N 196 N O N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H 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 N N 213 S C N 214 N C N 215 N O N 216 N C N 217 N C N 218 N C N 219 N O 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 H N 229 N N N 230 S C N 231 N C N 232 N O N 233 R C N 234 N O N 235 N C N 236 N O 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 O N 247 N P N 248 N O N 249 N O N 250 N O N 251 N C N 252 R C N 253 N O N 254 S C N 255 N O N 256 R C N 257 N O N 258 R C N 259 N N N 260 N C N 261 N O N 262 N N N 263 N C N 264 N O N 265 N C N 266 N C N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 N N N 281 S C N 282 N C N 283 N O N 284 N C N 285 N C N 286 N C N 287 N O N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N H N 296 N H N 297 N H N 298 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 sing N 45 N sing N 46 N doub 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 doub 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 doub 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 sing N 78 N sing N 79 N sing N 80 N sing 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 doub N 93 N sing N 94 N doub N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N doub 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 sing 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 doub N 122 N sing 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 Y 143 N sing Y 144 N sing Y 145 N doub N 146 N sing Y 147 N sing N 148 N sing Y 149 N doub N 150 N doub N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N doub 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 doub 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 doub 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 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 doub N 196 N sing N 197 N sing N 198 N sing 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 doub 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 sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N doub 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 sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N doub N 273 N sing N 274 N sing N 275 N sing N 276 N doub N 277 N sing N 278 N doub 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 doub 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 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 106 11931 11936 10.1073/pnas.0900629106 19584251 Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein 2009 10.2210/pdb2kdq/pdb pdb_00002kdq 1768.189 L-22 CYCLIC PEPTIDE 1 syn polymer 9307.555 HIV-1 TAR RNA 1 syn polymer no yes RVRTRKGRRIRI(DPR)P RVRTRKGRRIRIPP A polypeptide(L) no no GGCAGAUCUGAGCCUGGGAGCUCUCUGCC GGCAGAUCUGAGCCUGGGAGCUCUCUGCC B polyribonucleotide 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 -0.847 1 19 B 17 B 45 -2.191 B_G17:C45_B 1 0.785 -1.355 -0.016 -0.827 20.864 1 19 B 18 B 44 -2.020 B_G18:C44_B 2 -13.864 -1.394 0.419 -0.848 8.996 1 19 B 19 B 43 3.927 B_C19:G43_B 3 -8.524 -0.587 -0.188 -0.050 1.792 1 20 B 20 B 42 10.487 B_A20:U42_B 4 16.070 0.098 -0.092 -0.316 -6.343 1 19 B 21 B 41 3.720 B_G21:C41_B 5 -1.021 -0.363 0.018 -0.083 3.173 1 20 B 22 B 40 -7.385 B_A22:U40_B 6 8.850 1.233 -0.228 -0.296 -8.439 1 19 B 26 B 39 6.317 B_G26:C39_B 7 17.973 0.674 -0.079 -0.140 0.475 1 20 B 27 B 38 -2.452 B_A27:U38_B 8 9.461 -0.845 -0.245 -0.611 2.466 1 19 B 28 B 37 -7.370 B_G28:C37_B 9 22.094 0.375 -0.313 -0.224 10.355 1 19 B 29 B 36 9.566 B_C29:G36_B 10 29.734 -0.097 0.016 -0.269 3.125 35.071 B B 17 18 28.923 B B 45 44 2.950 16.756 0.244 1.120 BB_G17G18:C44C45_BB 1 -0.881 1.520 30.909 -0.634 -0.537 4.531 39.015 B B 18 19 1.278 B B 44 43 4.443 0.852 1.097 -0.061 BB_G18C19:G43C44_BB 2 4.234 -6.351 38.784 -0.233 -0.940 3.209 50.640 B B 19 20 35.053 B B 43 42 3.817 28.330 0.359 0.145 BB_C19A20:U42G43_BB 3 -7.419 9.179 41.776 -2.224 -1.046 4.665 32.758 B B 20 21 -7.418 B B 42 41 4.696 -4.169 -0.218 -0.256 BB_A20G21:C41U42_BB 4 2.339 -4.161 32.416 0.580 0.966 3.240 42.366 B B 21 22 18.046 B B 41 40 3.678 12.805 -0.454 -0.588 BB_G21A22:U40C41_BB 5 6.551 -9.232 39.956 -2.241 1.358 3.719 43.186 B B 22 26 9.277 B B 40 39 3.671 6.748 -1.173 -0.514 BB_A22G26:C39U40_BB 6 -9.789 13.458 41.593 -1.461 0.486 3.933 22.142 B B 26 27 -19.817 B B 39 38 3.608 -7.465 -0.729 -1.611 BB_G26A27:U38C39_BB 7 0.148 -0.393 20.860 -0.824 1.965 2.334 45.472 B B 27 28 13.338 B B 38 37 2.784 10.224 -0.443 -1.909 BB_A27G28:C37U38_BB 8 -2.973 3.879 44.272 -3.186 0.365 2.349 24.880 B B 28 29 20.460 B B 37 36 3.110 8.572 -0.151 -1.576 BB_G28C29:G36C37_BB 9 -5.200 12.413 22.800 -5.904 -1.012 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_ref_seq chem_comp_atom chem_comp_bond pdbx_entry_details pdbx_modification_feature repository Initial release Version format compliance Data collection Database references Derived calculations Data collection Structure summary 1 0 2009-06-23 1 1 2011-07-13 1 2 2022-03-16 1 3 2024-10-30 _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_atom_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_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end BIV TAR and cyclic peptide mimicking BIV Tat Unbound L-22 solution structure BMRB Y PDBJ 2009-01-14 REL REL THE L-22 PEPTIDE WAS SYNTHESIZED BY SOLID PHASE SYNTHESIS AND PURIFIED BY REVERSE PHASE HPLC sample RNA WAS TRANSCRIBED IN VITRO FROM DNA OLIGONUCLEOTIDE TEMPLATES WITH T7 RNA POLYMERASE PURIFIED IN HOUSE WITH UNLABELED OR 13C/15N ENRICHED NTPS (ISOTEC) AND PURIFIED BY DENATURING PAGE. sample Y A ARG 1 Non-standard linkage N A ARG 1 A PRO 14 C A PRO 14 1_555 1_555 None Lowest energy, least restraint violations 100 10 7 3D-13C HMQC NOESY, 3D HCCH TOCSY, IPAP-HSQC 15N HSQC 2D noesy 2D watergate NOESY F1fF2f-type noesy, F1fF2f-type tocsy, 2D HCCH-COSY 2D 1H-1H NOESY F1fF2f-type watergate noesy 1.0 mM 1.0 mM 1.0 mM 1.0 mM 1.0 mM [U-98% 13C; U-98% 15N] 1.0 mM 1.0 mM [U-98% 13C; U-98% 15N] 1.0 mM 1.0 mM [U-2H] 1.0 mM 10 mM potassium phosphate 6.6 ambient 298 K 10 mM potassium phosphate 6.6 ambient 277 K Structures of the HIV-1 TAR RNA/L-22 complex were calculated with Xplor-NIH. Backbone dihedral angle restraints for the peptide were estimated using chemical shift data and TALOS. Structures were originally calculated without RDCs to test for convergence and adherence to the NOE data. RDC restraints were then applied as susceptibility anisotropy restraints with a harmonic potential well. simulated annealing 1 lowest energy 1.0mM HIV-1 TAR RNA-1, 1.0mM L-22 CYCLIC PEPTIDE-2, 100% D2O 100% D2O 1.0mM HIV-1 TAR RNA-3, 1.0mM L-22 CYCLIC PEPTIDE-4, 90 % H2O, 10% D2O 90% H2O/10% D2O 1.0mM [U-98% 13C; U-98% 15N] HIV-1 TAR RNA-5, 1.0mM L-22 CYCLIC PEPTIDE-6, 100% D2O 100% D2O 1.0mM [U-98% 13C; U-98% 15N] HIV-1 TAR RNA-7, 1.0mM L-22 CYCLIC PEPTIDE-8, 90 % H2O, 10% D2O 90% H2O/10% D2O 1.0mM [U-2H] HIV-1 TAR RNA-9, 1.0mM L-22 CYCLIC PEPTIDE-10, 100% D2O 100% D2O C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore structure solution X-PLOR NIH 2.16.0 Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRPipe Bruker Biospin collection TopSpin Cornilescu, Delaglio and Bax data analysis TALOS Goddard peak picking Sparky C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore refinement X-PLOR NIH 2.16.0 500 Bruker DRX Bruker DRX 600 Bruker DMX Bruker DMX 800 Varian INOVA Varian Inova 600 Bruker AVIII Bruker AVIII ARG 1 n 1 ARG 1 A VAL 2 n 2 VAL 2 A ARG 3 n 3 ARG 3 A THR 4 n 4 THR 4 A ARG 5 n 5 ARG 5 A LYS 6 n 6 LYS 6 A GLY 7 n 7 GLY 7 A ARG 8 n 8 ARG 8 A ARG 9 n 9 ARG 9 A ILE 10 n 10 ILE 10 A ARG 11 n 11 ARG 11 A ILE 12 n 12 ILE 12 A DPR 13 n 13 DPR 13 A PRO 14 n 14 PRO 14 A G 17 n 1 G 17 B G 18 n 2 G 18 B C 19 n 3 C 19 B A 20 n 4 A 20 B G 21 n 5 G 21 B A 22 n 6 A 22 B U 23 n 7 U 23 B C 24 n 8 C 24 B U 25 n 9 U 25 B G 26 n 10 G 26 B A 27 n 11 A 27 B G 28 n 12 G 28 B C 29 n 13 C 29 B C 30 n 14 C 30 B U 31 n 15 U 31 B G 32 n 16 G 32 B G 33 n 17 G 33 B G 34 n 18 G 34 B A 35 n 19 A 35 B G 36 n 20 G 36 B C 37 n 21 C 37 B U 38 n 22 U 38 B C 39 n 23 C 39 B U 40 n 24 U 40 B C 41 n 25 C 41 B U 42 n 26 U 42 B G 43 n 27 G 43 B C 44 n 28 C 44 B C 45 n 29 C 45 B author_defined_assembly 2 dimeric 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 A N ARG 5 A N ARG 5 A O ARG 8 A O ARG 8 1 B B H3' H5' C U 24 25 1.25 1 B B H4' H5' G G 32 33 1.29 1 B B H2' H8 A G 27 28 1.30 1 A A HH21 HH12 ARG ARG 1 3 1.34 1 B B HO2' OP1 G A 34 35 1.42 1 B B OP1 HO2' C U 24 25 1.47 1 A A O H ARG ARG 5 8 1.50 1 B B HO2' O4' G C 18 19 1.52 1 B B N1 H3 A U 20 42 1.53 1 B B O4 H62 U A 23 27 1.55 1 B B OP2 HO2' U G 31 32 1.56 1 B B H4' O5' G G 33 34 1.56 1 A B O H2' ARG G 9 34 1.58 1 B B H3 N7 U A 23 27 1.59 2 B B H1' H1 G G 32 34 1.14 2 A B HH22 H3' ARG G 9 34 1.17 2 A B HH22 H3' ARG A 5 27 1.22 2 A B HH22 H8 ARG A 3 22 1.23 2 B B H5' H5' C U 24 25 1.24 2 B B O2' H5' G C 28 29 1.53 2 B B O4 H62 U A 23 27 1.53 2 B B HO2' OP1 U G 25 26 1.56 3 A B HH21 H2' ARG G 9 33 1.14 3 B B H2' H6 G C 36 37 1.32 3 B B HO2' O4' C U 39 40 1.44 3 B B O2' H5' A G 27 28 1.50 3 B B HO2' O3' G G 32 33 1.54 3 B B O4 H62 U A 23 27 1.57 3 B B H3 N7 U A 23 27 1.58 3 B B O6 H1 G G 28 34 1.58 3 A A N O ARG PRO 1 14 2.19 4 B B H5'' H5' C U 24 25 1.18 4 A A HH11 HH22 ARG ARG 9 11 1.23 4 B B H2' H4' G G 32 34 1.29 4 A B HE O3' ARG G 11 34 1.40 4 A B O H3' THR U 4 23 1.50 4 B B O2' H5' A G 27 28 1.50 4 B B HO2' O5' C U 39 40 1.53 4 B B O4 H62 U A 23 27 1.54 4 B B H4' OP1 A G 35 36 1.55 4 A A O H ARG ILE 1 12 1.57 4 A A O H ARG ARG 5 8 1.57 4 B B O2' H5' C U 37 38 1.58 4 A B NE O3' ARG G 11 34 2.16 5 A B HH22 H8 ARG A 3 22 1.11 5 B B H1' H5'' G G 32 33 1.17 5 B B H2' H6 G C 36 37 1.27 5 B B H3' H42 G C 28 30 1.29 5 B B H1' H3' G G 32 33 1.32 5 A B HH22 O2' ARG G 9 34 1.40 5 B B O2' H5' C U 37 38 1.51 5 B B O4 H62 U A 23 27 1.54 5 B B HO2' OP1 G G 33 34 1.55 5 B B O2' H5' A G 27 28 1.57 5 A B HH12 O2' ARG G 9 34 1.57 5 B B O2' H5' G C 28 29 1.58 6 A B HH22 H5'' ARG G 8 33 1.09 6 B B H5' H2' C U 24 25 1.18 6 A B HH12 HO2' ARG G 11 34 1.19 6 B B HO2' H5' G G 32 33 1.28 6 A B HE O2' ARG G 9 34 1.32 6 B B H4' H5 C U 30 31 1.35 6 B B HO2' O4' C U 39 40 1.41 6 A B HE OP2 ARG U 3 23 1.44 6 B B O2' H5' G C 28 29 1.52 6 A B H OP2 LYS C 6 24 1.53 6 B B O2' H5' A G 27 28 1.54 6 B B HO2' O4' U C 38 39 1.57 6 B B H3 N7 U A 23 27 1.60 7 A A HH21 HH21 ARG ARG 9 11 1.24 7 A A HH11 H ARG ARG 8 9 1.26 7 B B HO2' O5' G C 18 19 1.44 7 A A O H ARG ARG 5 8 1.53 7 B B O2' H5' A G 27 28 1.54 7 B B O4 H62 U A 23 27 1.54 7 B B HO2' O4' U C 38 39 1.58 8 A A HH21 HH21 ARG ARG 9 11 1.15 8 B B H3' H6 C U 24 25 1.23 8 B B HO2' H4' U C 23 24 1.32 8 A B HH22 N7 ARG A 1 22 1.48 8 A A O H ARG ARG 5 8 1.50 8 B B O4 H62 U A 23 27 1.51 8 B B HO2' O4' C U 39 40 1.51 8 B B O2' H5' C U 37 38 1.52 8 B B O2' H5' A G 27 28 1.52 8 B B O2' H5' G C 28 29 1.56 8 A B HE O2' ARG G 11 34 1.59 9 A B HH22 H8 ARG A 3 22 1.24 9 A B HE H5' ARG G 9 34 1.27 9 A A O H ARG ARG 5 8 1.42 9 B B O2' H5' A G 27 28 1.52 9 B B OP2 H2' C U 24 25 1.53 9 A A O H ARG ILE 1 12 1.57 9 B B O4 H62 U A 23 27 1.58 9 B B H3 N7 U A 23 27 1.59 9 B B O2' H5' C U 37 38 1.59 9 B B N1 H3 A U 20 42 1.59 10 A B HH21 H2' ARG G 9 34 1.23 10 A B HE H2' ARG U 8 31 1.25 10 B B H1' H5'' G G 32 34 1.26 10 A B HH22 H8 ARG G 9 32 1.28 10 A B HE H5 ARG U 3 23 1.29 10 B B H1 H41 G C 21 41 1.32 10 A A O H ARG ARG 5 8 1.41 10 B B O4 H62 U A 23 27 1.52 10 B B O2' H5' G C 28 29 1.58 10 B B O2 H2' U G 23 26 1.59 10 A A N O ARG PRO 1 14 2.15 8 B G 34 0.060 SIDE CHAIN 9 B G 34 0.053 SIDE CHAIN 1 -8.45 1.40 115.20 106.75 B B B C5' C4' C3' C C C 24 24 24 N 3 -10.91 1.40 115.20 104.29 B B B C5' C4' C3' A A A 35 35 35 N 5 -8.46 1.40 115.20 106.74 B B B C5' C4' C3' U U U 23 23 23 N 6 -8.49 1.40 115.20 106.71 B B B C5' C4' C3' U U U 23 23 23 N 6 -8.42 1.40 115.20 106.78 B B B C5' C4' C3' G G G 34 34 34 N 10 -8.46 1.40 115.20 106.74 B B B C5' C4' C3' C C C 24 24 24 N 10 -8.58 1.40 115.20 106.62 B B B C5' C4' C3' G G G 33 33 33 N 3 B B C4' C3' G G 34 34 0.090 0.011 1.527 1.617 N 2 A DPR 13 58.61 -108.43 3 A LYS 6 40.88 27.64 4 A LYS 6 40.54 28.45 4 A DPR 13 59.49 -108.72 5 A ARG 9 -65.91 93.62 6 A LYS 6 40.04 29.30 7 A LYS 6 38.71 29.13 8 A LYS 6 38.61 43.71 9 A LYS 6 42.89 28.17 9 A DPR 13 56.21 -103.56 10 A LYS 6 45.42 25.71 10 A DPR 13 48.71 -105.53 lowest energy, model 7 Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimic of Tat protein 1 N N 2 N N covale 1.313 both A ARG 1 A N ARG 1 1_555 A PRO 14 A C PRO 14 1_555 covale 1.309 both A ILE 12 A C ILE 12 1_555 A DPR 13 A N DPR 13 1_555 covale 1.306 both A DPR 13 A C DPR 13 1_555 A PRO 14 A N PRO 14 1_555 hydrog WATSON-CRICK B G 17 B N1 G 1 1_555 B C 45 B N3 C 29 1_555 hydrog WATSON-CRICK B G 17 B N2 G 1 1_555 B C 45 B O2 C 29 1_555 hydrog WATSON-CRICK B G 17 B O6 G 1 1_555 B C 45 B N4 C 29 1_555 hydrog WATSON-CRICK B G 18 B N1 G 2 1_555 B C 44 B N3 C 28 1_555 hydrog WATSON-CRICK B G 18 B N2 G 2 1_555 B C 44 B O2 C 28 1_555 hydrog WATSON-CRICK B G 18 B O6 G 2 1_555 B C 44 B N4 C 28 1_555 hydrog WATSON-CRICK B C 19 B N3 C 3 1_555 B G 43 B N1 G 27 1_555 hydrog WATSON-CRICK B C 19 B N4 C 3 1_555 B G 43 B O6 G 27 1_555 hydrog WATSON-CRICK B C 19 B O2 C 3 1_555 B G 43 B N2 G 27 1_555 hydrog WATSON-CRICK B A 20 B N1 A 4 1_555 B U 42 B N3 U 26 1_555 hydrog WATSON-CRICK B A 20 B N6 A 4 1_555 B U 42 B O4 U 26 1_555 hydrog WATSON-CRICK B G 21 B N1 G 5 1_555 B C 41 B N3 C 25 1_555 hydrog WATSON-CRICK B G 21 B N2 G 5 1_555 B C 41 B O2 C 25 1_555 hydrog WATSON-CRICK B G 21 B O6 G 5 1_555 B C 41 B N4 C 25 1_555 hydrog WATSON-CRICK B A 22 B N1 A 6 1_555 B U 40 B N3 U 24 1_555 hydrog WATSON-CRICK B A 22 B N6 A 6 1_555 B U 40 B O4 U 24 1_555 hydrog HOOGSTEEN B U 23 B N3 U 7 1_555 B A 27 B N7 A 11 1_555 hydrog HOOGSTEEN B U 23 B O4 U 7 1_555 B A 27 B N6 A 11 1_555 hydrog WATSON-CRICK B G 26 B N1 G 10 1_555 B C 39 B N3 C 23 1_555 hydrog WATSON-CRICK B G 26 B N2 G 10 1_555 B C 39 B O2 C 23 1_555 hydrog WATSON-CRICK B G 26 B O6 G 10 1_555 B C 39 B N4 C 23 1_555 hydrog WATSON-CRICK B A 27 B N1 A 11 1_555 B U 38 B N3 U 22 1_555 hydrog WATSON-CRICK B A 27 B N6 A 11 1_555 B U 38 B O4 U 22 1_555 hydrog WATSON-CRICK B G 28 B N1 G 12 1_555 B C 37 B N3 C 21 1_555 hydrog WATSON-CRICK B G 28 B N2 G 12 1_555 B C 37 B O2 C 21 1_555 hydrog WATSON-CRICK B G 28 B O6 G 12 1_555 B C 37 B N4 C 21 1_555 hydrog G-U MISPAIR B G 28 B O6 G 12 1_555 B U 38 B N3 U 22 1_555 hydrog WATSON-CRICK B C 29 B N3 C 13 1_555 B G 32 B N1 G 16 1_555 hydrog WATSON-CRICK B C 29 B N4 C 13 1_555 B G 32 B O6 G 16 1_555 hydrog WATSON-CRICK B C 29 B O2 C 13 1_555 B G 32 B N2 G 16 1_555 hydrog WATSON-CRICK B C 29 B N3 C 13 1_555 B G 36 B N1 G 20 1_555 hydrog WATSON-CRICK B C 29 B N4 C 13 1_555 B G 36 B O6 G 20 1_555 hydrog WATSON-CRICK B C 29 B O2 C 13 1_555 B G 36 B N2 G 20 1_555 RNA binding protein/RNA PEPTIDOMIMETICS, PEPTIDE STRUCTURE, RNA RECOGNITION, IMMUNODEFICIENCY VIRUS, TAR RNA, mimic of RNA binding protein, RNA binding protein-RNA COMPLEX 2KDQ PDB 1 1 2KDQ RVRTRKGRRIRIPP 2KDQ PDB 2 1 2KDQ GGCAGAUCUGAGCCUGGGAGCUCUCUGCC 1 14 2KDQ 1 14 2KDQ A 1 1 14 17 45 2KDQ 17 45 2KDQ B 2 1 29 2 anti-parallel A VAL 2 A VAL 2 A ARG 5 A ARG 5 A ARG 8 A ARG 8 A ARG 11 A ARG 11 1 P 1