1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Matsugami, A. Kobayashi, S. Ouhashi, K. Uesugi, S. Yamamoto, R. Taira, K. Nishikawa, S. Kumar, P.K.R. Katahira, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 C6 H15 N4 O2 1 175.209 n 2-AMINO-5-GUANIDINO-PENTANOIC ACID L-argininium(2+); L-argininediium L-peptide linking 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 O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 R C N 49 N O N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 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 O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 R C N 84 N O N 85 R C Y 86 N N Y 87 N C Y 88 N N Y 89 N C N 90 N C N 91 N O N 92 N N N 93 N C N 94 N N N 95 N N Y 96 N C 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 H N 111 S C N 112 N C N 113 N C N 114 N C N 115 N N N 116 N C N 117 N N N 118 N N N 119 N C N 120 N O N 121 N O N 122 N N N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H 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 O N 139 N P N 140 N O N 141 N O N 142 N O N 143 N C N 144 R C N 145 N O N 146 S C N 147 N O N 148 R C N 149 N O N 150 R C N 151 N N N 152 N C N 153 N O N 154 N N N 155 N C N 156 N O N 157 N C N 158 N C N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H 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 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 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 doub 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 doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub 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 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 Y 100 N sing Y 101 N sing Y 102 N doub N 103 N sing Y 104 N sing N 105 N sing Y 106 N doub N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing 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 sing N 128 N sing N 129 N sing N 130 N sing N 131 N doub N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N doub 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 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 sing 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 doub N 169 N sing N 170 N sing N 171 N sing N 172 N doub N 173 N sing N 174 N doub N 175 N sing N 176 N sing UK Structure STRUE6 2005 0969-2126 11 533 545 10.1016/S0969-2126(03)00069-8 12737819 Structural Basis of the Highly Efficient Trapping of the HIV Tat Protein by an RNA Aptamer 2003 10.2210/pdb1nbk/pdb pdb_00001nbk 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 10921.535 RNA aptamer 1 syn polymer 175.209 2-AMINO-5-GUANIDINO-PENTANOIC ACID 2 syn non-polymer no no GGGAGCUUGAUCCCGGAAACGGUCGAUCGCUCCC GGGAGCUUGAUCCCGGAAACGGUCGAUCGCUCCC A 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 4.019 1 19 A 1 A 34 -3.324 A_G1:C34_A 1 -1.217 -0.068 0.336 0.043 -0.026 1 19 A 2 A 33 -9.481 A_G2:C33_A 2 -2.743 -0.093 0.079 -0.338 -13.348 1 19 A 3 A 32 -14.224 A_G3:C32_A 3 -3.025 0.452 -0.803 -0.186 9.392 1 20 A 4 A 31 -10.397 A_A4:U31_A 4 6.216 0.861 0.258 0.110 5.522 1 19 A 5 A 30 -0.730 A_G5:C30_A 5 -1.224 0.600 -0.399 -0.136 10.335 1 19 A 6 A 29 -10.815 A_C6:G29_A 6 -11.134 0.636 0.006 -0.535 0.035 1 19 A 9 A 28 -9.242 A_G9:C28_A 7 -2.691 -0.284 0.268 -0.344 17.705 1 20 A 10 A 27 3.553 A_A10:U27_A 8 3.601 -0.052 -0.007 -0.253 -0.559 1 20 A 11 A 26 -0.874 A_U11:A26_A 9 -0.866 -0.580 -0.025 -0.067 0.424 1 19 A 12 A 25 -10.028 A_C12:G25_A 10 -1.160 -0.156 -0.148 -0.234 -12.621 1 19 A 13 A 22 1.077 A_C13:G22_A 11 -19.756 0.706 -0.741 -0.821 -10.232 1 19 A 14 A 21 0.095 A_C14:G21_A 12 12.854 -0.077 0.348 -0.007 45.560 1 19 A 15 A 20 -13.307 A_G15:C20_A 13 28.313 -0.141 -0.159 -0.373 6.972 10 11 A 16 A 19 -18.262 A_G16:A19_A 14 -28.147 6.810 0.201 -4.793 3.291 50.868 A A 1 2 22.929 A A 34 33 3.626 19.101 -1.822 -1.133 AA_G1G2:C33C34_AA 1 -11.718 14.067 45.964 -2.817 1.202 1.018 31.605 A A 2 3 43.175 A A 33 32 4.068 21.332 0.083 -2.917 AA_G2G3:C32C33_AA 2 5.749 -11.635 22.743 -8.963 0.821 2.946 43.547 A A 3 4 -21.731 A A 32 31 2.730 -15.787 0.942 -1.153 AA_G3A4:U31C32_AA 3 -0.671 0.923 40.709 -0.183 -1.328 2.712 22.847 A A 4 5 19.467 A A 31 30 3.765 7.485 -0.501 -1.848 AA_A4G5:C30U31_AA 4 5.769 -15.005 20.824 -7.436 3.401 2.628 36.495 A A 5 6 15.329 A A 30 29 3.020 9.483 -0.861 -1.436 AA_G5C6:G29C30_AA 5 -3.484 5.633 35.114 -3.449 0.951 2.712 55.217 A A 6 9 12.103 A A 29 28 3.327 11.143 -2.811 -1.888 AA_C6G9:C28G29_AA 6 4.162 -4.520 54.019 -2.651 3.262 2.964 18.521 A A 9 10 1.636 A A 28 27 3.015 0.526 0.310 -1.096 AA_G9A10:U27C28_AA 7 -0.920 2.859 18.491 -3.668 -1.419 5.232 36.507 A A 10 11 -19.745 A A 27 26 4.762 -12.146 -0.663 -2.188 AA_A10U11:A26U27_AA 8 -1.203 1.955 34.472 -0.848 0.796 2.057 27.970 A A 11 12 25.604 A A 26 25 3.151 11.968 0.349 -1.779 AA_U11C12:G25A26_AA 9 -2.839 6.073 25.169 -6.067 -1.288 3.034 65.368 A A 12 13 16.828 A A 25 22 3.691 17.974 2.536 -1.450 AA_C12C13:G22G25_AA 10 -5.048 4.727 62.931 -2.123 -2.567 1.136 35.506 A A 13 14 51.731 A A 22 21 3.051 27.564 -0.041 -1.015 AA_C13C14:G21G22_AA 11 -5.231 9.818 21.982 -4.903 -0.547 2.376 28.448 A A 14 15 -18.423 A A 21 20 2.127 -8.877 -0.497 -0.994 AA_C14G15:C20G21_AA 12 -4.058 8.421 26.754 -0.577 0.350 5.957 51.170 A A 15 16 6.775 A A 20 19 6.065 5.840 -2.275 -1.214 AA_G15G16:A19C20_AA 13 -1.398 1.622 50.840 -2.149 2.456 database_2 pdbx_struct_assembly pdbx_struct_oper_list struct_site chem_comp_atom chem_comp_bond chem_comp pdbx_entity_src_syn repository Initial release Version format compliance Version format compliance Database references Derived calculations Data collection Source and taxonomy Structure summary 1 0 2003-12-03 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 1 4 2024-05-29 1 5 2024-09-18 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _chem_comp.mon_nstd_flag _chem_comp.pdbx_synonyms RCSB Y PDBJ 2002-12-03 REL GND 2-AMINO-5-GUANIDINO-PENTANOIC ACID 32630 synthetic construct sample 1 3D_15N-separated_NOESY 3D_13C-separated_NOESY 2D NOESY 2D NOESY 2D TOCSY DQF-COSY 1H-31P HetCor spin echo difference CT 1H-13C HSQC HNN-COSY HNN-COSY 6.7 ambient 278 K 6.7 ambient 308 K simulated annealing 1 lowest energy 1.7mM RNA U-15N,13C; 6.8mM argininamide; 10mM sodium phosphate buffer; 30mM NaCl; 0.1mM EDTA 95% H2O/5% D2O 1.7mM RNA U-15N,13C; 6.8mM argininamide; 10mM sodium phosphate buffer; 30mM NaCl; 0.1mM EDTA 100% D2O 1.7mM RNA; 6.8mM argininamide; 10mM sodium phosphate buffer; 30mM NaCl; 0.1mM EDTA 95% H2O/5% D2O 1.7mM RNA; 6.8mM argininamide; 10mM sodium phosphate buffer; 30mM NaCl; 0.1mM EDTA 100% D2O Brunger structure solution X-PLOR 3.851 Brunger refinement X-PLOR 3.851 600 Bruker DRX ARG 35 2 GND GND 35 A ARG 36 2 GND GND 36 A G 1 n 1 G 1 A G 2 n 2 G 2 A G 3 n 3 G 3 A A 4 n 4 A 4 A G 5 n 5 G 5 A C 6 n 6 C 6 A U 7 n 7 U 7 A U 8 n 8 U 8 A G 9 n 9 G 9 A A 10 n 10 A 10 A U 11 n 11 U 11 A C 12 n 12 C 12 A C 13 n 13 C 13 A C 14 n 14 C 14 A G 15 n 15 G 15 A G 16 n 16 G 16 A A 17 n 17 A 17 A A 18 n 18 A 18 A A 19 n 19 A 19 A C 20 n 20 C 20 A G 21 n 21 G 21 A G 22 n 22 G 22 A U 23 n 23 U 23 A C 24 n 24 C 24 A G 25 n 25 G 25 A A 26 n 26 A 26 A U 27 n 27 U 27 A C 28 n 28 C 28 A G 29 n 29 G 29 A C 30 n 30 C 30 A U 31 n 31 U 31 A C 32 n 32 C 32 A C 33 n 33 C 33 A C 34 n 34 C 34 A author_defined_assembly 1 monomeric 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 A A H21 OP2 G A 16 19 1.39 1 A A O6 H41 G C 2 33 1.42 1 A A N7 HH22 G GND 25 36 1.47 1 A A H41 O6 C G 12 25 1.48 1 A A H41 O6 C G 6 29 1.48 1 A A O6 H41 G C 9 28 1.51 1 A A O6 H41 G C 15 20 1.51 1 A A H41 O6 C G 13 22 1.53 1 A A O2' H5' A U 26 27 1.57 1 A A O6 H41 G C 3 32 1.58 1 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 1 1 1 N 1 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 1 1 1 N 1 4.51 0.50 113.10 117.61 A A A N7 C8 N9 G G G 2 2 2 N 1 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 G G G 2 2 2 N 1 4.53 0.50 113.10 117.63 A A A N7 C8 N9 G G G 3 3 3 N 1 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 G G G 3 3 3 N 1 3.71 0.50 113.80 117.51 A A A N7 C8 N9 A A A 4 4 4 N 1 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 5 5 5 N 1 -2.62 0.40 106.40 103.78 A A A C8 N9 C4 G G G 5 5 5 N 1 4.37 0.50 113.10 117.47 A A A N7 C8 N9 G G G 9 9 9 N 1 -2.76 0.40 106.40 103.64 A A A C8 N9 C4 G G G 9 9 9 N 1 3.70 0.50 113.80 117.50 A A A N7 C8 N9 A A A 10 10 10 N 1 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 15 15 15 N 1 -2.61 0.40 106.40 103.79 A A A C8 N9 C4 G G G 15 15 15 N 1 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 16 16 16 N 1 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 16 16 16 N 1 3.80 0.50 113.80 117.60 A A A N7 C8 N9 A A A 17 17 17 N 1 3.84 0.50 113.80 117.64 A A A N7 C8 N9 A A A 18 18 18 N 1 3.85 0.50 113.80 117.65 A A A N7 C8 N9 A A A 19 19 19 N 1 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 21 21 21 N 1 -2.62 0.40 106.40 103.78 A A A C8 N9 C4 G G G 21 21 21 N 1 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 22 22 22 N 1 -2.62 0.40 106.40 103.78 A A A C8 N9 C4 G G G 22 22 22 N 1 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 25 25 25 N 1 -2.70 0.40 106.40 103.70 A A A C8 N9 C4 G G G 25 25 25 N 1 3.70 0.50 113.80 117.50 A A A N7 C8 N9 A A A 26 26 26 N 1 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 29 29 29 N 1 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 29 29 29 N The structure of RNA aptamer for HIV Tat complexed with two argininamide molecules 1 N N 2 N N 2 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 34 A N3 C 34 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 34 A O2 C 34 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 34 A N4 C 34 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 33 A N3 C 33 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 33 A O2 C 33 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 33 A N4 C 33 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 A C 32 A N3 C 32 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 A C 32 A O2 C 32 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 A C 32 A N4 C 32 1_555 hydrog WATSON-CRICK A A 4 A N1 A 4 1_555 A U 31 A N3 U 31 1_555 hydrog WATSON-CRICK A A 4 A N6 A 4 1_555 A U 31 A O4 U 31 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 30 A N3 C 30 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 30 A O2 C 30 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 30 A N4 C 30 1_555 hydrog WATSON-CRICK A C 6 A N3 C 6 1_555 A G 29 A N1 G 29 1_555 hydrog WATSON-CRICK A C 6 A N4 C 6 1_555 A G 29 A O6 G 29 1_555 hydrog WATSON-CRICK A C 6 A O2 C 6 1_555 A G 29 A N2 G 29 1_555 hydrog HOOGSTEEN A U 7 A N3 U 7 1_555 A A 10 A N7 A 10 1_555 hydrog HOOGSTEEN A U 7 A O4 U 7 1_555 A A 10 A N6 A 10 1_555 hydrog WATSON-CRICK A G 9 A N1 G 9 1_555 A C 28 A N3 C 28 1_555 hydrog WATSON-CRICK A G 9 A N2 G 9 1_555 A C 28 A O2 C 28 1_555 hydrog WATSON-CRICK A G 9 A O6 G 9 1_555 A C 28 A N4 C 28 1_555 hydrog WATSON-CRICK A A 10 A N1 A 10 1_555 A U 27 A N3 U 27 1_555 hydrog WATSON-CRICK A A 10 A N6 A 10 1_555 A U 27 A O4 U 27 1_555 hydrog WATSON-CRICK A U 11 A N3 U 11 1_555 A A 26 A N1 A 26 1_555 hydrog WATSON-CRICK A U 11 A O4 U 11 1_555 A A 26 A N6 A 26 1_555 hydrog WATSON-CRICK A C 12 A N3 C 12 1_555 A G 25 A N1 G 25 1_555 hydrog WATSON-CRICK A C 12 A N4 C 12 1_555 A G 25 A O6 G 25 1_555 hydrog WATSON-CRICK A C 12 A O2 C 12 1_555 A G 25 A N2 G 25 1_555 hydrog WATSON-CRICK A C 13 A N3 C 13 1_555 A G 22 A N1 G 22 1_555 hydrog WATSON-CRICK A C 13 A N4 C 13 1_555 A G 22 A O6 G 22 1_555 hydrog WATSON-CRICK A C 13 A O2 C 13 1_555 A G 22 A N2 G 22 1_555 hydrog WATSON-CRICK A C 14 A N3 C 14 1_555 A G 21 A N1 G 21 1_555 hydrog WATSON-CRICK A C 14 A N4 C 14 1_555 A G 21 A O6 G 21 1_555 hydrog WATSON-CRICK A C 14 A O2 C 14 1_555 A G 21 A N2 G 21 1_555 hydrog WATSON-CRICK A G 15 A N1 G 15 1_555 A C 20 A N3 C 20 1_555 hydrog WATSON-CRICK A G 15 A N2 G 15 1_555 A C 20 A O2 C 20 1_555 hydrog WATSON-CRICK A G 15 A O6 G 15 1_555 A C 20 A N4 C 20 1_555 hydrog G-G MISPAIR A G 15 A N1 G 15 1_555 A G 21 A N3 G 21 1_555 hydrog TYPE_11_PAIR A G 16 A N2 G 16 1_555 A A 19 A N7 A 19 1_555 hydrog TYPE_11_PAIR A G 16 A N3 G 16 1_555 A A 19 A N6 A 19 1_555 hydrog HOOGSTEEN A U 23 A N3 U 23 1_555 A A 26 A N7 A 26 1_555 hydrog HOOGSTEEN A U 23 A O4 U 23 1_555 A A 26 A N6 A 26 1_555 RNA RNA-LIGANDS COMPLEX, BASE TRIPLE, RNA APTAMER, HIV TAT, RNA 1NBK PDB 1 1NBK 1 34 1NBK 1 34 1NBK A 1 1 34 BINDING SITE FOR RESIDUE GND A 35 A GND 35 Software 6 BINDING SITE FOR RESIDUE GND A 36 A GND 36 Software 7 A C 6 A C 6 6 1_555 A U 7 A U 7 6 1_555 A G 9 A G 9 6 1_555 A U 27 A U 27 6 1_555 A C 28 A C 28 6 1_555 A G 29 A G 29 6 1_555 A U 7 A U 7 7 1_555 A A 10 A A 10 7 1_555 A U 11 A U 11 7 1_555 A C 12 A C 12 7 1_555 A G 22 A G 22 7 1_555 A U 23 A U 23 7 1_555 A G 25 A G 25 7 1_555