1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Yang, Y.S. Kochoyan, M. Burgstaller, P. Westhof, E. Famulok, 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 C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C6 H13 N3 O3 175.186 n CITRULLINE L-peptide linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA 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 C N 74 N O N 75 N O N 76 S C N 77 N N N 78 N C N 79 N C N 80 N C N 81 N N N 82 N C N 83 N O N 84 N N N 85 N H 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 O N 99 N P N 100 N O N 101 N O N 102 N O N 103 N C N 104 R C N 105 N O N 106 S C N 107 N O N 108 R C N 109 N O N 110 R C Y 111 N N Y 112 N C Y 113 N N Y 114 N C N 115 N C N 116 N O N 117 N N N 118 N C N 119 N N N 120 N N Y 121 N C N 122 N H 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 O N 137 N P N 138 N O N 139 N O N 140 N O N 141 N C N 142 R C N 143 N O N 144 S C N 145 N O N 146 R C N 147 N O N 148 R C N 149 N N N 150 N C N 151 N O N 152 N N N 153 N C N 154 N O N 155 N C N 156 N C N 157 N H N 158 N H 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 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 doub 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 sing N 93 N sing N 94 N sing N 95 N sing N 96 N doub N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N doub 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 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 Y 124 N sing Y 125 N sing Y 126 N doub N 127 N sing Y 128 N sing N 129 N sing Y 130 N doub N 131 N doub N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N doub N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N doub 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 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 doub N 167 N sing N 168 N sing N 169 N sing N 170 N doub N 171 N sing N 172 N doub N 173 N sing N 174 N sing US Science SCIEAS 0038 0036-8075 272 1343 1347 8650546 Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. 1996 UK Nucleic Acids Res. NARHAD 0389 0305-1048 23 4769 Structural Probing and Damage Selection of Citrulline-and Arginine-Specific RNA Aptamers Identify Base Positions Required for Binding 1995 10.2210/pdb1kod/pdb pdb_00001kod 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3610.226 RNA (5'-R(P*AP*GP*AP*AP*GP*GP*AP*GP*UP*GP*U)-3') 1 syn polymer 4479.691 RNA (5'-R(P*AP*CP*GP*GP*UP*UP*AP*GP*GP*UP*CP*GP*CP*U)-3') 1 syn polymer 175.186 CITRULLINE 1 syn non-polymer no no AGAAGGAGUGU AGAAGGAGUGU A polyribonucleotide no no ACGGUUAGGUCGCU ACGGUUAGGUCGCU 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 -2.274 1 20 A 5 B 40 7.876 A_A5:U40_B 1 -8.721 -0.412 -2.167 -0.563 -9.481 1 A 7 B 39 21.580 A_A7:C39_B 2 12.823 -1.172 1.051 -0.577 -16.307 B 34 B 38 -141.160 B_G34:G38_B 3 30.454 -0.139 -1.222 3.948 26.579 1 A 10 B 37 10.281 A_G10:C37_B 4 0.032 -0.808 0.301 0.211 -22.278 A 11 B 30 160.737 A_A11:G30_B 5 49.070 -0.679 -0.058 -4.191 47.975 A 12 A 9 108.561 A_G12:G9_A 6 -19.965 1.457 -0.431 -4.929 -17.695 A 13 B 29 -75.134 A_U13:G29_B 7 -41.512 -3.568 -1.453 0.780 -16.697 1 19 A 14 B 28 -0.559 A_G14:C28_B 8 -5.923 -0.539 -1.499 -0.705 43.986 1 20 A 15 B 27 8.745 A_U15:A27_B 9 3.814 -0.643 -1.293 0.215 46.568 5 B 33 B 35 -122.402 B_A33:G35_B 10 0.416 -2.798 1.130 4.394 4.726 44.541 A A 5 7 30.052 B B 40 39 5.680 21.881 -0.805 -0.611 AA_A5A7:C39U40_BB 1 -0.365 0.501 39.035 -4.250 1.005 1.299 -173.147 A B 7 34 60.694 B B 39 38 0.380 -120.166 3.616 -0.555 AB_A7G34:G38C39_BB 2 -113.444 -57.299 -124.474 0.428 1.670 -2.306 -170.074 B A 34 10 8.571 B B 38 37 -3.573 -16.907 1.958 2.584 BA_G34G10:C37G38_BB 3 -155.756 -78.967 -129.333 -1.367 1.630 3.713 -58.941 A A 10 11 44.321 B B 37 30 4.208 -39.981 4.201 -0.180 AA_G10A11:G30C37_BB 4 -10.193 -11.299 -43.048 3.160 3.510 0.586 76.519 A A 11 12 41.883 B A 30 9 1.956 48.808 -1.084 -1.651 AA_A11G12:G9G30_AB 5 4.638 -3.980 60.688 -1.984 0.937 3.652 125.701 A A 12 13 1.837 A B 9 29 3.660 3.266 -0.264 -1.125 AA_G12U13:G29G9_BA 6 -17.726 9.972 124.966 -0.662 -0.016 3.742 22.682 A A 13 14 15.206 B B 29 28 3.687 5.905 0.850 0.457 AA_U13G14:C28G29_BB 7 2.081 -5.360 21.812 -1.314 -1.288 2.043 31.295 A A 14 15 21.181 B B 28 27 2.560 9.960 -1.076 -1.009 AA_G14U15:A27C28_BB 8 -22.683 48.238 19.274 -3.530 -1.786 database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list struct_site atom_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Database references Derived calculations Other Atomic model Data collection 1 0 1996-11-08 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-23 2 0 2023-11-15 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _atom_site.auth_atom_id _atom_site.label_atom_id 1 STRUCTURE Y BNL 1996-03-28 REL CIR CITRULLINE 1 WESTHOF,DUMAS,MORAS refinement NUCLSQ CIR 1 3 CIR CIR 1 B A 5 n 1 A 5 A G 6 n 2 G 6 A A 7 n 3 A 7 A A 8 n 4 A 8 A G 9 n 5 G 9 A G 10 n 6 G 10 A A 11 n 7 A 11 A G 12 n 8 G 12 A U 13 n 9 U 13 A G 14 n 10 G 14 A U 15 n 11 U 15 A A 27 n 1 A 27 B C 28 n 2 C 28 B G 29 n 3 G 29 B G 30 n 4 G 30 B U 31 n 5 U 31 B U 32 n 6 U 32 B A 33 n 7 A 33 B G 34 n 8 G 34 B G 35 n 9 G 35 B U 36 n 10 U 36 B C 37 n 11 C 37 B G 38 n 12 G 38 B C 39 n 13 C 39 B U 40 n 14 U 40 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 1 -9.26 1.50 119.60 110.34 A A A OP1 P OP2 A A A 5 5 5 N 1 4.85 0.80 101.50 106.35 A A A C3' C2' C1' A A A 5 5 5 N 1 3.85 0.50 113.80 117.65 A A A N7 C8 N9 A A A 5 5 5 N 1 4.97 0.80 101.50 106.47 A A A C3' C2' C1' G G G 6 6 6 N 1 4.63 0.50 113.10 117.73 A A A N7 C8 N9 G G G 6 6 6 N 1 -2.73 0.40 106.40 103.67 A A A C8 N9 C4 G G G 6 6 6 N 1 3.70 0.50 113.80 117.50 A A A N7 C8 N9 A A A 7 7 7 N 1 3.77 0.50 113.80 117.57 A A A N7 C8 N9 A A A 8 8 8 N 1 4.67 0.50 113.10 117.77 A A A N7 C8 N9 G G G 9 9 9 N 1 4.42 0.50 113.10 117.52 A A A N7 C8 N9 G G G 10 10 10 N 1 -2.86 0.40 106.40 103.54 A A A C8 N9 C4 G G G 10 10 10 N 1 3.99 0.50 113.80 117.79 A A A N7 C8 N9 A A A 11 11 11 N 1 4.61 0.70 108.50 113.11 A A A O4' C1' N9 G G G 12 12 12 N 1 4.45 0.50 113.10 117.55 A A A N7 C8 N9 G G G 12 12 12 N 1 -2.73 0.40 106.40 103.67 A A A C8 N9 C4 G G G 12 12 12 N 1 5.09 0.50 113.10 118.19 A A A N7 C8 N9 G G G 14 14 14 N 1 -2.76 0.40 106.40 103.64 A A A C8 N9 C4 G G G 14 14 14 N 1 4.91 0.80 101.50 106.41 A A A C3' C2' C1' U U U 15 15 15 N 1 -9.25 1.50 119.60 110.35 B B B OP1 P OP2 A A A 27 27 27 N 1 3.67 0.50 113.80 117.47 B B B N7 C8 N9 A A A 27 27 27 N 1 4.53 0.50 113.10 117.63 B B B N7 C8 N9 G G G 29 29 29 N 1 -2.79 0.40 106.40 103.61 B B B C8 N9 C4 G G G 29 29 29 N 1 4.90 0.80 101.50 106.40 B B B C3' C2' C1' G G G 30 30 30 N 1 4.32 0.50 113.10 117.42 B B B N7 C8 N9 G G G 30 30 30 N 1 -2.78 0.40 106.40 103.62 B B B C8 N9 C4 G G G 30 30 30 N 1 4.92 0.80 101.50 106.42 B B B C3' C2' C1' U U U 31 31 31 N 1 4.87 0.80 101.50 106.37 B B B C3' C2' C1' U U U 32 32 32 N 1 3.80 0.50 113.80 117.60 B B B N7 C8 N9 A A A 33 33 33 N 1 4.83 0.50 113.10 117.93 B B B N7 C8 N9 G G G 34 34 34 N 1 -2.95 0.40 106.40 103.45 B B B C8 N9 C4 G G G 34 34 34 N 1 6.08 0.70 108.50 114.58 B B B O4' C1' N9 G G G 35 35 35 N 1 5.47 0.50 113.10 118.57 B B B N7 C8 N9 G G G 35 35 35 N 1 -2.81 0.40 106.40 103.59 B B B C8 N9 C4 G G G 35 35 35 N 1 4.53 0.70 108.50 113.03 B B B O4' C1' N1 U U U 36 36 36 N 1 4.41 0.50 113.10 117.51 B B B N7 C8 N9 G G G 38 38 38 N 1 -2.52 0.40 106.40 103.88 B B B C8 N9 C4 G G G 38 38 38 N 1 5.42 0.80 101.50 106.92 B B B C3' C2' C1' C C C 39 39 39 N 1 4.40 0.70 108.50 112.90 B B B O4' C1' N1 C C C 39 39 39 N model building X-PLOR refinement X-PLOR phasing X-PLOR RNA APTAMER COMPLEXED WITH CITRULLINE, NMR 1 N N 2 N N 3 N N hydrog WATSON-CRICK A A 5 A N1 A 1 1_555 B U 40 B N3 U 14 1_555 hydrog WATSON-CRICK A A 5 A N6 A 1 1_555 B U 40 B O4 U 14 1_555 hydrog WATSON-CRICK A G 6 A N1 G 2 1_555 B C 39 B N3 C 13 1_555 hydrog WATSON-CRICK A G 6 A N2 G 2 1_555 B C 39 B O2 C 13 1_555 hydrog WATSON-CRICK A G 6 A O6 G 2 1_555 B C 39 B N4 C 13 1_555 hydrog G-U MISPAIR A G 6 A N1 G 2 1_555 B U 40 B O2 U 14 1_555 hydrog TYPE_8_PAIR A A 7 A N1 A 3 1_555 B G 38 B N1 G 12 1_555 hydrog TYPE_8_PAIR A A 7 A N6 A 3 1_555 B G 38 B O6 G 12 1_555 hydrog A-C MISPAIR A A 7 A N6 A 3 1_555 B C 39 B N3 C 13 1_555 hydrog G-G MISPAIR A G 9 A N1 G 5 1_555 A G 12 A N7 G 8 1_555 hydrog G-C PAIR A G 10 A N1 G 6 1_555 B C 37 B O2 C 11 1_555 hydrog A-G MISPAIR A A 11 A N6 A 7 1_555 B G 30 B O6 G 4 1_555 hydrog A-U PAIR A A 11 A N1 A 7 1_555 B U 36 B N3 U 10 1_555 hydrog TYPE_6_PAIR A G 12 A N1 G 8 1_555 B G 35 B O6 G 9 1_555 hydrog TYPE_6_PAIR A G 12 A N2 G 8 1_555 B G 35 B N7 G 9 1_555 hydrog U-G MISPAIR A U 13 A O4 U 9 1_555 B G 29 B N1 G 3 1_555 hydrog WATSON-CRICK A G 14 A N1 G 10 1_555 B C 28 B N3 C 2 1_555 hydrog WATSON-CRICK A G 14 A N2 G 10 1_555 B C 28 B O2 C 2 1_555 hydrog WATSON-CRICK A G 14 A O6 G 10 1_555 B C 28 B N4 C 2 1_555 hydrog WATSON-CRICK A U 15 A N3 U 11 1_555 B A 27 B N1 A 1 1_555 hydrog WATSON-CRICK A U 15 A O4 U 11 1_555 B A 27 B N6 A 1 1_555 hydrog A-G MISPAIR B A 33 B N3 A 7 1_555 B G 35 B N1 G 9 1_555 hydrog G-C PAIR B G 34 B O6 G 8 1_555 B C 37 B N4 C 11 1_555 hydrog G-G MISPAIR B G 34 B N1 G 8 1_555 B G 38 B O6 G 12 1_555 RNA IN VITRO SELECTED RNA, RNA APTAMER, RNA 1KOD PDB 1 1KOD 1KOD PDB 2 1KOD 5 15 1KOD 5 15 1KOD A 1 1 11 27 40 1KOD 27 40 1KOD B 2 1 14 BINDING SITE FOR RESIDUE CIR B 1 B CIR 1 Software 6 A G 12 A G 8 6 1_555 A U 13 A U 9 6 1_555 B G 30 B G 4 6 1_555 B U 31 B U 5 6 1_555 B A 33 B A 7 6 1_555 B G 35 B G 9 6 1_555 1 P 1