1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Katahira, M. Mashima, T. Matsugami, A. Nishikawa, F. Nishikawa, S. 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 C10 H14 N5 O8 P 363.221 y GUANOSINE-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 Y 51 N N Y 52 N C Y 53 N N Y 54 N C N 55 N C N 56 N O N 57 N N N 58 N C N 59 N N N 60 N N Y 61 N C 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 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 Y 64 N sing Y 65 N sing Y 66 N doub N 67 N sing Y 68 N sing N 69 N sing Y 70 N doub N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 37 6249 6258 10.1093/nar/gkp647 19666719 Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein 2009 10.2210/pdb2rqj/pdb pdb_00002rqj 4033.512 RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') 2 syn polymer no no GGAGGAGGAGGA GGAGGAGGAGGA A,B polyribonucleotide n n n n n n n n n n n n refined structure 0.376 3 6 A 2 A 11 97.799 A_G2:G11_A 1 -0.973 -0.643 0.170 -3.514 3.148 3 6 A 5 A 8 -88.943 A_G5:G8_A 2 0.249 0.339 -0.349 3.799 0.765 3 6 A 1 A 4 -86.907 A_G1:G4_A 3 -1.248 0.528 0.007 3.864 5.387 6 A 7 A 10 -98.276 A_G7:G10_A 4 5.868 1.300 -0.207 3.493 2.138 3 6 B 23 B 20 90.662 B_G23:G20_B 5 -0.033 -0.510 -0.014 -3.857 5.077 6 B 19 B 22 -98.053 B_G19:G22_B 6 8.231 1.116 -0.291 3.607 -1.580 3 6 B 16 B 13 88.183 B_G16:G13_B 7 0.798 -0.423 -0.009 -3.841 -0.088 176.433 A A 2 5 1.443 A A 11 8 -0.084 2.885 -1.158 -3.923 AA_G2G5:G8G11_AA 1 3.346 -1.674 176.431 -1.962 0.579 -3.216 -126.549 A A 5 1 -1.817 A A 8 4 -3.162 3.245 -0.096 3.744 AA_G5G1:G4G8_AA 2 -2.703 -1.513 -126.510 -2.070 -0.032 -3.179 -31.513 B B 23 19 4.046 B B 20 22 -3.201 -2.185 0.760 1.435 BB_G23G19:G22G20_BB 3 5.513 10.210 -30.963 -3.043 0.388 -0.054 174.977 B B 19 16 1.381 B B 22 13 -0.050 2.759 -0.832 -3.833 BB_G19G16:G13G22_BB 4 -0.668 0.334 174.976 -1.918 0.417 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list chem_comp_atom chem_comp_bond repository Initial release Version format compliance Data collection Database references Derived calculations Data collection 1 0 2009-11-17 1 1 2011-07-13 1 2 2022-03-16 1 3 2024-05-29 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name BMRB Y PDBJ 2009-07-18 REL REL structures with the lowest energy 200 9 1 2D 1H-1H NOESY 2D 1H-1H NOESY 2D 1H-1H NOESY 2D 1H-1H TOCSY 2D 1H-1H TOCSY 2D DQF-COSY 2D 1H-13C HSQC JRHMBC 1 mM 10 mM 100 mM 0.01 mM 3 mM 1 mM 10 mM 100 mM 0.01 mM 3 mM 0.1 6.2 ambient atm 278 K 0.1 6.2 ambient atm 303 K simulated annealing 1 lowest energy 1mM RNA-1, 10mM potassium phosphate-2, 100mM potassium chloride-3, 0.01mM DSS-4, 3mM sodium azide-5, 95% H2O/5% D2O 95% H2O/5% D2O 1mM RNA-6, 10mM potassium phosphate-7, 100mM potassium chloride-8, 0.01mM DSS-9, 3mM sodium azide-10, 95% H2O/5% D2O 100% D2O Schwieters, Kuszewski, Tjandra and Clore structure solution X-PLOR NIH 2.20 Bruker Biospin collection XwinNMR Bruker Biospin collection TopSpin Goddard chemical shift assignment Sparky Goddard peak picking Sparky Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRPipe Garrett chemical shift assignment PIPP Garrett peak picking PIPP Schwieters, Kuszewski, Tjandra and Clore refinement X-PLOR NIH 2.20 800 Bruker DRX Bruker DRX 600 Bruker DRX Bruker DRX G 1 n 1 G 1 A G 2 n 2 G 2 A A 3 n 3 A 3 A G 4 n 4 G 4 A G 5 n 5 G 5 A A 6 n 6 A 6 A G 7 n 7 G 7 A G 8 n 8 G 8 A A 9 n 9 A 9 A G 10 n 10 G 10 A G 11 n 11 G 11 A A 12 n 12 A 12 A G 13 n 1 G 13 B G 14 n 2 G 14 B A 15 n 3 A 15 B G 16 n 4 G 16 B G 17 n 5 G 17 B A 18 n 6 A 18 B G 19 n 7 G 19 B G 20 n 8 G 20 B A 21 n 9 A 21 B G 22 n 10 G 22 B G 23 n 11 G 23 B A 24 n 12 A 24 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 A A HO2' O5' G G 1 2 1.54 1 A A N7 H21 G G 1 10 1.59 1 B B N7 H21 G G 13 22 1.60 2 A A HO2' OP2 G G 1 2 1.49 2 A A N7 H21 G G 1 10 1.60 3 A B HO2' O2' G A 10 18 1.39 3 A A HO2' OP2 G G 1 2 1.50 3 A A HO2' N1 G A 4 6 1.51 3 B B N7 H21 G G 13 22 1.58 3 A A HO2' O5' G G 7 8 1.58 3 A A N7 H21 G G 1 10 1.59 4 A B O2' HO2' A G 6 22 1.41 4 A A N7 H21 G G 1 10 1.58 4 B B N7 H21 G G 13 22 1.59 5 B B HO2' N1 G A 16 18 1.41 5 A A N7 H21 G G 1 10 1.59 6 B B HO2' OP2 G G 13 14 1.48 6 B B HO2' O5' G A 23 24 1.52 6 B B O2' H5' G G 16 17 1.56 6 A B O2' HO2' G A 10 18 1.58 6 A A N7 H21 G G 1 10 1.59 6 A B O2' O2' A G 6 22 2.14 7 A A HO2' N1 G A 4 6 1.39 7 A A HO2' OP2 G G 1 2 1.39 7 B B N7 H21 G G 13 22 1.59 7 A A N7 H21 G G 1 10 1.60 8 A A OP1 H61 G A 2 3 1.49 8 B B N7 H21 G G 13 22 1.58 9 A B HO2' O2' A G 6 22 1.36 9 B B HO2' O5' G G 19 20 1.50 9 A A HO2' OP2 G G 7 8 1.57 9 A B O2' O2' A G 6 22 2.12 lowest energy, model 1 Quadruplex structure of an RNA aptamer against bovine prion protein 1 N N 1 N N hydrog TYPE_11_PAIR A G 1 A N2 G 1 1_555 A A 3 A N7 A 3 1_555 hydrog TYPE_11_PAIR A G 1 A N3 G 1 1_555 A A 3 A N6 A 3 1_555 hydrog TYPE_6_PAIR A G 1 A N1 G 1 1_555 A G 4 A O6 G 4 1_555 hydrog TYPE_6_PAIR A G 1 A N2 G 1 1_555 A G 4 A N7 G 4 1_555 hydrog TYPE_6_PAIR A G 1 A N7 G 1 1_555 A G 10 A N2 G 10 1_555 hydrog TYPE_6_PAIR A G 1 A O6 G 1 1_555 A G 10 A N1 G 10 1_555 hydrog TYPE_6_PAIR A G 2 A N1 G 2 1_555 A G 5 A O6 G 5 1_555 hydrog TYPE_6_PAIR A G 2 A N2 G 2 1_555 A G 5 A N7 G 5 1_555 hydrog TYPE_6_PAIR A G 2 A N7 G 2 1_555 A G 11 A N2 G 11 1_555 hydrog TYPE_6_PAIR A G 2 A O6 G 2 1_555 A G 11 A N1 G 11 1_555 hydrog TYPE_6_PAIR A G 4 A N1 G 4 1_555 A G 7 A O6 G 7 1_555 hydrog TYPE_6_PAIR A G 4 A N2 G 4 1_555 A G 7 A N7 G 7 1_555 hydrog TYPE_6_PAIR A G 5 A N1 G 5 1_555 A G 8 A O6 G 8 1_555 hydrog TYPE_6_PAIR A G 5 A N2 G 5 1_555 A G 8 A N7 G 8 1_555 hydrog TYPE_11_PAIR A G 7 A N2 G 7 1_555 A A 9 A N7 A 9 1_555 hydrog TYPE_11_PAIR A G 7 A N3 G 7 1_555 A A 9 A N6 A 9 1_555 hydrog TYPE_6_PAIR A G 7 A N1 G 7 1_555 A G 10 A O6 G 10 1_555 hydrog TYPE_6_PAIR A G 7 A N2 G 7 1_555 A G 10 A N7 G 10 1_555 hydrog TYPE_6_PAIR A G 8 A N1 G 8 1_555 A G 11 A O6 G 11 1_555 hydrog TYPE_6_PAIR A G 8 A N2 G 8 1_555 A G 11 A N7 G 11 1_555 hydrog TYPE_11_PAIR B G 13 B N2 G 1 1_555 B A 15 B N7 A 3 1_555 hydrog TYPE_11_PAIR B G 13 B N3 G 1 1_555 B A 15 B N6 A 3 1_555 hydrog TYPE_6_PAIR B G 13 B N1 G 1 1_555 B G 16 B O6 G 4 1_555 hydrog TYPE_6_PAIR B G 13 B N2 G 1 1_555 B G 16 B N7 G 4 1_555 hydrog TYPE_6_PAIR B G 13 B N7 G 1 1_555 B G 22 B N2 G 10 1_555 hydrog TYPE_6_PAIR B G 13 B O6 G 1 1_555 B G 22 B N1 G 10 1_555 hydrog TYPE_6_PAIR B G 14 B N1 G 2 1_555 B G 17 B O6 G 5 1_555 hydrog TYPE_6_PAIR B G 14 B N2 G 2 1_555 B G 17 B N7 G 5 1_555 hydrog TYPE_6_PAIR B G 14 B N7 G 2 1_555 B G 23 B N2 G 11 1_555 hydrog TYPE_6_PAIR B G 14 B O6 G 2 1_555 B G 23 B N1 G 11 1_555 hydrog TYPE_6_PAIR B G 16 B N1 G 4 1_555 B G 19 B O6 G 7 1_555 hydrog TYPE_6_PAIR B G 16 B N2 G 4 1_555 B G 19 B N7 G 7 1_555 hydrog TYPE_6_PAIR B G 17 B N1 G 5 1_555 B G 20 B O6 G 8 1_555 hydrog TYPE_6_PAIR B G 17 B N2 G 5 1_555 B G 20 B N7 G 8 1_555 hydrog TYPE_11_PAIR B G 19 B N2 G 7 1_555 B A 21 B N7 A 9 1_555 hydrog TYPE_11_PAIR B G 19 B N3 G 7 1_555 B A 21 B N6 A 9 1_555 hydrog TYPE_6_PAIR B G 19 B N1 G 7 1_555 B G 22 B O6 G 10 1_555 hydrog TYPE_6_PAIR B G 19 B N2 G 7 1_555 B G 22 B N7 G 10 1_555 hydrog TYPE_6_PAIR B G 20 B N1 G 8 1_555 B G 23 B O6 G 11 1_555 hydrog TYPE_6_PAIR B G 20 B N2 G 8 1_555 B G 23 B N7 G 11 1_555 RNA Aptamer, Prion, Quadruplex, RNA 2RQJ PDB 1 2RQJ 1 12 2RQJ 1 12 2RQJ A 1 1 12 13 24 2RQJ 13 24 2RQJ B 1 1 12 1 P 1