1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Lynch, S.R. Puglisi, J.D. 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 C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C23 H45 N5 O14 615.628 PAROMOMYCIN PAROMOMYCIN I; AMMINOSIDIN; CATENULIN; CRESTOMYCIN; MONOMYCIN A; NEOMYCIN E non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking UK J.Mol.Biol. JMOBAK 0070 0022-2836 306 1037 1058 10.1006/jmbi.2000.4420 11237617 Structural origins of aminoglycoside specificity for prokaryotic ribosomes. 2001 10.2210/pdb1fyp/pdb pdb_00001fyp 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 EUKARYOTIC DECODING REGION A-SITE RNA 8672.185 FRAGMENT OF 18S RIBOSOMAL RNA 18S RNA - NUCLEOTIDES 1404-1412, 1488-1497 (E. COLI NUMBERING) U1410A, A1490U 1 syn polymer 615.628 PAROMOMYCIN PAROMOMYCIN 1 syn non-polymer no no GGCGUCGCACCUUCGGGUGAAGUCGCC GGCGUCGCACCUUCGGGUGAAGUCGCC 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 3.247 1 19 A 1 A 27 -1.816 A_G1:C27_A 1 -22.660 -0.286 -0.060 -0.222 -0.640 1 19 A 2 A 26 -4.658 A_G2:C26_A 2 -10.567 -0.425 0.021 -0.313 9.244 1 19 A 3 A 25 -1.687 A_C3:G25_A 3 -19.296 0.566 -0.058 -0.333 -21.306 1 19 A 4 A 24 -5.591 A_G4:C24_A 4 -37.146 -0.238 -0.036 -0.273 -16.032 1 19 A 6 A 22 0.561 A_C6:G22_A 5 -20.148 0.425 -0.068 -0.330 -19.146 1 8 A 7 A 21 -11.700 A_G7:A21_A 6 -0.306 0.471 0.932 1.277 1.833 1 19 A 8 A 19 -10.312 A_C8:G19_A 7 -20.512 0.191 0.574 -0.293 -1.868 1 20 A 9 A 18 -11.460 A_A9:U18_A 8 -31.325 0.151 0.252 -0.243 1.317 1 19 A 10 A 17 -3.410 A_C10:G17_A 9 -15.274 0.092 0.103 -0.152 8.426 1 19 A 11 A 16 -2.421 A_C11:G16_A 10 -11.329 0.474 -0.309 -0.312 -12.693 A 12 A 15 -79.759 A_U12:G15_A 11 -32.331 1.853 0.947 -4.892 2.827 44.775 A A 1 2 16.117 A A 27 26 2.852 12.027 -1.701 -0.939 AA_G1G2:C26C27_AA 1 -10.776 14.440 41.902 -2.219 1.349 2.738 36.706 A A 2 3 6.352 A A 26 25 2.856 3.993 0.281 -1.006 AA_G2C3:G25C26_AA 2 0.508 -0.808 36.492 -2.066 -0.387 2.416 48.752 A A 3 4 32.056 A A 25 24 3.454 25.259 0.591 -1.263 AA_C3G4:C24G25_AA 3 5.126 -6.505 41.740 -3.418 -0.333 5.154 64.938 A A 4 6 10.901 A A 24 22 5.563 11.653 -0.827 -2.167 AA_G4C6:G22C24_AA 4 -0.999 0.934 63.989 -2.824 0.701 2.230 31.831 A A 6 7 19.554 A A 22 21 2.828 10.532 0.813 -1.356 AA_C6G7:A21G22_AA 5 -0.293 0.544 30.080 -4.005 -1.525 2.643 54.117 A A 7 8 19.163 A A 21 19 3.799 16.928 1.325 -1.516 AA_G7C8:G19A21_AA 6 -16.478 18.653 49.043 -2.753 -2.514 2.462 39.618 A A 8 9 21.066 A A 19 18 3.004 13.990 -0.166 -1.037 AA_C8A9:U18G19_AA 7 1.557 -2.344 37.127 -2.946 0.403 3.116 37.244 A A 9 10 -5.310 A A 18 17 3.020 -3.386 0.886 -0.975 AA_A9C10:G17U18_AA 8 1.031 -1.616 37.082 -1.104 -1.258 2.632 31.939 A A 10 11 12.105 A A 17 16 2.930 6.610 -0.343 -1.036 AA_C10C11:G16G17_AA 9 2.117 -3.877 31.195 -2.914 0.954 2.864 101.392 A A 11 12 9.919 A A 16 15 2.938 15.309 0.606 -0.814 AA_C11U12:G15G16_AA 10 9.033 -5.853 100.247 -0.733 -0.269 chem_comp database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Structure summary 1 0 2001-03-14 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Eukaryotic decoding region A-site RNA, free in solution Prokaryotic decoding region A-site RNA, bound to paromomycin Prokaryotic decoding region A-site RNA, free in solution RCSB Y RCSB 2000-10-02 REL PAR PAROMOMYCIN This sequence of 18S RNA occurs in Tetrahymena thermophila sample structures with the least restraint violations,structures with the lowest energy 100 29 DQF-COSY 3D_15N-separated_NOESY 3D_13C-separated_NOESY 2D NOESY 10 mM 6.3 1 atm 308 K 605 NOEs, 122 dihedral constraints, and 36 hydrogen bonds simulated annealing molecular dynamics 11 3 mM RNA, 3 mM paromomycin, 10 mM Naphosphate, pH 6.3, 13C/15N RNA 10% D2O/ 90% H2O; 100% D2O collection VNMR 6.1 processing VNMR 6.1 processing Felix 98 Brunger refinement X-PLOR 3.83 Brunger structure solution X-PLOR 3.83 500 Varian INOVA 800 Varian INOVA PAR 28 2 PAR PAR 28 A G 1 n 1 G 1 A G 2 n 2 G 2 A C 3 n 3 C 3 A G 4 n 4 G 4 A U 5 n 5 U 5 A C 6 n 6 C 6 A G 7 n 7 G 7 A C 8 n 8 C 8 A A 9 n 9 A 9 A C 10 n 10 C 10 A C 11 n 11 C 11 A U 12 n 12 U 12 A U 13 n 13 U 13 A C 14 n 14 C 14 A G 15 n 15 G 15 A G 16 n 16 G 16 A G 17 n 17 G 17 A U 18 n 18 U 18 A G 19 n 19 G 19 A A 20 n 20 A 20 A A 21 n 21 A 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 C 26 n 26 C 26 A C 27 n 27 C 27 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 17 A A HO2' O4' A A 20 21 1.57 28 A A HO2' O4' A A 20 21 1.53 EUKARYOTIC DECODING REGION A-SITE RNA-PAROMOMYCIN COMPLEX 1 N N 2 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 27 A N3 C 27 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 27 A O2 C 27 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 27 A N4 C 27 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 26 A N3 C 26 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 26 A O2 C 26 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 26 A N4 C 26 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 25 A N1 G 25 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 25 A O6 G 25 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 25 A N2 G 25 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 A C 24 A N3 C 24 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 A C 24 A O2 C 24 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 A C 24 A N4 C 24 1_555 hydrog WATSON-CRICK A C 6 A N3 C 6 1_555 A G 22 A N1 G 22 1_555 hydrog WATSON-CRICK A C 6 A N4 C 6 1_555 A G 22 A O6 G 22 1_555 hydrog WATSON-CRICK A C 6 A O2 C 6 1_555 A G 22 A N2 G 22 1_555 hydrog TYPE_8_PAIR A G 7 A N1 G 7 1_555 A A 21 A N1 A 21 1_555 hydrog TYPE_8_PAIR A G 7 A O6 G 7 1_555 A A 21 A N6 A 21 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 A G 19 A N1 G 19 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 A G 19 A O6 G 19 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 A G 19 A N2 G 19 1_555 hydrog C-A MISPAIR A C 8 A O2 C 8 1_555 A A 20 A N6 A 20 1_555 hydrog WATSON-CRICK A A 9 A N1 A 9 1_555 A U 18 A N3 U 18 1_555 hydrog WATSON-CRICK A A 9 A N6 A 9 1_555 A U 18 A O4 U 18 1_555 hydrog WATSON-CRICK A C 10 A N3 C 10 1_555 A G 17 A N1 G 17 1_555 hydrog WATSON-CRICK A C 10 A N4 C 10 1_555 A G 17 A O6 G 17 1_555 hydrog WATSON-CRICK A C 10 A O2 C 10 1_555 A G 17 A N2 G 17 1_555 hydrog WATSON-CRICK A C 11 A N3 C 11 1_555 A G 16 A N1 G 16 1_555 hydrog WATSON-CRICK A C 11 A N4 C 11 1_555 A G 16 A O6 G 16 1_555 hydrog WATSON-CRICK A C 11 A O2 C 11 1_555 A G 16 A N2 G 16 1_555 hydrog U-G MISPAIR A U 12 A O2 U 12 1_555 A G 15 A N1 G 15 1_555 RNA RNA-paromomycin complex, aminoglycoside, stem-internal loop-stem-tetraloop, RNA-drug, G-A base pair, RNA 1FYP PDB 1 1FYP 1 27 1FYP 1 27 1FYP A 1 1 27 BINDING SITE FOR RESIDUE PAR A 28 A PAR 28 Software 13 A G 2 A G 2 13 1_555 A C 3 A C 3 13 1_555 A G 4 A G 4 13 1_555 A U 5 A U 5 13 1_555 A C 6 A C 6 13 1_555 A G 7 A G 7 13 1_555 A G 17 A G 17 13 1_555 A U 18 A U 18 13 1_555 A G 19 A G 19 13 1_555 A A 20 A A 20 13 1_555 A A 21 A A 21 13 1_555 A G 22 A G 22 13 1_555 A U 23 A U 23 13 1_555 1 P 1