#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
15Z1I|1|A (rep)RNA (5'-R(P*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-fluoro sisomicinX-ray diffraction1.92018-05-30
22PWT|1|A+ 2PWT|1|B22-mer of the ribosomal decoding siteCrystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA groupX-ray diffraction1.82007-09-18
35ZEG|1|A+ 5ZEG|1|B+ 5ZEG|1|CRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the bacterial A1408me1A-mutant ribosomal decoding siteX-ray diffraction2.42018-03-21
46JBF|1|A+ 6JBF|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F)X-ray diffraction2.62020-01-29
53TD1|1|B+ 3TD1|1|ARNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the bacterial A1408G-mutant and the protozoa cytoplasmic ribosomal decoding site in complex with geneticinX-ray diffraction2.12011-12-07
64K32|1|A+ 4K32|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')LeishmaniaCrystal structure of geneticin bound to the leishmanial rRNA A-siteX-ray diffraction2.52013-07-31
75ZEI|1|A+ 5ZEI|1|BRNA (5'-R(P*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'), RNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with geneticinX-ray diffraction2.12018-03-21
83BNL|1|A+ 3BNL|1|BA site of bacterial ribosomeCrystal structure of the bacterial ribosomal decoding A site in the presence of [Co(NH3)6]Cl3X-ray diffraction2.62008-06-24
96JBF|1|C+ 6JBF|1|DRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F)X-ray diffraction2.62020-01-29
105XZ1|1|C+ 5XZ1|1|DRNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418X-ray diffraction3.012018-07-18
114P3S|1|B+ 4P3S|1|A5'-R(*UP*UP*GP*CP*GP*UP*CP*CP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'synthetic constructCrystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticinX-ray diffraction2.32016-05-04
125XZ1|1|A+ 5XZ1|1|BRNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418X-ray diffraction3.012018-07-18
132ET5|1|A+ 2ET5|1|B5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Complex Between Ribostamycin and the 16S-RRNA A-SiteX-ray diffraction2.22005-12-13
144PDQ|1|A+ 4PDQ|1|BRNA (5'-*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C-3')synthetic constructCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neomycin analogX-ray diffraction32015-01-07
154GPY|1|A+ 4GPY|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the bacterial ribosomal decoding site in complex with 6'-hydroxysisomicinX-ray diffraction2.82013-04-03
166JBG|1|C+ 6JBG|1|DRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (equatorial 4'-F)X-ray diffraction3.12020-01-29
174GPW|1|A+ 4GPW|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P21212 form)X-ray diffraction32013-04-03
181MWL|1|A+ 1MWL|1|B5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Crystal structure of geneticin bound to the eubacterial 16S rRNA A siteX-ray diffraction2.42003-02-18
192ET4|1|A+ 2ET4|1|B5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Complex Between Neomycin B and the 16S-RRNA A-SiteX-ray diffraction2.42005-12-13
204GPX|1|A+ 4GPX|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P212121 form)X-ray diffraction2.62013-04-03
216JBG|1|A+ 6JBG|1|BRNA (5'-R(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (equatorial 4'-F)X-ray diffraction3.12020-01-29
222ESJ|1|A+ 2ESJ|1|B5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Complex between Lividomycin A and the 16S-Rrna A SiteX-ray diffraction2.22005-12-20
235Z1H|1|B+ 5Z1H|1|ARNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the bacterial ribosomal decoding site in complex with 6'-fluoro sisomicinX-ray diffraction2.42018-05-30
242ESI|1|A+ 2ESI|1|B5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Complex between Kanamycin A and the 16S-Rrna A Site.X-ray diffraction32005-12-20
254F8V|1|A+ 4F8V|1|BRNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the bacterial ribosomal decoding site in complex with sisomicin (P21212 form)X-ray diffraction2.82012-08-15
263WRU|1|A+ 3WRU|1|BRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the bacterial ribosomal decoding site in complex with synthetic aminoglycoside with F-HABA groupX-ray diffraction2.32014-11-05
274F8U|1|A+ 4F8U|1|BRNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'), RNA (5'-R(P*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the bacterial ribosomal decoding site in complex with sisomicin (C2 form)X-ray diffraction22012-08-15
283S4P|1|A+ 3S4P|1|BRNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')Crystal structure of the bacterial ribosomal decoding site complexed with an amphiphilic paromomycin O2''-ether analogueX-ray diffraction2.562011-09-21
294P20|1|A+ 4P20|1|B5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'synthetic constructCrystal structures of the bacterial ribosomal decoding site complexed with amikacinX-ray diffraction2.72014-05-07
301LC4|1|A+ 1LC4|1|B5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Crystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A SiteX-ray diffraction2.542003-04-08
312ET3|1|A+ 2ET3|1|B5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Complex Between Gentamicin C1A and the 16S-RRNA A-SiteX-ray diffraction2.82005-12-13
325ZEJ|1|A+ 5ZEJ|1|BRNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycinX-ray diffraction3.52018-03-21
335ZEM|1|A+ 5ZEM|1|BRNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in the presence of gentamicinX-ray diffraction3.12018-03-21
345Z71|1|B+ 5Z71|1|ARNA (5'-R(P*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')synthetic constructCrystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418 (P21212 form)X-ray diffraction2.52019-01-30
352BE0|1|A+ 2BE0|1|B5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Complex Between Paromomycin Derivative JS5-39 and the 16S-Rrna A-Site.X-ray diffraction2.632005-12-20
362BEE|1|A+ 2BEE|1|B5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Complex Between Paromomycin derivative JS4 and the 16S-Rrna A SiteX-ray diffraction2.62005-12-20
371J7T|1|A+ 1J7T|1|B5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Complex between Paromomycin and the 16S-rRNA A-site at 2.5 A resolutionX-ray diffraction2.52002-05-18
381YRJ|1|A+ 1YRJ|1|BBacterial 16 S Ribosomal RNA A Site OligonucleotideCrystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotideX-ray diffraction2.72005-06-07
392F4T|1|B+ 2F4T|1|A5'-R(*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3', 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'Asite RNA + designer antibioticX-ray diffraction32006-05-02

Release history

Release3.1513.1523.1533.1543.1553.1563.1573.1583.1593.1603.1613.1623.1633.1643.1653.1663.1673.1683.1693.1703.1713.1723.1733.1743.1753.1763.1773.1783.1793.1803.1813.1823.1833.1843.1853.1863.1873.1883.1893.1903.1913.1923.1933.1943.1953.1963.1973.1983.1993.2003.2013.2023.2033.2043.2053.2063.2073.2083.2093.2103.2113.2123.2133.2143.2153.2163.2173.2183.2193.2203.221
Date2020-11-042020-11-112020-11-182020-11-252020-12-022020-12-092020-12-162020-12-232020-12-302021-01-062021-01-132021-01-202021-01-272021-02-032021-02-102021-02-172021-02-242021-03-032021-03-102021-03-172021-03-242021-03-312021-04-072021-04-142021-04-212021-04-282021-05-052021-05-122021-05-192021-05-262021-06-022021-06-092021-06-162021-06-232021-06-302021-07-072021-07-142021-07-212021-07-282021-08-042021-08-112021-08-182021-08-252021-09-012021-09-082021-09-152021-09-222021-09-292021-10-062021-10-132021-10-202021-10-272021-11-032021-11-102021-11-172021-11-242021-12-012021-12-082021-12-152021-12-222021-12-292022-01-052022-01-122022-01-192022-01-262022-02-022022-02-092022-02-162022-02-232022-03-022022-03-09

Instances are ordered to put similar structures near each other. Select one instance to see its 3D structure. Selecting two or more instances will show their superposition, but only chains with identical numbers of observed nucleotides will superpose well. Large structures are slow to display; this tool is not designed for that.

#SViewPDBTitleMethodResolutionLength
14PDQ|1|A+ 4PDQ|1|BCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neomycin analogX-RAY DIFFRACTION323
23BNL|1|A+ 3BNL|1|BCrystal structure of the bacterial ribosomal decoding A site in the presence of [Co(NH3)6]Cl3X-RAY DIFFRACTION2.622
36JBG|1|C+ 6JBG|1|DCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (equatorial 4'-F)X-RAY DIFFRACTION3.123
46JBF|1|C+ 6JBF|1|DCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F)X-RAY DIFFRACTION2.623
55ZEG|1|A+ 5ZEG|1|B+ 5ZEG|1|CCrystal structure of the bacterial A1408me1A-mutant ribosomal decoding siteX-RAY DIFFRACTION2.422
66JBG|1|A+ 6JBG|1|BCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (equatorial 4'-F)X-RAY DIFFRACTION3.122
76JBF|1|A+ 6JBF|1|BCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F)X-RAY DIFFRACTION2.623
82BE0|1|A+ 2BE0|1|BComplex Between Paromomycin Derivative JS5-39 and the 16S-Rrna A-Site.X-RAY DIFFRACTION2.6321
92BEE|1|A+ 2BEE|1|BComplex Between Paromomycin derivative JS4 and the 16S-Rrna A SiteX-RAY DIFFRACTION2.621
102PWT|1|A+ 2PWT|1|BCrystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA groupX-RAY DIFFRACTION1.821
113S4P|1|A+ 3S4P|1|BCrystal structure of the bacterial ribosomal decoding site complexed with an amphiphilic paromomycin O2''-ether analogueX-RAY DIFFRACTION2.5621
122F4T|1|B+ 2F4T|1|AAsite RNA + designer antibioticX-RAY DIFFRACTION323
135Z1H|1|B+ 5Z1H|1|ACrystal structure of the bacterial ribosomal decoding site in complex with 6'-fluoro sisomicinX-RAY DIFFRACTION2.423
144GPY|1|A+ 4GPY|1|BCrystal structure of the bacterial ribosomal decoding site in complex with 6'-hydroxysisomicinX-RAY DIFFRACTION2.822
154P20|1|A+ 4P20|1|BCrystal structures of the bacterial ribosomal decoding site complexed with amikacinX-RAY DIFFRACTION2.721
161LC4|1|A+ 1LC4|1|BCrystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A SiteX-RAY DIFFRACTION2.5421
172ESI|1|A+ 2ESI|1|BComplex between Kanamycin A and the 16S-Rrna A Site.X-RAY DIFFRACTION323
183WRU|1|A+ 3WRU|1|BCrystal structure of the bacterial ribosomal decoding site in complex with synthetic aminoglycoside with F-HABA groupX-RAY DIFFRACTION2.321
191MWL|1|A+ 1MWL|1|BCrystal structure of geneticin bound to the eubacterial 16S rRNA A siteX-RAY DIFFRACTION2.424
201YRJ|1|A+ 1YRJ|1|BCrystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotideX-RAY DIFFRACTION2.723
212ESJ|1|A+ 2ESJ|1|BComplex between Lividomycin A and the 16S-Rrna A SiteX-RAY DIFFRACTION2.221
222ET5|1|A+ 2ET5|1|BComplex Between Ribostamycin and the 16S-RRNA A-SiteX-RAY DIFFRACTION2.221
231J7T|1|A+ 1J7T|1|BComplex between Paromomycin and the 16S-rRNA A-site at 2.5 A resolutionX-RAY DIFFRACTION2.521
242ET4|1|A+ 2ET4|1|BComplex Between Neomycin B and the 16S-RRNA A-SiteX-RAY DIFFRACTION2.421
254F8V|1|A+ 4F8V|1|BCrystal structure of the bacterial ribosomal decoding site in complex with sisomicin (P21212 form)X-RAY DIFFRACTION2.821
262ET3|1|A+ 2ET3|1|BComplex Between Gentamicin C1A and the 16S-RRNA A-SiteX-RAY DIFFRACTION2.821
274F8U|1|A+ 4F8U|1|BCrystal structure of the bacterial ribosomal decoding site in complex with sisomicin (C2 form)X-RAY DIFFRACTION222
285XZ1|1|A+ 5XZ1|1|BCrystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418X-RAY DIFFRACTION3.0122
294K32|1|A+ 4K32|1|BCrystal structure of geneticin bound to the leishmanial rRNA A-siteX-RAY DIFFRACTION2.521
304GPW|1|A+ 4GPW|1|BCrystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P21212 form)X-RAY DIFFRACTION322
314GPX|1|A+ 4GPX|1|BCrystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P212121 form)X-RAY DIFFRACTION2.621
325XZ1|1|C+ 5XZ1|1|DCrystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418X-RAY DIFFRACTION3.0122
335Z71|1|B+ 5Z71|1|ACrystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418 (P21212 form)X-RAY DIFFRACTION2.522
345Z1I|1|ACrystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-fluoro sisomicinX-RAY DIFFRACTION1.921
353TD1|1|B+ 3TD1|1|ACrystal structure of the bacterial A1408G-mutant and the protozoa cytoplasmic ribosomal decoding site in complex with geneticinX-RAY DIFFRACTION2.122
364P3S|1|B+ 4P3S|1|ACrystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticinX-RAY DIFFRACTION2.321
375ZEI|1|A+ 5ZEI|1|BCrystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with geneticinX-RAY DIFFRACTION2.121
385ZEJ|1|A+ 5ZEJ|1|BCrystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycinX-RAY DIFFRACTION3.521
395ZEM|1|A+ 5ZEM|1|BCrystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in the presence of gentamicinX-RAY DIFFRACTION3.121

Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. The ordering in the heat map is the same as in the table. The colorbar ranges from 0 to the maximum observed discrepancy. Click above the diagonal to select a range of structures, below the diagonal to select two structures.


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