Equivalence class NR_2.5_97151.3 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 5Z1I|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 construct | Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-fluoro sisomicin | X-ray diffraction | 1.9 | 2018-05-30 | |||
| 2 | 2PWT|1|A+ 2PWT|1|B | 22-mer of the ribosomal decoding site | Crystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA group | X-ray diffraction | 1.8 | 2007-09-18 | ||||
| 3 | 3TD1|1|B+ 3TD1|1|A | RNA (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 geneticin | X-ray diffraction | 2.1 | 2011-12-07 | ||||
| 4 | 4K32|1|A+ 4K32|1|B | RNA (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') | Leishmania | Crystal structure of geneticin bound to the leishmanial rRNA A-site | X-ray diffraction | 2.5 | 2013-07-31 | |||
| 5 | 4P3S|1|B+ 4P3S|1|A | 5'-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 construct | Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin | X-ray diffraction | 2.3 | 2016-05-04 | |||
| 6 | 2ET5|1|A+ 2ET5|1|B | 5'-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-Site | X-ray diffraction | 2.2 | 2005-12-13 | ||||
| 7 | 4WCP|1|A+ 4WCP|1|B+ 4WCP|1|C | RNA (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') | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site | X-ray diffraction | 2.4 | 2015-09-09 | ||||
| 8 | 1MWL|1|A+ 1MWL|1|B | 5'-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 site | X-ray diffraction | 2.4 | 2003-02-18 | ||||
| 9 | 2ET4|1|A+ 2ET4|1|B | 5'-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-Site | X-ray diffraction | 2.4 | 2005-12-13 | ||||
| 10 | 2ESJ|1|A+ 2ESJ|1|B | 5'-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 Site | X-ray diffraction | 2.2 | 2005-12-20 | ||||
| 11 | 5Z1H|1|B+ 5Z1H|1|A | RNA (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 construct | Crystal structure of the bacterial ribosomal decoding site in complex with 6'-fluoro sisomicin | X-ray diffraction | 2.4 | 2018-05-30 | |||
| 12 | 4WCQ|1|A+ 4WCQ|1|B | RNA (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') | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with geneticin | X-ray diffraction | 2.1 | 2015-09-09 | ||||
| 13 | 3WRU|1|A+ 3WRU|1|B | RNA (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 group | X-ray diffraction | 2.3 | 2014-11-05 | ||||
| 14 | 4F8U|1|A+ 4F8U|1|B | 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'), RNA (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 (C2 form) | X-ray diffraction | 2 | 2012-08-15 | ||||
| 15 | 5Z71|1|B+ 5Z71|1|A | RNA (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 construct | Crystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418 (P21212 form) | X-ray diffraction | 2.5 | 2019-01-30 | |||
| 16 | 1J7T|1|A+ 1J7T|1|B | 5'-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 resolution | X-ray diffraction | 2.5 | 2002-05-18 |
Release history
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_2.5_97151.3 | NR_2.5_19598.3 | 3.59 | (2) 5Z1I|1|A, 5Z1H|1|B+5Z1H|1|A | (14) 2ESJ|1|A+2ESJ|1|B, 1J7T|1|A+1J7T|1|B, 3TD1|1|B+3TD1|1|A, 2ET5|1|A+2ET5|1|B, 4WCP|1|A+4WCP|1|B+4WCP|1|C, 4K32|1|A+4K32|1|B, 5Z71|1|B+5Z71|1|A, 4F8U|1|A+4F8U|1|B, 1MWL|1|A+1MWL|1|B, 4P3S|1|B+4P3S|1|A, 2ET4|1|A+2ET4|1|B, 4WCQ|1|A+4WCQ|1|B, 2PWT|1|A+2PWT|1|B, 3WRU|1|A+3WRU|1|B | (2) 5ZEG|1|A+5ZEG|1|B+5ZEG|1|C, 5ZEI|1|A+5ZEI|1|B |
| NR_2.5_97151.3 | NR_2.5_97151.2 | 3.59 | (13) 2ESJ|1|A+2ESJ|1|B, 2PWT|1|A+2PWT|1|B, 4F8U|1|A+4F8U|1|B, 1MWL|1|A+1MWL|1|B, 4WCP|1|A+4WCP|1|B+4WCP|1|C, 2ET5|1|A+2ET5|1|B, 3WRU|1|A+3WRU|1|B, 4P3S|1|B+4P3S|1|A, 1J7T|1|A+1J7T|1|B, 2ET4|1|A+2ET4|1|B, 3TD1|1|B+3TD1|1|A, 4K32|1|A+4K32|1|B, 4WCQ|1|A+4WCQ|1|B | (3) 5Z71|1|B+5Z71|1|A, 5Z1H|1|B+5Z1H|1|A, 5Z1I|1|A | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_2.5_97151.3 | NR_2.5_71199.1 | 3.75 | (16) 3TD1|1|B+3TD1|1|A, 5Z1I|1|A, 2PWT|1|A+2PWT|1|B, 5Z1H|1|B+5Z1H|1|A, 2ET5|1|A+2ET5|1|B, 4WCQ|1|A+4WCQ|1|B, 2ET4|1|A+2ET4|1|B, 4WCP|1|A+4WCP|1|B+4WCP|1|C, 2ESJ|1|A+2ESJ|1|B, 4P3S|1|B+4P3S|1|A, 1MWL|1|A+1MWL|1|B, 4K32|1|A+4K32|1|B, 1J7T|1|A+1J7T|1|B, 4F8U|1|A+4F8U|1|B, 3WRU|1|A+3WRU|1|B, 5Z71|1|B+5Z71|1|A | (0) | (2) 5ZEG|1|A+5ZEG|1|B+5ZEG|1|C, 5ZEI|1|A+5ZEI|1|B |
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5
#S - ordering by similarity (same as in the heat map).| #S | PDB | Title | Method | Resolution | Length |
|---|---|---|---|---|---|
| 1 | 4WCP|1|A+4WCP|1|B+4WCP|1|C | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site | X-RAY DIFFRACTION | 2.4 | 22 |
| 2 | 3TD1|1|B+3TD1|1|A | Crystal structure of the bacterial A1408G-mutant and the protozoa cytoplasmic ribosomal decoding site in complex with geneticin | X-RAY DIFFRACTION | 2.1 | 22 |
| 3 | 4WCQ|1|A+4WCQ|1|B | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with geneticin | X-RAY DIFFRACTION | 2.1 | 21 |
| 4 | 4P3S|1|B+4P3S|1|A | Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin | X-RAY DIFFRACTION | 2.3 | 21 |
| 5 | 5Z1H|1|B+5Z1H|1|A | Crystal structure of the bacterial ribosomal decoding site in complex with 6'-fluoro sisomicin | X-RAY DIFFRACTION | 2.4 | 23 |
| 6 | 2PWT|1|A+2PWT|1|B | Crystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA group | X-RAY DIFFRACTION | 1.8 | 21 |
| 7 | 2ET5|1|A+2ET5|1|B | Complex Between Ribostamycin and the 16S-RRNA A-Site | X-RAY DIFFRACTION | 2.2 | 21 |
| 8 | 2ET4|1|A+2ET4|1|B | Complex Between Neomycin B and the 16S-RRNA A-Site | X-RAY DIFFRACTION | 2.4 | 21 |
| 9 | 1J7T|1|A+1J7T|1|B | Complex between Paromomycin and the 16S-rRNA A-site at 2.5 A resolution | X-RAY DIFFRACTION | 2.5 | 21 |
| 10 | 2ESJ|1|A+2ESJ|1|B | Complex between Lividomycin A and the 16S-Rrna A Site | X-RAY DIFFRACTION | 2.2 | 21 |
| 11 | 3WRU|1|A+3WRU|1|B | Crystal structure of the bacterial ribosomal decoding site in complex with synthetic aminoglycoside with F-HABA group | X-RAY DIFFRACTION | 2.3 | 21 |
| 12 | 1MWL|1|A+1MWL|1|B | Crystal structure of geneticin bound to the eubacterial 16S rRNA A site | X-RAY DIFFRACTION | 2.4 | 24 |
| 13 | 4F8U|1|A+4F8U|1|B | Crystal structure of the bacterial ribosomal decoding site in complex with sisomicin (C2 form) | X-RAY DIFFRACTION | 2 | 22 |
| 14 | 5Z1I|1|A | Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-fluoro sisomicin | X-RAY DIFFRACTION | 1.9 | 21 |
| 15 | 5Z71|1|B+5Z71|1|A | Crystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418 (P21212 form) | X-RAY DIFFRACTION | 2.5 | 22 |
| 16 | 4K32|1|A+4K32|1|B | Crystal structure of geneticin bound to the leishmanial rRNA A-site | X-RAY DIFFRACTION | 2.5 | 21 |