Equivalence class NR_2.5_97151.2 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2PWT|1|A+ 2PWT|1|B (rep) | 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 | ||||
| 2 | 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 | ||||
| 3 | 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 | |||
| 4 | 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 | |||
| 5 | 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 | ||||
| 6 | 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 | ||||
| 7 | 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 | ||||
| 8 | 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 | ||||
| 9 | 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 | ||||
| 10 | 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 | ||||
| 11 | 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 | ||||
| 12 | 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 | ||||
| 13 | 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
| Release | 3.0 | 3.1 | 3.2 | 3.3 | 3.4 | 3.5 | 3.6 | 3.7 | 3.8 | 3.9 | 3.10 | 3.11 | 3.12 | 3.13 | 3.14 | 3.15 | 3.16 | 3.17 | 3.18 | 3.19 | 3.20 | 3.21 | 3.22 | 3.23 | 3.24 | 3.25 | 3.26 | 3.27 | 3.28 | 3.29 | 3.30 | 3.31 | 3.32 | 3.33 | 3.34 | 3.35 | 3.36 | 3.37 | 3.38 | 3.39 | 3.40 | 3.41 | 3.42 | 3.43 | 3.44 | 3.45 | 3.46 | 3.47 | 3.48 | 3.49 | 3.50 | 3.51 | 3.52 | 3.53 | 3.54 | 3.55 | 3.56 | 3.57 | 3.58 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2017-12-15 | 2017-12-22 | 2017-12-29 | 2018-01-05 | 2018-01-12 | 2018-01-19 | 2018-01-26 | 2018-02-02 | 2018-02-09 | 2018-02-16 | 2018-02-23 | 2018-03-01 | 2018-03-08 | 2018-03-15 | 2018-03-22 | 2018-03-29 | 2018-04-06 | 2018-04-13 | 2018-04-20 | 2018-04-27 | 2018-05-04 | 2018-05-11 | 2018-05-18 | 2018-05-25 | 2018-06-01 | 2018-06-08 | 2018-06-15 | 2018-06-22 | 2018-06-29 | 2018-07-06 | 2018-07-13 | 2018-07-20 | 2018-07-27 | 2018-08-03 | 2018-08-10 | 2018-08-17 | 2018-08-24 | 2018-08-31 | 2018-09-07 | 2018-09-14 | 2018-09-21 | 2018-09-28 | 2018-10-05 | 2018-10-12 | 2018-10-19 | 2018-10-26 | 2018-11-02 | 2018-11-09 | 2018-11-16 | 2018-11-23 | 2018-11-30 | 2018-12-07 | 2018-12-14 | 2018-12-21 | 2018-12-28 | 2019-01-04 | 2019-01-11 | 2019-01-18 | 2019-01-25 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_2.5_97151.2 | NR_2.5_97151.1 | 3.0 | (13) 1J7T|1|A+1J7T|1|B, 4WCP|1|A+4WCP|1|B+4WCP|1|C, 4P3S|1|B+4P3S|1|A, 4K32|1|A+4K32|1|B, 4F8U|1|A+4F8U|1|B, 3WRU|1|A+3WRU|1|B, 3TD1|1|B+3TD1|1|A, 2PWT|1|A+2PWT|1|B, 2ET5|1|A+2ET5|1|B, 2ET4|1|A+2ET4|1|B, 2ESJ|1|A+2ESJ|1|B, 1MWL|1|A+1MWL|1|B, 4WCQ|1|A+4WCQ|1|B | (0) | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_2.5_97151.2 | NR_2.5_97151.3 | 3.59 | (13) 3WRU|1|A+3WRU|1|B, 2ESJ|1|A+2ESJ|1|B, 4WCQ|1|A+4WCQ|1|B, 1MWL|1|A+1MWL|1|B, 3TD1|1|B+3TD1|1|A, 4WCP|1|A+4WCP|1|B+4WCP|1|C, 1J7T|1|A+1J7T|1|B, 2PWT|1|A+2PWT|1|B, 4P3S|1|B+4P3S|1|A, 2ET5|1|A+2ET5|1|B, 4K32|1|A+4K32|1|B, 2ET4|1|A+2ET4|1|B, 4F8U|1|A+4F8U|1|B | (0) | (3) 5Z71|1|B+5Z71|1|A, 5Z1I|1|A, 5Z1H|1|B+5Z1H|1|A |
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 | 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 |
| 2 | 1MWL|1|A+1MWL|1|B | Crystal structure of geneticin bound to the eubacterial 16S rRNA A site | X-RAY DIFFRACTION | 2.4 | 24 |
| 3 | 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 |
| 4 | 2ET5|1|A+2ET5|1|B | Complex Between Ribostamycin and the 16S-RRNA A-Site | X-RAY DIFFRACTION | 2.2 | 21 |
| 5 | 2ET4|1|A+2ET4|1|B | Complex Between Neomycin B and the 16S-RRNA A-Site | X-RAY DIFFRACTION | 2.4 | 21 |
| 6 | 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 |
| 7 | 2ESJ|1|A+2ESJ|1|B | Complex between Lividomycin A and the 16S-Rrna A Site | X-RAY DIFFRACTION | 2.2 | 21 |
| 8 | 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 |
| 9 | 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 |
| 10 | 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 |
| 11 | 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 |
| 12 | 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 |
| 13 | 4K32|1|A+4K32|1|B | Crystal structure of geneticin bound to the leishmanial rRNA A-site | X-RAY DIFFRACTION | 2.5 | 21 |