Equivalence class NR_2.5_71199.3 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 | 5ZEG|1|A+ 5ZEG|1|B+ 5ZEG|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') | synthetic construct | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site | X-ray diffraction | 2.4 | 2018-03-21 | |||
| 4 | 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 | ||||
| 5 | 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 | |||
| 6 | 5ZEI|1|A+ 5ZEI|1|B | RNA (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 construct | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with geneticin | X-ray diffraction | 2.1 | 2018-03-21 | |||
| 7 | 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 | |||
| 8 | 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 | ||||
| 9 | 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 | ||||
| 10 | 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 | ||||
| 11 | 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 | ||||
| 12 | 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 | |||
| 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*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 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
| Release | 3.151 | 3.152 | 3.153 | 3.154 | 3.155 | 3.156 | 3.157 | 3.158 | 3.159 | 3.160 | 3.161 | 3.162 | 3.163 | 3.164 | 3.165 | 3.166 | 3.167 | 3.168 | 3.169 | 3.170 | 3.171 | 3.172 | 3.173 | 3.174 | 3.175 | 3.176 | 3.177 | 3.178 | 3.179 | 3.180 | 3.181 | 3.182 | 3.183 | 3.184 | 3.185 | 3.186 | 3.187 | 3.188 | 3.189 | 3.190 | 3.191 | 3.192 | 3.193 | 3.194 | 3.195 | 3.196 | 3.197 | 3.198 | 3.199 | 3.200 | 3.201 | 3.202 | 3.203 | 3.204 | 3.205 | 3.206 | 3.207 | 3.208 | 3.209 | 3.210 | 3.211 | 3.212 | 3.213 | 3.214 | 3.215 | 3.216 | 3.217 | 3.218 | 3.219 | 3.220 | 3.221 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2020-11-04 | 2020-11-11 | 2020-11-18 | 2020-11-25 | 2020-12-02 | 2020-12-09 | 2020-12-16 | 2020-12-23 | 2020-12-30 | 2021-01-06 | 2021-01-13 | 2021-01-20 | 2021-01-27 | 2021-02-03 | 2021-02-10 | 2021-02-17 | 2021-02-24 | 2021-03-03 | 2021-03-10 | 2021-03-17 | 2021-03-24 | 2021-03-31 | 2021-04-07 | 2021-04-14 | 2021-04-21 | 2021-04-28 | 2021-05-05 | 2021-05-12 | 2021-05-19 | 2021-05-26 | 2021-06-02 | 2021-06-09 | 2021-06-16 | 2021-06-23 | 2021-06-30 | 2021-07-07 | 2021-07-14 | 2021-07-21 | 2021-07-28 | 2021-08-04 | 2021-08-11 | 2021-08-18 | 2021-08-25 | 2021-09-01 | 2021-09-08 | 2021-09-15 | 2021-09-22 | 2021-09-29 | 2021-10-06 | 2021-10-13 | 2021-10-20 | 2021-10-27 | 2021-11-03 | 2021-11-10 | 2021-11-17 | 2021-11-24 | 2021-12-01 | 2021-12-08 | 2021-12-15 | 2021-12-22 | 2021-12-29 | 2022-01-05 | 2022-01-12 | 2022-01-19 | 2022-01-26 | 2022-02-02 | 2022-02-09 | 2022-02-16 | 2022-02-23 | 2022-03-02 | 2022-03-09 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_2.5_71199.3 | NR_2.5_71199.2 | 3.151 | (16) 1J7T|1|A+1J7T|1|B, 1MWL|1|A+1MWL|1|B, 2ESJ|1|A+2ESJ|1|B, 2ET4|1|A+2ET4|1|B, 2ET5|1|A+2ET5|1|B, 2PWT|1|A+2PWT|1|B, 3TD1|1|B+3TD1|1|A, 3WRU|1|A+3WRU|1|B, 4F8U|1|A+4F8U|1|B, 4K32|1|A+4K32|1|B, 4P3S|1|B+4P3S|1|A, 5Z1H|1|B+5Z1H|1|A, 5Z1I|1|A, 5Z71|1|B+5Z71|1|A, 5ZEG|1|A+5ZEG|1|B+5ZEG|1|C, 5ZEI|1|A+5ZEI|1|B | (0) | (2) 4WCP|1|A+4WCP|1|B+4WCP|1|C, 4WCQ|1|A+4WCQ|1|B |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_2.5_71199.3 | NR_2.5_71199.4 | 3.222 | (16) 1J7T|1|A+1J7T|1|B, 1MWL|1|A+1MWL|1|B, 2ESJ|1|A+2ESJ|1|B, 2ET4|1|A+2ET4|1|B, 2ET5|1|A+2ET5|1|B, 2PWT|1|A+2PWT|1|B, 3TD1|1|B+3TD1|1|A, 3WRU|1|A+3WRU|1|B, 4F8U|1|A+4F8U|1|B, 4K32|1|A+4K32|1|B, 4P3S|1|B+4P3S|1|A, 5Z1H|1|B+5Z1H|1|A, 5Z1I|1|A, 5Z71|1|B+5Z71|1|A, 5ZEG|1|A+5ZEG|1|B+5ZEG|1|C, 5ZEI|1|A+5ZEI|1|B | (0) | (0) |
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.
| #S | View | PDB | Title | Method | Resolution | Length |
|---|---|---|---|---|---|---|
| 1 | 5ZEG|1|A+ 5ZEG|1|B+ 5ZEG|1|C | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site | X-RAY DIFFRACTION | 2.4 | 22 | |
| 2 | 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 | |
| 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 | 1MWL|1|A+ 1MWL|1|B | Crystal structure of geneticin bound to the eubacterial 16S rRNA A site | X-RAY DIFFRACTION | 2.4 | 24 | |
| 10 | 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 | |
| 11 | 5ZEI|1|A+ 5ZEI|1|B | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with geneticin | X-RAY DIFFRACTION | 2.1 | 21 | |
| 12 | 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 | |
| 13 | 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 | |
| 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 |
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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