Equivalence class NR_4.0_74841.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3TD1|1|B+ 3TD1|1|A (rep) | 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 | ||||
| 2 | 2ESI|1|A+ 2ESI|1|B | 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' | Complex between Kanamycin A and the 16S-Rrna A Site. | X-ray diffraction | 3 | 2005-12-20 | ||||
| 3 | 1YRJ|1|A+ 1YRJ|1|B | Bacterial 16 S Ribosomal RNA A Site Oligonucleotide | Crystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotide | X-ray diffraction | 2.7 | 2005-06-07 | ||||
| 4 | 2F4T|1|B+ 2F4T|1|A | 5'-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 antibiotic | X-ray diffraction | 3 | 2006-05-02 | ||||
| 5 | 4GPW|1|A+ 4GPW|1|B | RNA (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 diffraction | 3 | 2013-04-03 | ||||
| 6 | 4GPY|1|A+ 4GPY|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 6'-hydroxysisomicin | X-ray diffraction | 2.8 | 2013-04-03 | ||||
| 7 | 1LC4|1|A+ 1LC4|1|B | 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' | Crystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A Site | X-ray diffraction | 2.54 | 2003-04-08 | ||||
| 8 | 4WCR|1|A+ 4WCR|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 paromomycin | X-ray diffraction | 3.5 | 2015-09-09 | ||||
| 9 | 4P20|1|A+ 4P20|1|B | 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' | synthetic construct | Synthetic | Crystal structures of the bacterial ribosomal decoding site complexed with amikacin | X-ray diffraction | 2.7 | 2014-05-07 | ||
| 10 | 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 | ||||
| 11 | 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 | Eukarya | Crystal structure of geneticin bound to the leishmanial rRNA A-site | X-ray diffraction | 2.5 | 2013-07-31 | ||
| 12 | 4GPX|1|A+ 4GPX|1|B | RNA (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 diffraction | 2.6 | 2013-04-03 | ||||
| 13 | 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 | ||||
| 14 | 4WCS|1|A+ 4WCS|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 the presence of gentamicin | X-ray diffraction | 3.1 | 2015-09-09 | ||||
| 15 | 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 | Synthetic | Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin | X-ray diffraction | 2.3 | 2016-05-04 |
Release history
| Release | 5.0 |
|---|---|
| Date | 2016-07-25 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_4.0_74841.1 | NR_all_33419.1 | 5.0 | (15) 2F4T|1|B+2F4T|1|A, 4P3S|1|B+4P3S|1|A, 3TD1|1|B+3TD1|1|A, 1LC4|1|A+1LC4|1|B, 4WCQ|1|A+4WCQ|1|B, 4GPY|1|A+4GPY|1|B, 3WRU|1|A+3WRU|1|B, 1YRJ|1|A+1YRJ|1|B, 4WCS|1|A+4WCS|1|B, 4P20|1|A+4P20|1|B, 4GPX|1|A+4GPX|1|B, 4WCR|1|A+4WCR|1|B, 4K32|1|A+4K32|1|B, 4GPW|1|A+4GPW|1|B, 2ESI|1|A+2ESI|1|B | (0) | (24) 2O3V|1|A+2O3V|1|B, 3TD0|1|B+3TD0|1|A, 3BNS|1|A+3BNS|1|B, 5BWS|1|A+5BWS|1|B, 4PDQ|1|A+4PDQ|1|B, 2O3X|1|A+2O3X|1|B, 3BNQ|1|C+3BNQ|1|D, 2O3Y|1|A+2O3Y|1|B, 4P3U|1|B+4P3U|1|A, 4K31|1|B+4K31|1|C, 5BXK|1|C+5BXK|1|D, 5BWS|1|C+5BWS|1|D, 2FQN|1|A+2FQN|1|B, 3BNR|1|A+3BNR|1|B, 4P3U|1|C+4P3U|1|D, 4WCP|1|A+4WCP|1|B+4WCP|1|C, 2O3W|1|A+2O3W|1|B, 3BNS|1|C+3BNS|1|D, 4P3T|1|A+4P3T|1|B, 5BXK|1|A+5BXK|1|B, 3BNQ|1|A+3BNQ|1|B, 3BNR|1|C+3BNR|1|D, 4P43|1|B+4P43|1|A, 2G5K|1|A+2G5K|1|B |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_4.0_74841.1 | NR_4.0_88720.1 | 6.0 | (1) 3TD1|1|B+3TD1|1|A | (14) 1LC4|1|A+1LC4|1|B, 1YRJ|1|A+1YRJ|1|B, 2ESI|1|A+2ESI|1|B, 2F4T|1|B+2F4T|1|A, 3WRU|1|A+3WRU|1|B, 4GPW|1|A+4GPW|1|B, 4GPX|1|A+4GPX|1|B, 4GPY|1|A+4GPY|1|B, 4K32|1|A+4K32|1|B, 4P20|1|A+4P20|1|B, 4P3S|1|B+4P3S|1|A, 4WCQ|1|A+4WCQ|1|B, 4WCR|1|A+4WCR|1|B, 4WCS|1|A+4WCS|1|B | (0) |
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 | NAKB_NA_annotation | NAKB_protein_annotation |
|---|---|---|---|---|---|---|---|
| 1 | 4K32|1|A+4K32|1|B | Title: Crystal structure of geneticin bound to the leishmanial rRNA A-site | X-RAY DIFFRACTION | 2.5 | 21 | ||
| 2 | 4GPX|1|A+4GPX|1|B | Title: Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P212121 form) | X-RAY DIFFRACTION | 2.6 | 21 | ||
| 3 | 4GPW|1|A+4GPW|1|B | Title: Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P21212 form) | X-RAY DIFFRACTION | 3 | 22 | ||
| 4 | 4WCQ|1|A+4WCQ|1|B | Title: Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with geneticin | X-RAY DIFFRACTION | 2.1 | 21 | ||
| 5 | 2F4T|1|B+2F4T|1|A | Title: Asite RNA + designer antibiotic | X-RAY DIFFRACTION | 3 | 23 | ||
| 6 | 4WCS|1|A+4WCS|1|B | Title: Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in the presence of gentamicin | X-RAY DIFFRACTION | 3.1 | 21 | ||
| 7 | 4GPY|1|A+4GPY|1|B | Title: Crystal structure of the bacterial ribosomal decoding site in complex with 6'-hydroxysisomicin | X-RAY DIFFRACTION | 2.8 | 22 | ||
| 8 | 4P20|1|A+4P20|1|B | Title: Crystal structures of the bacterial ribosomal decoding site complexed with amikacin | X-RAY DIFFRACTION | 2.7 | 21 | ||
| 9 | 1LC4|1|A+1LC4|1|B | Title: Crystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A Site | X-RAY DIFFRACTION | 2.54 | 21 | ||
| 10 | 2ESI|1|A+2ESI|1|B | Title: Complex between Kanamycin A and the 16S-Rrna A Site. | X-RAY DIFFRACTION | 3 | 23 | ||
| 11 | 3WRU|1|A+3WRU|1|B | Title: Crystal structure of the bacterial ribosomal decoding site in complex with synthetic aminoglycoside with F-HABA group | X-RAY DIFFRACTION | 2.3 | 21 | ||
| 12 | 4P3S|1|B+4P3S|1|A | Title: 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 | Title: 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 | 4WCR|1|A+4WCR|1|B | Title: Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycin | X-RAY DIFFRACTION | 3.5 | 21 | ||
| 15 | 1YRJ|1|A+1YRJ|1|B | Title: Crystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotide | X-RAY DIFFRACTION | 2.7 | 23 |
Coloring options: