Equivalence class NR_all_43554.2 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 | 4PDQ|1|A+ 4PDQ|1|B | RNA (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 construct | Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neomycin analog | X-ray diffraction | 3 | 2015-01-07 | |||
| 5 | 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 | ||||
| 6 | 2O3Y|1|A+ 2O3Y|1|B | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3') | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in Presence of Paromamine Derivative NB30 | X-ray diffraction | 2.7 | 2007-11-06 | ||||
| 7 | 2O3V|1|A+ 2O3V|1|B | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3') | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with paromamine derivative NB33 | X-ray diffraction | 2.8 | 2007-11-06 | ||||
| 8 | 3BNS|1|A+ 3BNS|1|B | A site of human mitochondrial ribosome, chain three, A site of human mitochondrial ribosome, chain two | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G mutant, Br-derivative) | X-ray diffraction | 1.9 | 2008-06-24 | ||||
| 9 | 2G5K|1|A+ 2G5K|1|B | 5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3' | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with Apramycin | X-ray diffraction | 2.8 | 2006-06-20 | ||||
| 10 | 3BNR|1|A+ 3BNR|1|B | A site of human mitochondrial ribosome, chain one, A site of human mitochondrial ribosome, chain two | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative) | X-ray diffraction | 2.1 | 2008-06-24 | ||||
| 11 | 2FQN|1|A+ 2FQN|1|B | 5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3' | Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site | X-ray diffraction | 2.3 | 2006-02-14 | ||||
| 12 | 2O3W|1|A+ 2O3W|1|B | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3') | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in presence of paromomycin | X-ray diffraction | 2.8 | 2007-11-06 | ||||
| 13 | 3BNQ|1|A+ 3BNQ|1|B | A site of human mitochondrial ribosome, A chain | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative) | X-ray diffraction | 2 | 2008-06-24 | ||||
| 14 | 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 | ||||
| 15 | 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 | ||||
| 16 | 4K31|1|B+ 4K31|1|C | 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 apramycin bound to the leishmanial rRNA A-site | X-ray diffraction | 1.41 | 2013-07-31 | |||
| 17 | 3TD0|1|B+ 3TD0|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 | X-ray diffraction | 1.6 | 2011-12-07 | ||||
| 18 | 3BNR|1|C+ 3BNR|1|D | A site of human mitochondrial ribosome, chain one, A site of human mitochondrial ribosome, chain three | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative) | X-ray diffraction | 2.1 | 2008-06-24 | ||||
| 19 | 3BNQ|1|C+ 3BNQ|1|D | A site of human mitochondrial ribosome, A chain, A site of human mitochondrial ribosome, B chain | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative) | X-ray diffraction | 2 | 2008-06-24 | ||||
| 20 | 3BNS|1|C+ 3BNS|1|D | A site of human mitochondrial ribosome, chain three | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G mutant, Br-derivative) | X-ray diffraction | 1.9 | 2008-06-24 | ||||
| 21 | 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 | ||||
| 22 | 2O3X|1|A+ 2O3X|1|B | RNA (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 the Prokaryotic Ribosomal Decoding Site Complexed with Paromamine Derivative NB30 | X-ray diffraction | 2.9 | 2007-11-06 | ||||
| 23 | 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 | ||||
| 24 | 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 | |||
| 25 | 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 | ||||
| 26 | 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 | Crystal structures of the bacterial ribosomal decoding site complexed with amikacin | X-ray diffraction | 2.7 | 2014-05-07 |
Release history
| Release | 2.5 | 2.6 | 2.7 | 2.8 | 2.9 | 2.10 | 2.11 | 2.12 | 2.13 | 2.14 | 2.15 | 2.16 | 2.17 | 2.18 | 2.19 | 2.20 | 2.21 | 2.22 | 2.23 | 2.24 | 2.25 | 2.26 | 2.27 | 2.28 | 2.29 | 2.30 | 2.31 | 2.32 | 2.33 | 2.34 | 2.35 | 2.36 | 2.37 | 2.38 | 2.39 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2015-01-09 | 2015-01-16 | 2015-01-23 | 2015-01-30 | 2015-02-06 | 2015-02-13 | 2015-02-20 | 2015-02-27 | 2015-03-06 | 2015-03-13 | 2015-03-20 | 2015-03-27 | 2015-04-03 | 2015-04-10 | 2015-04-17 | 2015-04-24 | 2015-05-01 | 2015-05-08 | 2015-05-15 | 2015-05-22 | 2015-05-29 | 2015-06-05 | 2015-06-12 | 2015-06-19 | 2015-06-26 | 2015-07-03 | 2015-07-10 | 2015-07-17 | 2015-07-24 | 2015-07-31 | 2015-08-07 | 2015-08-14 | 2015-08-21 | 2015-08-28 | 2015-09-04 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_all_43554.2 | NR_all_43554.1 | 2.5 | (25) 2FQN|1|A+2FQN|1|B, 2F4T|1|B+2F4T|1|A, 2ESI|1|A+2ESI|1|B, 1YRJ|1|A+1YRJ|1|B, 1LC4|1|A+1LC4|1|B, 4P20|1|A+4P20|1|B, 4K32|1|A+4K32|1|B, 4K31|1|B+4K31|1|C, 4GPY|1|A+4GPY|1|B, 4GPX|1|A+4GPX|1|B, 4GPW|1|A+4GPW|1|B, 3WRU|1|A+3WRU|1|B, 3TD1|1|B+3TD1|1|A, 3TD0|1|B+3TD0|1|A, 3BNS|1|C+3BNS|1|D, 3BNS|1|A+3BNS|1|B, 3BNR|1|C+3BNR|1|D, 3BNR|1|A+3BNR|1|B, 3BNQ|1|C+3BNQ|1|D, 3BNQ|1|A+3BNQ|1|B, 2O3Y|1|A+2O3Y|1|B, 2O3X|1|A+2O3X|1|B, 2O3W|1|A+2O3W|1|B, 2O3V|1|A+2O3V|1|B, 2G5K|1|A+2G5K|1|B | (1) 4PDQ|1|A+4PDQ|1|B | (0) |
Children
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 | 2O3X|1|A+2O3X|1|B | Crystal Structure of the Prokaryotic Ribosomal Decoding Site Complexed with Paromamine Derivative NB30 | X-RAY DIFFRACTION | 2.9 | 21 |
| 2 | 1YRJ|1|A+1YRJ|1|B | Crystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotide | X-RAY DIFFRACTION | 2.7 | 23 |
| 3 | 2F4T|1|B+2F4T|1|A | Asite RNA + designer antibiotic | X-RAY DIFFRACTION | 3 | 23 |
| 4 | 4GPY|1|A+4GPY|1|B | Crystal structure of the bacterial ribosomal decoding site in complex with 6'-hydroxysisomicin | X-RAY DIFFRACTION | 2.8 | 22 |
| 5 | 4P20|1|A+4P20|1|B | Crystal structures of the bacterial ribosomal decoding site complexed with amikacin | X-RAY DIFFRACTION | 2.7 | 21 |
| 6 | 1LC4|1|A+1LC4|1|B | Crystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A Site | X-RAY DIFFRACTION | 2.54 | 21 |
| 7 | 2ESI|1|A+2ESI|1|B | Complex between Kanamycin A and the 16S-Rrna A Site. | X-RAY DIFFRACTION | 3 | 23 |
| 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 | 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 |
| 10 | 4GPX|1|A+4GPX|1|B | Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P212121 form) | X-RAY DIFFRACTION | 2.6 | 21 |
| 11 | 4GPW|1|A+4GPW|1|B | Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P21212 form) | X-RAY DIFFRACTION | 3 | 22 |
| 12 | 4K32|1|A+4K32|1|B | Crystal structure of geneticin bound to the leishmanial rRNA A-site | X-RAY DIFFRACTION | 2.5 | 21 |
| 13 | 4K31|1|B+4K31|1|C | Crystal structure of apramycin bound to the leishmanial rRNA A-site | X-RAY DIFFRACTION | 1.41 | 22 |
| 14 | 2G5K|1|A+2G5K|1|B | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with Apramycin | X-RAY DIFFRACTION | 2.8 | 22 |
| 15 | 2O3W|1|A+2O3W|1|B | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in presence of paromomycin | X-RAY DIFFRACTION | 2.8 | 22 |
| 16 | 2FQN|1|A+2FQN|1|B | Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site | X-RAY DIFFRACTION | 2.3 | 22 |
| 17 | 2O3Y|1|A+2O3Y|1|B | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in Presence of Paromamine Derivative NB30 | X-RAY DIFFRACTION | 2.7 | 22 |
| 18 | 2O3V|1|A+2O3V|1|B | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with paromamine derivative NB33 | X-RAY DIFFRACTION | 2.8 | 22 |
| 19 | 4PDQ|1|A+4PDQ|1|B | Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neomycin analog | X-RAY DIFFRACTION | 3 | 23 |
| 20 | 3TD0|1|B+3TD0|1|A | Crystal structure of the bacterial A1408G-mutant and the protozoa cytoplasmic ribosomal decoding site | X-RAY DIFFRACTION | 1.6 | 22 |
| 21 | 3BNQ|1|A+3BNQ|1|B | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative) | X-RAY DIFFRACTION | 2 | 22 |
| 22 | 3BNR|1|A+3BNR|1|B | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative) | X-RAY DIFFRACTION | 2.1 | 22 |
| 23 | 3BNS|1|A+3BNS|1|B | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G mutant, Br-derivative) | X-RAY DIFFRACTION | 1.9 | 22 |
| 24 | 3BNS|1|C+3BNS|1|D | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G mutant, Br-derivative) | X-RAY DIFFRACTION | 1.9 | 22 |
| 25 | 3BNR|1|C+3BNR|1|D | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative) | X-RAY DIFFRACTION | 2.1 | 22 |
| 26 | 3BNQ|1|C+3BNQ|1|D | Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative) | X-RAY DIFFRACTION | 2 | 22 |
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