Equivalence class NR_4.0_43554.3 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 | 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 | ||||
| 3 | 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 | ||||
| 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 | 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 | ||||
| 7 | 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 | ||||
| 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 | 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 | ||||
| 12 | 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 | ||||
| 13 | 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 | ||||
| 14 | 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 | ||||
| 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 | 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 | ||||
| 17 | 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 | |||
| 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 | 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 | ||||
| 20 | 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 | ||||
| 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 | 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 | ||||
| 23 | 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 | ||||
| 24 | 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 | ||||
| 25 | 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 | ||||
| 26 | 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 | ||||
| 27 | 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 | |||
| 28 | 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 | ||||
| 29 | 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 | 2.40 | 2.41 | 2.42 | 2.43 | 2.44 | 2.45 | 2.46 | 2.47 | 2.48 | 2.49 | 2.50 | 2.51 | 2.52 | 2.53 | 2.54 | 2.55 | 2.56 | 2.57 | 2.58 | 2.59 | 2.60 | 2.61 | 2.62 | 2.63 | 2.64 | 2.65 | 2.66 | 2.67 | 2.68 | 2.69 | 2.70 | 2.71 | 2.72 | 2.73 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2015-09-11 | 2015-09-18 | 2015-09-25 | 2015-10-02 | 2015-10-09 | 2015-10-16 | 2015-10-23 | 2015-10-30 | 2015-11-06 | 2015-11-13 | 2015-11-20 | 2015-11-27 | 2015-12-04 | 2015-12-11 | 2015-12-18 | 2015-12-25 | 2016-01-01 | 2016-01-08 | 2016-01-15 | 2016-01-22 | 2016-01-29 | 2016-02-05 | 2016-02-12 | 2016-02-19 | 2016-02-26 | 2016-03-04 | 2016-03-11 | 2016-03-18 | 2016-03-25 | 2016-04-01 | 2016-04-08 | 2016-04-15 | 2016-04-22 | 2016-04-29 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_4.0_43554.3 | NR_all_43554.2 | 2.40 | (26) 1LC4|1|A+1LC4|1|B, 1YRJ|1|A+1YRJ|1|B, 2ESI|1|A+2ESI|1|B, 2F4T|1|B+2F4T|1|A, 2FQN|1|A+2FQN|1|B, 2G5K|1|A+2G5K|1|B, 2O3V|1|A+2O3V|1|B, 2O3W|1|A+2O3W|1|B, 2O3X|1|A+2O3X|1|B, 2O3Y|1|A+2O3Y|1|B, 3BNQ|1|A+3BNQ|1|B, 3BNQ|1|C+3BNQ|1|D, 3BNR|1|A+3BNR|1|B, 3BNR|1|C+3BNR|1|D, 3BNS|1|A+3BNS|1|B, 3BNS|1|C+3BNS|1|D, 3TD0|1|B+3TD0|1|A, 3TD1|1|B+3TD1|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, 4K31|1|B+4K31|1|C, 4K32|1|A+4K32|1|B, 4P20|1|A+4P20|1|B, 4PDQ|1|A+4PDQ|1|B | (3) 4WCQ|1|A+4WCQ|1|B, 4WCR|1|A+4WCR|1|B, 4WCS|1|A+4WCS|1|B | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|
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 | 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 | 4WCR|1|A+4WCR|1|B | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycin | X-RAY DIFFRACTION | 3.5 | 21 |
| 3 | 1YRJ|1|A+1YRJ|1|B | Crystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotide | X-RAY DIFFRACTION | 2.7 | 23 |
| 4 | 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 |
| 5 | 2ESI|1|A+2ESI|1|B | Complex between Kanamycin A and the 16S-Rrna A Site. | X-RAY DIFFRACTION | 3 | 23 |
| 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 | 4P20|1|A+4P20|1|B | Crystal structures of the bacterial ribosomal decoding site complexed with amikacin | X-RAY DIFFRACTION | 2.7 | 21 |
| 8 | 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 |
| 9 | 2F4T|1|B+2F4T|1|A | Asite RNA + designer antibiotic | X-RAY DIFFRACTION | 3 | 23 |
| 10 | 4WCS|1|A+4WCS|1|B | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in the presence of gentamicin | X-RAY DIFFRACTION | 3.1 | 21 |
| 11 | 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 |
| 12 | 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 |
| 13 | 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 |
| 14 | 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 |
| 15 | 4K32|1|A+4K32|1|B | Crystal structure of geneticin bound to the leishmanial rRNA A-site | X-RAY DIFFRACTION | 2.5 | 21 |
| 16 | 4K31|1|B+4K31|1|C | Crystal structure of apramycin bound to the leishmanial rRNA A-site | X-RAY DIFFRACTION | 1.41 | 22 |
| 17 | 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 |
| 18 | 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 |
| 19 | 2FQN|1|A+2FQN|1|B | Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site | X-RAY DIFFRACTION | 2.3 | 22 |
| 20 | 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 |
| 21 | 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 |
| 22 | 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 |
| 23 | 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 |
| 24 | 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 |
| 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 | 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 |
| 27 | 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 |
| 28 | 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 |
| 29 | 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 |
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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