Equivalence class NR_3.5_88987.7 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 4IOA|1|X (rep) | Large subunit ribosomal RNA | 23S ribosomal RNA | Deinococcus radiodurans | Bacteria | RF02541 | Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans | X-ray diffraction | 3.2 | 2013-03-06 |
| 2 | 4IO9|1|X | Large subunit ribosomal RNA | 23S ribosomal RNA | Deinococcus radiodurans | Bacteria | RF02541 | Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans | X-ray diffraction | 3.2 | 2013-03-06 |
| 3 | 5JVG|1|X | Large subunit ribosomal RNA | 23S ribosomal RNA | Deinococcus radiodurans | Bacteria | RF02541 | The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin | X-ray diffraction | 3.43 | 2016-11-09 |
| 4 | 5DM6|1|X | Large subunit ribosomal RNA | 23S ribosomal RNA | Deinococcus radiodurans | Bacteria | RF02541 | Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans | X-ray diffraction | 2.9 | 2015-11-11 |
| 5 | 3PIO|1|X | Large subunit ribosomal RNA | RIBOSOMAL 23S RNA | Deinococcus radiodurans | Bacteria | RF02541 | Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit | X-ray diffraction | 3.25 | 2011-02-23 |
| 6 | 5DM7|1|X | Large subunit ribosomal RNA | 23S ribosomal RNA | Deinococcus radiodurans | Bacteria | RF02541 | Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A | X-ray diffraction | 3 | 2015-11-11 |
| 7 | 3PIP|1|X | Large subunit ribosomal RNA | RIBOSOMAL 23S RNA | Deinococcus radiodurans | Bacteria | RF02541 | Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit | X-ray diffraction | 3.45 | 2011-02-23 |
| 8 | 3DLL|1|X | Large subunit ribosomal RNA | rRNA-23S ribosomal RNA | Deinococcus radiodurans | Bacteria | RF02541 | The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning | X-ray diffraction | 3.5 | 2008-09-16 |
| 9 | 1OND|1|0 | Large subunit ribosomal RNA | 23S RIBOSOMAL RNA | Deinococcus radiodurans | Bacteria | RF02541 | THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTIC | X-ray diffraction | 3.4 | 2003-04-15 |
| 10 | 2AAR|1|0 | Large subunit ribosomal RNA | 23S ribosomal RNA | Deinococcus radiodurans | Bacteria | RF02541 | Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome. | X-ray diffraction | 3.5 | 2005-08-23 |
| 11 | 1Y69|1|0 | Large subunit ribosomal RNA | 23S ribosomal RNA | Deinococcus radiodurans | Bacteria | RF02541 | RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans | X-ray diffraction | 3.33 | 2005-03-01 |
| 12 | 2ZJR|1|X | Large subunit ribosomal RNA | ribosomal 23S RNA | Deinococcus radiodurans | Bacteria | RF02541 | Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans | X-ray diffraction | 2.91 | 2008-06-17 |
| 13 | 3CF5|1|X | Large subunit ribosomal RNA | RRNA-23S RIBOSOMAL RNA | Deinococcus radiodurans | Bacteria | RF02541 | Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans | X-ray diffraction | 3.3 | 2008-06-17 |
| 14 | 2ZJQ|1|X | Large subunit ribosomal RNA | ribosomal 23S RNA | Deinococcus radiodurans | Bacteria | RF02541 | Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit | X-ray diffraction | 3.3 | 2008-06-17 |
| 15 | 2OGM|1|0 | Large subunit ribosomal RNA | 23S ribosomal RNA | Deinococcus radiodurans | Bacteria | RF02541 | The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519 | X-ray diffraction | 3.5 | 2007-05-01 |
| 16 | 1JZX|1|A | Large subunit ribosomal RNA | 23S rRNA | Deinococcus radiodurans | Bacteria | RF02541 | Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria | X-ray diffraction | 3.1 | 2001-10-26 |
| 17 | 1NKW|1|0 | Large subunit ribosomal RNA | 23S ribosomal RNA | Deinococcus radiodurans | Bacteria | RF02541 | Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans | X-ray diffraction | 3.1 | 2003-02-11 |
| 18 | 1NWY|1|0 | Large subunit ribosomal RNA | 23S RIBOSOMAL RRNA | Deinococcus radiodurans | Bacteria | RF02541 | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN | X-ray diffraction | 3.3 | 2003-03-18 |
| 19 | 1NJP|1|0 | Large subunit ribosomal RNA | 23S ribosomal RNA | Deinococcus radiodurans | Bacteria | RF02541 | The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) | X-ray diffraction | 3.5 | 2003-02-11 |
| 20 | 1NWX|1|0 | Large subunit ribosomal RNA | 23S RIBOSOMAL RNA | Deinococcus radiodurans | Bacteria | RF02541 | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 | X-ray diffraction | 3.5 | 2003-03-18 |
| 21 | 1J5A|1|A | Large subunit ribosomal RNA | 23S RRNA | Deinococcus radiodurans | Bacteria | RF02541 | STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA | X-ray diffraction | 3.5 | 2002-03-08 |
| 22 | 1JZY|1|A | Large subunit ribosomal RNA | 23S rRNA | Deinococcus radiodurans | Bacteria | RF02541 | Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria | X-ray diffraction | 3.5 | 2001-10-26 |
| 23 | 1K01|1|A | Large subunit ribosomal RNA | 23S rRNA | Deinococcus radiodurans | Bacteria | RF02541 | Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria | X-ray diffraction | 3.5 | 2001-10-26 |
| 24 | 1SM1|1|0 | Large subunit ribosomal RNA | 23S RIBOSOMAL RNA | Deinococcus radiodurans | Bacteria | RF02541 | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN | X-ray diffraction | 3.42 | 2004-08-03 |
| 25 | 1P9X|1|0 | Large subunit ribosomal RNA | 23S RIBOSOMAL RNA | Deinococcus radiodurans | Bacteria | RF02541 | THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TELITHROMYCIN KETOLIDE ANTIBIOTIC | X-ray diffraction | 3.4 | 2003-08-05 |
| 26 | 2D3O|1|0 | Large subunit ribosomal RNA | 23S RIBOSOMAL RNA | Deinococcus radiodurans | Bacteria | RF02541 | Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans | X-ray diffraction | 3.35 | 2005-12-06 |
| 27 | 1XBP|1|0 | Large subunit ribosomal RNA | 23S RIBOSOMAL RNA | Deinococcus radiodurans | Bacteria | RF02541 | Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin | X-ray diffraction | 3.5 | 2005-03-01 |
| 28 | 2O44|1|A | Large subunit ribosomal RNA | 23S rRNA | Deinococcus radiodurans | Bacteria | RF02541 | Structure of 23S rRNA of the large ribosomal subunit from Deinococcus radiodurans in complex with the macrolide josamycin | X-ray diffraction | 3.3 | 2007-12-04 |
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.5_88987.7 | NR_3.5_88987.6 | 3.151 | (28) 2D3O|1|0, 1P9X|1|0, 1NJP|1|0, 5DM7|1|X, 3PIO|1|X, 2OGM|1|0, 1XBP|1|0, 1NWX|1|0, 1JZX|1|A, 4IO9|1|X, 2ZJR|1|X, 2AAR|1|0, 1OND|1|0, 1K01|1|A, 5DM6|1|X, 3DLL|1|X, 2O44|1|A, 1SM1|1|0, 1NKW|1|0, 1J5A|1|A, 5JVG|1|X, 3PIP|1|X, 2ZJQ|1|X, 1Y69|1|0, 1NWY|1|0, 1JZY|1|A, 4IOA|1|X, 3CF5|1|X | (0) | (1) 5DM8|1|X |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.5_88987.7 | NR_3.5_88987.8 | 3.192 | (28) 1JZX|1|A, 1P9X|1|0, 2ZJQ|1|X, 5DM6|1|X, 1J5A|1|A, 1OND|1|0, 2OGM|1|0, 4IOA|1|X, 1NWY|1|0, 2O44|1|A, 4IO9|1|X, 1NWX|1|0, 2D3O|1|0, 3PIP|1|X, 1NKW|1|0, 2AAR|1|0, 3PIO|1|X, 1NJP|1|0, 1Y69|1|0, 3DLL|1|X, 1K01|1|A, 1XBP|1|0, 3CF5|1|X, 5JVG|1|X, 1JZY|1|A, 1SM1|1|0, 2ZJR|1|X, 5DM7|1|X | (0) | (2) 7A0R|1|X, 7A0S|1|X |
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 | 2D3O|1|0 | Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans | X-RAY DIFFRACTION | 3.35 | 2802 |
| 2 | 3PIO|1|X | Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit | X-RAY DIFFRACTION | 3.25 | 2657 |
| 3 | 3PIP|1|X | Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit | X-RAY DIFFRACTION | 3.45 | 2644 |
| 4 | 3CF5|1|X | Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans | X-RAY DIFFRACTION | 3.3 | 2686 |
| 5 | 2ZJQ|1|X | Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit | X-RAY DIFFRACTION | 3.3 | 2686 |
| 6 | 2ZJR|1|X | Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans | X-RAY DIFFRACTION | 2.91 | 2686 |
| 7 | 4IO9|1|X | Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans | X-RAY DIFFRACTION | 3.2 | 2686 |
| 8 | 4IOA|1|X | Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans | X-RAY DIFFRACTION | 3.2 | 2686 |
| 9 | 3DLL|1|X | The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning | X-RAY DIFFRACTION | 3.5 | 2686 |
| 10 | 5DM6|1|X | Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans | X-RAY DIFFRACTION | 2.9 | 2780 |
| 11 | 5DM7|1|X | Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A | X-RAY DIFFRACTION | 3 | 2780 |
| 12 | 5JVG|1|X | The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin | X-RAY DIFFRACTION | 3.43 | 2711 |
| 13 | 2O44|1|A | Structure of 23S rRNA of the large ribosomal subunit from Deinococcus radiodurans in complex with the macrolide josamycin | X-RAY DIFFRACTION | 3.3 | 2766 |
| 14 | 2OGM|1|0 | The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519 | X-RAY DIFFRACTION | 3.5 | 2766 |
| 15 | 2AAR|1|0 | Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome. | X-RAY DIFFRACTION | 3.5 | 2766 |
| 16 | 1P9X|1|0 | THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TELITHROMYCIN KETOLIDE ANTIBIOTIC | X-RAY DIFFRACTION | 3.4 | 2738 |
| 17 | 1NJP|1|0 | The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) | X-RAY DIFFRACTION | 3.5 | 2766 |
| 18 | 1NWY|1|0 | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN | X-RAY DIFFRACTION | 3.3 | 2766 |
| 19 | 1NWX|1|0 | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 | X-RAY DIFFRACTION | 3.5 | 2766 |
| 20 | 1NKW|1|0 | Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans | X-RAY DIFFRACTION | 3.1 | 2766 |
| 21 | 1OND|1|0 | THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTIC | X-RAY DIFFRACTION | 3.4 | 2765 |
| 22 | 1XBP|1|0 | Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin | X-RAY DIFFRACTION | 3.5 | 2766 |
| 23 | 1SM1|1|0 | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN | X-RAY DIFFRACTION | 3.42 | 2766 |
| 24 | 1Y69|1|0 | RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans | X-RAY DIFFRACTION | 3.33 | 2766 |
| 25 | 1J5A|1|A | STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA | X-RAY DIFFRACTION | 3.5 | 2774 |
| 26 | 1JZY|1|A | Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria | X-RAY DIFFRACTION | 3.5 | 2774 |
| 27 | 1JZX|1|A | Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria | X-RAY DIFFRACTION | 3.1 | 2774 |
| 28 | 1K01|1|A | Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria | X-RAY DIFFRACTION | 3.5 | 2774 |