Equivalence class NR_3.5_88987.5 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 | 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 |
| 4 | 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 |
| 5 | 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 |
| 6 | 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 |
| 7 | 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 |
| 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 | 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 |
| 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 | 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 |
| 12 | 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 |
| 13 | 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 |
| 14 | 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 |
| 15 | 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 |
| 16 | 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 |
| 17 | 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 |
| 18 | 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 |
| 19 | 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 |
| 20 | 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 |
| 21 | 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 |
| 22 | 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 |
| 23 | 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 |
| 24 | 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 |
| 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 | 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 |
| 27 | 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 |
| 28 | 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 |
Release history
| Release | 2.101 | 2.102 | 2.103 | 2.104 | 2.105 | 2.106 | 2.107 | 2.108 | 2.109 | 2.110 | 2.111 | 2.112 | 2.113 | 2.114 | 2.115 | 2.116 | 2.117 | 2.118 | 2.119 | 2.120 | 2.121 | 2.122 | 2.123 | 2.124 | 2.125 | 2.126 | 2.127 | 2.128 | 2.129 | 2.130 | 2.131 | 2.132 | 2.133 | 2.134 | 2.135 | 2.136 | 2.137 | 2.138 | 2.139 | 2.140 | 2.141 | 2.142 | 2.143 | 2.144 | 2.145 | 2.146 | 2.147 | 2.148 | 2.149 | 2.150 | 2.151 | 2.152 | 2.153 | 2.154 | 2.155 | 2.156 | 2.157 | 2.158 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2016-11-11 | 2016-11-18 | 2016-11-25 | 2016-12-02 | 2016-12-09 | 2016-12-16 | 2016-12-23 | 2016-12-30 | 2017-01-06 | 2017-01-13 | 2017-01-20 | 2017-01-27 | 2017-02-03 | 2017-02-10 | 2017-02-17 | 2017-02-24 | 2017-03-03 | 2017-03-10 | 2017-03-17 | 2017-03-24 | 2017-03-31 | 2017-04-11 | 2017-04-15 | 2017-04-26 | 2017-04-29 | 2017-05-09 | 2017-05-15 | 2017-05-20 | 2017-05-27 | 2017-06-07 | 2017-06-11 | 2017-06-21 | 2017-06-24 | 2017-06-28 | 2017-07-04 | 2017-07-10 | 2017-07-15 | 2017-07-26 | 2017-07-31 | 2017-08-05 | 2017-08-12 | 2017-08-19 | 2017-08-26 | 2017-09-03 | 2017-09-09 | 2017-09-16 | 2017-09-23 | 2017-09-30 | 2017-10-07 | 2017-10-14 | 2017-10-21 | 2017-10-28 | 2017-11-03 | 2017-11-10 | 2017-11-17 | 2017-11-24 | 2017-12-01 | 2017-12-08 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.5_88987.5 | NR_3.5_88987.4 | 2.101 | (27) 1J5A|1|A, 1JZX|1|A, 1JZY|1|A, 1K01|1|A, 1NJP|1|0, 1NKW|1|0, 1NWX|1|0, 1NWY|1|0, 1OND|1|0, 1P9X|1|0, 1SM1|1|0, 1XBP|1|0, 1Y69|1|0, 2AAR|1|0, 2D3O|1|0, 2O44|1|A, 2OGM|1|0, 2ZJQ|1|X, 2ZJR|1|X, 3CF5|1|X, 3DLL|1|X, 3PIO|1|X, 3PIP|1|X, 4IO9|1|X, 4IOA|1|X, 5DM6|1|X, 5DM7|1|X | (1) 5JVG|1|X | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.5_88987.5 | NR_3.5_88987.6 | 3.0 | (28) 1J5A|1|A, 1JZX|1|A, 1JZY|1|A, 1K01|1|A, 1NJP|1|0, 1NKW|1|0, 1NWX|1|0, 1NWY|1|0, 1OND|1|0, 1P9X|1|0, 1SM1|1|0, 1XBP|1|0, 1Y69|1|0, 2AAR|1|0, 2D3O|1|0, 2O44|1|A, 2OGM|1|0, 2ZJQ|1|X, 2ZJR|1|X, 3CF5|1|X, 3DLL|1|X, 3PIO|1|X, 3PIP|1|X, 4IO9|1|X, 4IOA|1|X, 5DM6|1|X, 5DM7|1|X, 5JVG|1|X | (0) | (1) 5DM8|1|X |
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 | 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 | 3DLL|1|X | The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning | X-RAY DIFFRACTION | 3.5 | 2686 | |
| 3 | 2ZJQ|1|X | Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit | X-RAY DIFFRACTION | 3.3 | 2686 | |
| 4 | 3CF5|1|X | Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans | X-RAY DIFFRACTION | 3.3 | 2686 | |
| 5 | 2ZJR|1|X | Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans | X-RAY DIFFRACTION | 2.91 | 2686 | |
| 6 | 4IO9|1|X | Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans | X-RAY DIFFRACTION | 3.2 | 2686 | |
| 7 | 4IOA|1|X | Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans | X-RAY DIFFRACTION | 3.2 | 2686 | |
| 8 | 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 | |
| 9 | 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 | |
| 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 | 1SM1|1|0 | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN | X-RAY DIFFRACTION | 3.42 | 2766 | |
| 18 | 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 | |
| 19 | 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 | |
| 20 | 1NKW|1|0 | Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans | X-RAY DIFFRACTION | 3.1 | 2766 | |
| 21 | 1NWX|1|0 | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 | X-RAY DIFFRACTION | 3.5 | 2766 | |
| 22 | 1NWY|1|0 | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN | X-RAY DIFFRACTION | 3.3 | 2766 | |
| 23 | 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 | |
| 24 | 1J5A|1|A | STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA | X-RAY DIFFRACTION | 3.5 | 2774 | |
| 25 | 1JZY|1|A | Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria | X-RAY DIFFRACTION | 3.5 | 2774 | |
| 26 | 1JZX|1|A | Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria | X-RAY DIFFRACTION | 3.1 | 2774 | |
| 27 | 1K01|1|A | Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria | X-RAY DIFFRACTION | 3.5 | 2774 | |
| 28 | 1Y69|1|0 | RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans | X-RAY DIFFRACTION | 3.33 | 2766 |
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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