Equivalence class NR_3.5_88987.4 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 | 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 |
7 | 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 |
8 | 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 |
9 | 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 |
10 | 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 |
11 | 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 |
12 | 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 |
13 | 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 |
14 | 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 |
15 | 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 |
16 | 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 |
17 | 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 |
18 | 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 |
19 | 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 |
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 | 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 |
22 | 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 |
23 | 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 |
24 | 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 |
25 | 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 |
26 | 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 |
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 |
Release history
Release | 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 | 2.74 | 2.75 | 2.76 | 2.77 | 2.78 | 2.79 | 2.80 | 2.81 | 2.82 | 2.83 | 2.84 | 2.85 | 2.86 | 2.87 | 2.88 | 2.89 | 2.90 | 2.91 | 2.92 | 2.93 | 2.94 | 2.95 | 2.96 | 2.97 | 2.98 | 2.99 | 2.100 |
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Date | 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 | 2016-05-06 | 2016-05-13 | 2016-05-20 | 2016-05-27 | 2016-06-03 | 2016-06-10 | 2016-06-17 | 2016-06-24 | 2016-07-01 | 2016-07-08 | 2016-07-15 | 2016-07-22 | 2016-07-29 | 2016-08-05 | 2016-08-12 | 2016-08-19 | 2016-08-26 | 2016-09-02 | 2016-09-09 | 2016-09-16 | 2016-09-23 | 2016-09-30 | 2016-10-07 | 2016-10-14 | 2016-10-21 | 2016-10-28 | 2016-11-04 |
Parents
This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
---|---|---|---|---|---|
NR_3.5_88987.4 | NR_all_88987.3 | 2.55 | (27) 3DLL|1|X, 1OND|1|0, 1JZX|1|A, 3PIP|1|X, 2O44|1|A, 1SM1|1|0, 1K01|1|A, 4IOA|1|X, 2ZJR|1|X, 1Y69|1|0, 1NKW|1|0, 3CF5|1|X, 1NWY|1|0, 1J5A|1|A, 2ZJQ|1|X, 5DM7|1|X, 3PIO|1|X, 1P9X|1|0, 1JZY|1|A, 2D3O|1|0, 4IO9|1|X, 2OGM|1|0, 1XBP|1|0, 1NJP|1|0, 2AAR|1|0, 1NWX|1|0, 5DM6|1|X | (0) | (14) 1Z58|1|2, 1NJN|1|0, 2OGO|1|0, 3FWO|1|A, 2O45|1|A, 4IOC|1|X, 1JZZ|1|A, 4U67|1|X, 3JQ4|1|A, 1NJO|1|0, 2O43|1|A, 1NJM|1|0, 2OGN|1|0, 2ZJP|1|X |
Children
This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
---|---|---|---|---|---|
NR_3.5_88987.4 | NR_3.5_88987.5 | 2.101 | (27) 1NKW|1|0, 3PIO|1|X, 1NJP|1|0, 3DLL|1|X, 1K01|1|A, 3CF5|1|X, 1JZY|1|A, 2ZJR|1|X, 1JZX|1|A, 2ZJQ|1|X, 1J5A|1|A, 2OGM|1|0, 2O44|1|A, 2D3O|1|0, 2AAR|1|0, 1Y69|1|0, 1XBP|1|0, 1SM1|1|0, 5DM7|1|X, 1P9X|1|0, 5DM6|1|X, 1OND|1|0, 4IOA|1|X, 1NWY|1|0, 4IO9|1|X, 1NWX|1|0, 3PIP|1|X | (0) | (1) 5JVG|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 | 5DM7|1|X | Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A | X-RAY DIFFRACTION | 3 | 2780 |
3 | 5DM6|1|X | Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans | X-RAY DIFFRACTION | 2.9 | 2780 |
4 | 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 |
5 | 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 |
6 | 4IOA|1|X | Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans | X-RAY DIFFRACTION | 3.2 | 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 | 2ZJR|1|X | Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans | X-RAY DIFFRACTION | 2.91 | 2686 |
9 | 3CF5|1|X | Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans | X-RAY DIFFRACTION | 3.3 | 2686 |
10 | 2ZJQ|1|X | Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit | X-RAY DIFFRACTION | 3.3 | 2686 |
11 | 3DLL|1|X | The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning | X-RAY DIFFRACTION | 3.5 | 2686 |
12 | 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 |
13 | 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 |
14 | 2AAR|1|0 | Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome. | X-RAY DIFFRACTION | 3.5 | 2766 |
15 | 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 |
16 | 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 |
17 | 1NWY|1|0 | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN | X-RAY DIFFRACTION | 3.3 | 2766 |
18 | 1NWX|1|0 | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 | X-RAY DIFFRACTION | 3.5 | 2766 |
19 | 1NKW|1|0 | Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans | X-RAY DIFFRACTION | 3.1 | 2766 |
20 | 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 |
21 | 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 |
22 | 1SM1|1|0 | COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN | X-RAY DIFFRACTION | 3.42 | 2766 |
23 | 1Y69|1|0 | RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans | X-RAY DIFFRACTION | 3.33 | 2766 |
24 | 1K01|1|A | Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria | X-RAY DIFFRACTION | 3.5 | 2774 |
25 | 1JZX|1|A | Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria | X-RAY DIFFRACTION | 3.1 | 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 | 1J5A|1|A | STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA | X-RAY DIFFRACTION | 3.5 | 2774 |