Equivalence class NR_4.0_94729.10 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 4NLF|1|A (rep) | 23S ribosomal RNA Sarcin Ricin Loop | 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL | X-ray diffraction | 1 | 2014-11-19 | ||||
| 2 | 5D99|1|A | RNA (27-MER) hairpin from sarcin-ricin domain of E. coli 23S rRNA | Enterobacteria phage L1 | 3DW4 redetermined by direct methods starting from random phase angles | X-ray diffraction | 0.97 | 2016-04-13 | |||
| 3 | 6Y0Y|1|A | RNA (27-MER) | synthetic construct | Sarcin Ricin Loop, mutant C2666U | X-ray diffraction | 0.95 | 2021-02-17 | |||
| 4 | 1Q9A|1|A | Sarcin/ricin 23S rRNA | Crystal structure of the sarcin/ricin domain from E.coli 23S rRNA at 1.04 resolution | X-ray diffraction | 1.04 | 2003-11-25 | ||||
| 5 | 7QP2|1|A | RNA (27-MER) | synthetic construct | 1-deazaguanosine modified-RNA Sarcin Ricin Loop | X-ray diffraction | 0.9 | 2022-07-20 | |||
| 6 | 4NMG|1|A | 23S ribosomal RNA Sarcin Ricin Loop | 2'-Trifluoromethylthio-2'-deoxyuridine-modified SRL | X-ray diffraction | 1.01 | 2014-11-19 | ||||
| 7 | 6ZYB|1|A | Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification | synthetic construct | Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification | X-ray diffraction | 0.9 | 2020-12-16 | |||
| 8 | 3DW4|1|A | Sarcin/Ricin Domain from E. Coli 23 S rRNA | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-OCH3 modified | X-ray diffraction | 0.97 | 2009-03-24 | ||||
| 9 | 3DW6|1|A | Sarcin/Ricin Domain from E. Coli 23 S rRNA | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-SECH3 modified | X-ray diffraction | 1 | 2009-03-24 | ||||
| 10 | 7L3R|1|A | RNA (27-MER) | synthetic construct | 23S Sarcin Ricin Loop with a 3-deazapurine A2670 | X-ray diffraction | 1.01 | 2021-05-05 | |||
| 11 | 4Y27|1|A | 27-mer 23S Sarcin-Ricil Loop | Escherichia coli | E.coli 23S Sarcin-Ricil Loop, modified with a 2-Me on G2661 and a methylphosphonate on A2662 | X-ray diffraction | 1 | 2015-11-18 | |||
| 12 | 7JJE|1|A | RNA (27-MER) | synthetic construct | Sarcin-ricin loop with guanosine dithiophosphate residue. | X-ray diffraction | 1.25 | 2020-12-23 | |||
| 13 | 3DVZ|1|A | Sarcin/Ricin Domain from E. Coli 23 S rRNA | Crystal Structure of the Sarcin/Ricin Domain from E. coli 23 S rRNA | X-ray diffraction | 1 | 2009-03-24 | ||||
| 14 | 4NXH|1|A | 23S ribosomal RNA Sarcin Ricin Loop | Escherichia coli | 2'-Trifluoromethylthiouridine-modified E. coli 23S rRNA Sarcin Ricin Loop | X-ray diffraction | 1.16 | 2014-12-10 | |||
| 15 | 5NQI|1|A | E.Coli 27-mer SRL RNA | Escherichia coli | E.coli 16S rRNA Sarcin-Ricin Loop containing a 5-hydroxymethylcytosine modification | X-ray diffraction | 0.85 | 2017-07-26 | |||
| 16 | 3S7C|1|A | Ecoli 23 S rRNA Sarcin Ricin loop | Crystal structure of a 2'-azido-uridine-modified RNA | X-ray diffraction | 1.1 | 2012-04-11 | ||||
| 17 | 5MRX|1|A | RNA (27-MER) | Escherichia coli | 27-nt SRL with a 5-hydroxymethyl cytidine modification | X-ray diffraction | 0.85 | 2018-01-17 | |||
| 18 | 7QSH|1|A | 23S ribosomal RNA Sarcin Ricin Loop 27-nucleotide fragment | synthetic construct | 23S ribosomal RNA Sarcin Ricin Loop 27-nt fragment containing a Xanthosine residue at position 2648 | X-ray diffraction | 0.86 | 2023-01-25 | |||
| 19 | 3DW5|1|A | Sarcin/Ricin Domain from E. Coli 23 S rRNA | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23S rRNA, U2656-OCH3 modified | X-ray diffraction | 0.96 | 2009-03-24 | ||||
| 20 | 3DW7|1|A | Sarcin/Ricin Domain from E. Coli 23 S rRNA | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2656-SeCH3 modified | X-ray diffraction | 1 | 2009-03-24 | ||||
| 21 | 483D|1|A | SARCIN/RICIN RRNA DOMAIN | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | X-ray diffraction | 1.11 | 1999-10-08 | ||||
| 22 | 3S8U|1|A | Ecoli 23 S rRNA Sarcin Ricin loop | Escherichia coli | Crystal structure of a 2-azido-adenine-modified RNA | X-ray diffraction | 1.2 | 2012-04-11 | |||
| 23 | 7JJD|1|A | RNA (27-MER) | synthetic construct | Sarcin-ricin loop with guanosine monothiophosphate residue. | X-ray diffraction | 1.21 | 2020-12-23 | |||
| 24 | 1MSY|1|A | SARCIN/RICIN DOMAIN FROM 23 S RRNA | GUAA tetraloop mutant of Sarcin/Ricin domain from E. Coli 23 S rRNA | X-ray diffraction | 1.41 | 2003-02-25 | ||||
| 25 | 480D|1|A | SARCIN/RICIN DOMAIN FROM 23 S RRNA | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | X-ray diffraction | 1.5 | 1999-10-08 | ||||
| 26 | 6Y0T|1|B | RNA (27-MER) | synthetic construct | Sarcin Ricin Loop, mutant C2666A U2653G C2667A | X-ray diffraction | 1.393 | 2021-02-17 | |||
| 27 | 6Y0T|1|A | RNA (27-MER) | synthetic construct | Sarcin Ricin Loop, mutant C2666A U2653G C2667A | X-ray diffraction | 1.393 | 2021-02-17 | |||
| 28 | 7M3V|1|A | RNA (27-MER) | synthetic construct | RNA bulged-G motif | X-ray diffraction | 2.19 | 2022-03-23 | |||
| 29 | 7JJF|1|A | RNA/DNA (27-mer) | Escherichia coli | Sarcin-ricin loop with modified residue. | X-ray diffraction | 1.2 | 2020-12-23 | |||
| 30 | 1JBR|1|D | 31-mer SRD RNA analog | Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor | X-ray diffraction | 2.15 | 2001-10-26 | ||||
| 31 | 7EEN|1|A | DNA/RNA (27-MER) | synthetic construct | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-ray diffraction | 1.7 | 2022-03-23 | |||
| 32 | 7EEN|1|B | DNA/RNA (27-MER) | synthetic construct | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-ray diffraction | 1.7 | 2022-03-23 | |||
| 33 | 7EEM|1|A | RNA (27-MER) | synthetic construct | RNA bulged-G motif | X-ray diffraction | 2.593 | 2022-03-23 | |||
| 34 | 1JBT|1|C | 29-MER SARCIN/RICIN DOMAIN RNA ANALOG | CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG | X-ray diffraction | 2.7 | 2001-10-26 | ||||
| 35 | 6ZXZ|1|B | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | synthetic construct | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-ray diffraction | 2.44 | 2020-12-16 | |||
| 36 | 7EEN|1|D | DNA/RNA (27-MER) | synthetic construct | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-ray diffraction | 1.7 | 2022-03-23 | |||
| 37 | 1JBT|1|D | 29-MER SARCIN/RICIN DOMAIN RNA ANALOG | CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG | X-ray diffraction | 2.7 | 2001-10-26 | ||||
| 38 | 1JBS|1|D | 29-mer sarcin/ricin domain RNA analog | Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog | X-ray diffraction | 1.97 | 2001-10-26 | ||||
| 39 | 7EEN|1|C | DNA/RNA (27-MER) | synthetic construct | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-ray diffraction | 1.7 | 2022-03-23 | |||
| 40 | 6ZXZ|1|A | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | synthetic construct | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-ray diffraction | 2.44 | 2020-12-16 | |||
| 41 | 6ZXZ|1|C | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | synthetic construct | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-ray diffraction | 2.44 | 2020-12-16 | |||
| 42 | 1JBS|1|C | 29-mer sarcin/ricin domain RNA analog | Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog | X-ray diffraction | 1.97 | 2001-10-26 | ||||
| 43 | 7EEO|1|A | DNA/RNA (27-MER) | synthetic construct | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-ray diffraction | 2.701 | 2022-03-23 | |||
| 44 | 7EEO|1|B | DNA/RNA (27-MER) | synthetic construct | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-ray diffraction | 2.701 | 2022-03-23 | |||
| 45 | 7UCR|1|A | Sarcin-Ricin loop RNA | Homo sapiens | Joint X-ray/neutron structure of the Sarcin-Ricin loop RNA | X-ray diffraction | 1 | 2022-07-20 |
Release history
| Release | 3.267 | 3.268 | 3.269 | 3.270 | 3.271 | 3.272 | 3.273 | 3.274 | 3.275 | 3.276 | 3.277 | 3.278 | 3.279 | 3.280 | 3.281 | 3.282 | 3.283 | 3.284 | 3.285 | 3.286 | 3.287 | 3.288 | 3.289 | 3.290 | 3.291 | 3.292 | 3.293 | 3.294 | 3.295 | 3.296 | 3.297 | 3.298 | 3.299 | 3.300 | 3.301 | 3.302 | 3.303 | 3.304 | 3.305 | 3.306 | 3.307 | 3.308 | 3.309 | 3.310 | 3.311 | 3.312 | 3.313 | 3.314 | 3.315 | 3.316 | 3.317 | 3.318 | 3.319 | 3.320 | 3.321 | 3.322 | 3.323 | 3.324 | 3.325 | 3.326 | 3.327 | 3.328 | 3.329 | 3.330 | 3.331 | 3.332 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2023-01-25 | 2023-02-01 | 2023-02-08 | 2023-02-15 | 2023-02-22 | 2023-03-01 | 2023-03-08 | 2023-03-15 | 2023-03-22 | 2023-03-29 | 2023-04-05 | 2023-04-12 | 2023-04-19 | 2023-04-26 | 2023-05-03 | 2023-05-10 | 2023-05-17 | 2023-05-24 | 2023-05-31 | 2023-06-07 | 2023-06-14 | 2023-06-21 | 2023-06-28 | 2023-07-05 | 2023-07-12 | 2023-07-19 | 2023-07-26 | 2023-08-02 | 2023-08-09 | 2023-08-16 | 2023-08-23 | 2023-08-30 | 2023-09-06 | 2023-09-13 | 2023-09-20 | 2023-09-27 | 2023-10-04 | 2023-10-11 | 2023-10-18 | 2023-10-25 | 2023-11-01 | 2023-11-08 | 2023-11-15 | 2023-11-24 | 2023-11-29 | 2023-12-06 | 2023-12-13 | 2023-12-20 | 2023-12-27 | 2024-01-03 | 2024-01-10 | 2024-01-17 | 2024-01-24 | 2024-01-31 | 2024-02-07 | 2024-02-14 | 2024-02-21 | 2024-02-28 | 2024-03-06 | 2024-03-13 | 2024-03-20 | 2024-03-27 | 2024-04-03 | 2024-04-10 | 2024-04-17 | 2024-04-24 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_4.0_94729.10 | NR_4.0_94729.9 | 3.267 | (44) 3S7C|1|A, 3DW7|1|A, 7UCR|1|A, 3DW6|1|A, 7QP2|1|A, 3DW5|1|A, 7M3V|1|A, 3DW4|1|A, 7L3R|1|A, 3DVZ|1|A, 7JJF|1|A, 1Q9A|1|A, 7JJE|1|A, 7JJD|1|A, 1MSY|1|A, 7EEO|1|B, 1JBT|1|D, 7EEO|1|A, 1JBT|1|C, 7EEN|1|D, 1JBS|1|D, 7EEN|1|C, 1JBS|1|C, 7EEN|1|B, 1JBR|1|D, 7EEN|1|A, 7EEM|1|A, 6ZYB|1|A, 6ZXZ|1|C, 6ZXZ|1|B, 6ZXZ|1|A, 6Y0Y|1|A, 6Y0T|1|B, 6Y0T|1|A, 5NQI|1|A, 5MRX|1|A, 5D99|1|A, 4Y27|1|A, 4NXH|1|A, 4NMG|1|A, 4NLF|1|A, 483D|1|A, 480D|1|A, 3S8U|1|A | (1) 7QSH|1|A | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|
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 | 1MSY|1|A | GUAA tetraloop mutant of Sarcin/Ricin domain from E. Coli 23 S rRNA | X-RAY DIFFRACTION | 1.41 | 31 |
| 2 | 6Y0Y|1|A | Sarcin Ricin Loop, mutant C2666U | X-RAY DIFFRACTION | 0.95 | 27 |
| 3 | 6Y0T|1|A | Sarcin Ricin Loop, mutant C2666A U2653G C2667A | X-RAY DIFFRACTION | 1.393 | 30 |
| 4 | 6Y0T|1|B | Sarcin Ricin Loop, mutant C2666A U2653G C2667A | X-RAY DIFFRACTION | 1.393 | 30 |
| 5 | 7EEM|1|A | RNA bulged-G motif | X-RAY DIFFRACTION | 2.593 | 26 |
| 6 | 7QSH|1|A | 23S ribosomal RNA Sarcin Ricin Loop 27-nt fragment containing a Xanthosine residue at position 2648 | X-RAY DIFFRACTION | 0.86 | 34 |
| 7 | 3S8U|1|A | Crystal structure of a 2-azido-adenine-modified RNA | X-RAY DIFFRACTION | 1.2 | 34 |
| 8 | 7L3R|1|A | 23S Sarcin Ricin Loop with a 3-deazapurine A2670 | X-RAY DIFFRACTION | 1.01 | 30 |
| 9 | 3DW5|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23S rRNA, U2656-OCH3 modified | X-RAY DIFFRACTION | 0.96 | 32 |
| 10 | 4NMG|1|A | 2'-Trifluoromethylthio-2'-deoxyuridine-modified SRL | X-RAY DIFFRACTION | 1.01 | 36 |
| 11 | 3DW7|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2656-SeCH3 modified | X-RAY DIFFRACTION | 1 | 37 |
| 12 | 7QP2|1|A | 1-deazaguanosine modified-RNA Sarcin Ricin Loop | X-RAY DIFFRACTION | 0.9 | 32 |
| 13 | 7UCR|1|A | Joint X-ray/neutron structure of the Sarcin-Ricin loop RNA | X-RAY DIFFRACTION | 1 | 56 |
| 14 | 1Q9A|1|A | Crystal structure of the sarcin/ricin domain from E.coli 23S rRNA at 1.04 resolution | X-RAY DIFFRACTION | 1.04 | 38 |
| 15 | 483D|1|A | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | X-RAY DIFFRACTION | 1.11 | 39 |
| 16 | 7JJF|1|A | Sarcin-ricin loop with modified residue. | X-RAY DIFFRACTION | 1.2 | 27 |
| 17 | 4Y27|1|A | E.coli 23S Sarcin-Ricil Loop, modified with a 2-Me on G2661 and a methylphosphonate on A2662 | X-RAY DIFFRACTION | 1 | 25 |
| 18 | 5NQI|1|A | E.coli 16S rRNA Sarcin-Ricin Loop containing a 5-hydroxymethylcytosine modification | X-RAY DIFFRACTION | 0.85 | 34 |
| 19 | 5MRX|1|A | 27-nt SRL with a 5-hydroxymethyl cytidine modification | X-RAY DIFFRACTION | 0.85 | 34 |
| 20 | 7JJE|1|A | Sarcin-ricin loop with guanosine dithiophosphate residue. | X-RAY DIFFRACTION | 1.25 | 29 |
| 21 | 7JJD|1|A | Sarcin-ricin loop with guanosine monothiophosphate residue. | X-RAY DIFFRACTION | 1.21 | 29 |
| 22 | 3DVZ|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. coli 23 S rRNA | X-RAY DIFFRACTION | 1 | 35 |
| 23 | 6ZYB|1|A | Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification | X-RAY DIFFRACTION | 0.9 | 30 |
| 24 | 7M3V|1|A | RNA bulged-G motif | X-RAY DIFFRACTION | 2.19 | 27 |
| 25 | 4NXH|1|A | 2'-Trifluoromethylthiouridine-modified E. coli 23S rRNA Sarcin Ricin Loop | X-RAY DIFFRACTION | 1.16 | 32 |
| 26 | 480D|1|A | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | X-RAY DIFFRACTION | 1.5 | 27 |
| 27 | 3S7C|1|A | Crystal structure of a 2'-azido-uridine-modified RNA | X-RAY DIFFRACTION | 1.1 | 32 |
| 28 | 3DW6|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-SECH3 modified | X-RAY DIFFRACTION | 1 | 28 |
| 29 | 3DW4|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-OCH3 modified | X-RAY DIFFRACTION | 0.97 | 26 |
| 30 | 5D99|1|A | 3DW4 redetermined by direct methods starting from random phase angles | X-RAY DIFFRACTION | 0.97 | 30 |
| 31 | 4NLF|1|A | 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL | X-RAY DIFFRACTION | 1 | 28 |
| 32 | 7EEO|1|B | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 2.701 | 14 |
| 33 | 7EEO|1|A | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 2.701 | 14 |
| 34 | 7EEN|1|A | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 1.7 | 14 |
| 35 | 7EEN|1|B | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 1.7 | 15 |
| 36 | 7EEN|1|C | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 1.7 | 14 |
| 37 | 7EEN|1|D | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 1.7 | 14 |
| 38 | 6ZXZ|1|A | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-RAY DIFFRACTION | 2.44 | 25 |
| 39 | 6ZXZ|1|C | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-RAY DIFFRACTION | 2.44 | 25 |
| 40 | 6ZXZ|1|B | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-RAY DIFFRACTION | 2.44 | 25 |
| 41 | 1JBT|1|C | CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG | X-RAY DIFFRACTION | 2.7 | 29 |
| 42 | 1JBS|1|C | Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog | X-RAY DIFFRACTION | 1.97 | 17 |
| 43 | 1JBS|1|D | Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog | X-RAY DIFFRACTION | 1.97 | 17 |
| 44 | 1JBT|1|D | CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG | X-RAY DIFFRACTION | 2.7 | 29 |
| 45 | 1JBR|1|D | Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor | X-RAY DIFFRACTION | 2.15 | 31 |