Equivalence class NR_2.5_94729.8 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 4NLF|1|A (rep) | 23S ribosomal RNA Sarcin Ricin Loop | 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL | X-ray diffraction | 1 | 27 | 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 | 27 | 2016-04-13 | |||
| 3 | 6Y0Y|1|A | RNA (27-MER) | synthetic construct | Sarcin Ricin Loop, mutant C2666U | X-ray diffraction | 0.95 | 27 | 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 | 27 | 2003-11-25 | ||||
| 5 | 4NMG|1|A | 23S ribosomal RNA Sarcin Ricin Loop | 2'-Trifluoromethylthio-2'-deoxyuridine-modified SRL | X-ray diffraction | 1.01 | 27 | 2014-11-19 | ||||
| 6 | 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 | 27 | 2020-12-16 | |||
| 7 | 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 | 27 | 2009-03-24 | ||||
| 8 | 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 | 27 | 2009-03-24 | ||||
| 9 | 7L3R|1|A | RNA (27-MER) | synthetic construct | 23S Sarcin Ricin Loop with a 3-deazapurine A2670 | X-ray diffraction | 1.01 | 27 | 2021-05-05 | |||
| 10 | 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 | 27 | 2015-11-18 | |||
| 11 | 7JJE|1|A | RNA (27-MER) | synthetic construct | Sarcin-ricin loop with guanosine dithiophosphate residue. | X-ray diffraction | 1.25 | 27 | 2020-12-23 | |||
| 12 | 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 | 27 | 2009-03-24 | ||||
| 13 | 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 | 27 | 2014-12-10 | |||
| 14 | 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 | 27 | 2017-07-26 | |||
| 15 | 3S7C|1|A | Ecoli 23 S rRNA Sarcin Ricin loop | Crystal structure of a 2'-azido-uridine-modified RNA | X-ray diffraction | 1.1 | 27 | 2012-04-11 | ||||
| 16 | 5MRX|1|A | RNA (27-MER) | Escherichia coli | 27-nt SRL with a 5-hydroxymethyl cytidine modification | X-ray diffraction | 0.85 | 27 | 2018-01-17 | |||
| 17 | 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 | 27 | 2009-03-24 | ||||
| 18 | 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 | 27 | 2009-03-24 | ||||
| 19 | 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 | 27 | 1999-10-08 | ||||
| 20 | 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 | 27 | 2012-04-11 | |||
| 21 | 7JJD|1|A | RNA (27-MER) | synthetic construct | Sarcin-ricin loop with guanosine monothiophosphate residue. | X-ray diffraction | 1.21 | 27 | 2020-12-23 | |||
| 22 | 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 | 27 | 2003-02-25 | ||||
| 23 | 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 | 27 | 1999-10-08 | ||||
| 24 | 6Y0T|1|B | RNA (27-MER) | synthetic construct | Sarcin Ricin Loop, mutant C2666A U2653G C2667A | X-ray diffraction | 1.393 | 27 | 2021-02-17 | |||
| 25 | 6Y0T|1|A | RNA (27-MER) | synthetic construct | Sarcin Ricin Loop, mutant C2666A U2653G C2667A | X-ray diffraction | 1.393 | 27 | 2021-02-17 | |||
| 26 | 7M3V|1|A | RNA (27-MER) | synthetic construct | RNA bulged-G motif | X-ray diffraction | 2.19 | 27 | 2022-03-23 | |||
| 27 | 7JJF|1|A | RNA/DNA (27-mer) | Escherichia coli | Sarcin-ricin loop with modified residue. | X-ray diffraction | 1.2 | 27 | 2020-12-23 | |||
| 28 | 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 | 31 | 2001-10-26 | ||||
| 29 | 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 | 26 | 2022-03-23 | |||
| 30 | 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 | 27 | 2022-03-23 | |||
| 31 | 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 | 26 | 2020-12-16 | |||
| 32 | 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 | 26 | 2022-03-23 | |||
| 33 | 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 | 29 | 2001-10-26 | ||||
| 34 | 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 | 26 | 2022-03-23 | |||
| 35 | 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 | 26 | 2020-12-16 | |||
| 36 | 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 | 26 | 2020-12-16 | |||
| 37 | 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 | 29 | 2001-10-26 |
Release history
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_2.5_94729.8 | NR_2.5_94729.7 | 3.223 | (32) 1JBR|1|D, 1JBS|1|C, 1JBS|1|D, 1MSY|1|A, 1Q9A|1|A, 3DVZ|1|A, 3DW4|1|A, 3DW5|1|A, 3DW6|1|A, 3DW7|1|A, 3S7C|1|A, 3S8U|1|A, 480D|1|A, 483D|1|A, 4NLF|1|A, 4NMG|1|A, 4NXH|1|A, 4Y27|1|A, 5D99|1|A, 5MRX|1|A, 5NQI|1|A, 6Y0T|1|A, 6Y0T|1|B, 6Y0Y|1|A, 6ZXZ|1|A, 6ZXZ|1|B, 6ZXZ|1|C, 6ZYB|1|A, 7JJD|1|A, 7JJE|1|A, 7JJF|1|A, 7L3R|1|A | (5) 7EEN|1|A, 7EEN|1|B, 7EEN|1|C, 7EEN|1|D, 7M3V|1|A | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_2.5_94729.8 | NR_2.5_94729.9 | 3.240 | (37) 1JBR|1|D, 1JBS|1|C, 1JBS|1|D, 1MSY|1|A, 1Q9A|1|A, 3DVZ|1|A, 3DW4|1|A, 3DW5|1|A, 3DW6|1|A, 3DW7|1|A, 3S7C|1|A, 3S8U|1|A, 480D|1|A, 483D|1|A, 4NLF|1|A, 4NMG|1|A, 4NXH|1|A, 4Y27|1|A, 5D99|1|A, 5MRX|1|A, 5NQI|1|A, 6Y0T|1|A, 6Y0T|1|B, 6Y0Y|1|A, 6ZXZ|1|A, 6ZXZ|1|B, 6ZXZ|1|C, 6ZYB|1|A, 7EEN|1|A, 7EEN|1|B, 7EEN|1|C, 7EEN|1|D, 7JJD|1|A, 7JJE|1|A, 7JJF|1|A, 7L3R|1|A, 7M3V|1|A | (0) | (2) 7QP2|1|A, 7UCR|1|A |
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 | #NTs |
|---|---|---|---|---|---|---|
| 1 | 7EEN|1|B | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 1.7 | 27 | |
| 2 | 7EEN|1|A | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 1.7 | 26 | |
| 3 | 7EEN|1|C | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 1.7 | 26 | |
| 4 | 7EEN|1|D | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 1.7 | 26 | |
| 5 | 6ZXZ|1|B | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-RAY DIFFRACTION | 2.44 | 26 | |
| 6 | 6ZXZ|1|C | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-RAY DIFFRACTION | 2.44 | 26 | |
| 7 | 6ZXZ|1|A | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-RAY DIFFRACTION | 2.44 | 26 | |
| 8 | 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 | 27 | |
| 9 | 7JJF|1|A | Sarcin-ricin loop with modified residue. | X-RAY DIFFRACTION | 1.2 | 27 | |
| 10 | 5NQI|1|A | E.coli 16S rRNA Sarcin-Ricin Loop containing a 5-hydroxymethylcytosine modification | X-RAY DIFFRACTION | 0.85 | 27 | |
| 11 | 5MRX|1|A | 27-nt SRL with a 5-hydroxymethyl cytidine modification | X-RAY DIFFRACTION | 0.85 | 27 | |
| 12 | 483D|1|A | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | X-RAY DIFFRACTION | 1.11 | 27 | |
| 13 | 1Q9A|1|A | Crystal structure of the sarcin/ricin domain from E.coli 23S rRNA at 1.04 resolution | X-RAY DIFFRACTION | 1.04 | 27 | |
| 14 | 3DW7|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2656-SeCH3 modified | X-RAY DIFFRACTION | 1 | 27 | |
| 15 | 4NMG|1|A | 2'-Trifluoromethylthio-2'-deoxyuridine-modified SRL | X-RAY DIFFRACTION | 1.01 | 27 | |
| 16 | 7M3V|1|A | RNA bulged-G motif | X-RAY DIFFRACTION | 2.19 | 27 | |
| 17 | 6ZYB|1|A | Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification | X-RAY DIFFRACTION | 0.9 | 27 | |
| 18 | 7JJE|1|A | Sarcin-ricin loop with guanosine dithiophosphate residue. | X-RAY DIFFRACTION | 1.25 | 27 | |
| 19 | 3DVZ|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. coli 23 S rRNA | X-RAY DIFFRACTION | 1 | 27 | |
| 20 | 7JJD|1|A | Sarcin-ricin loop with guanosine monothiophosphate residue. | X-RAY DIFFRACTION | 1.21 | 27 | |
| 21 | 3S8U|1|A | Crystal structure of a 2-azido-adenine-modified RNA | X-RAY DIFFRACTION | 1.2 | 27 | |
| 22 | 7L3R|1|A | 23S Sarcin Ricin Loop with a 3-deazapurine A2670 | X-RAY DIFFRACTION | 1.01 | 27 | |
| 23 | 3DW5|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23S rRNA, U2656-OCH3 modified | X-RAY DIFFRACTION | 0.96 | 27 | |
| 24 | 4NXH|1|A | 2'-Trifluoromethylthiouridine-modified E. coli 23S rRNA Sarcin Ricin Loop | X-RAY DIFFRACTION | 1.16 | 27 | |
| 25 | 5D99|1|A | 3DW4 redetermined by direct methods starting from random phase angles | X-RAY DIFFRACTION | 0.97 | 27 | |
| 26 | 3DW4|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-OCH3 modified | X-RAY DIFFRACTION | 0.97 | 27 | |
| 27 | 3DW6|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-SECH3 modified | X-RAY DIFFRACTION | 1 | 27 | |
| 28 | 3S7C|1|A | Crystal structure of a 2'-azido-uridine-modified RNA | X-RAY DIFFRACTION | 1.1 | 27 | |
| 29 | 480D|1|A | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | X-RAY DIFFRACTION | 1.5 | 27 | |
| 30 | 4NLF|1|A | 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL | X-RAY DIFFRACTION | 1 | 27 | |
| 31 | 6Y0T|1|B | Sarcin Ricin Loop, mutant C2666A U2653G C2667A | X-RAY DIFFRACTION | 1.393 | 27 | |
| 32 | 6Y0T|1|A | Sarcin Ricin Loop, mutant C2666A U2653G C2667A | X-RAY DIFFRACTION | 1.393 | 27 | |
| 33 | 6Y0Y|1|A | Sarcin Ricin Loop, mutant C2666U | X-RAY DIFFRACTION | 0.95 | 27 | |
| 34 | 1MSY|1|A | GUAA tetraloop mutant of Sarcin/Ricin domain from E. Coli 23 S rRNA | X-RAY DIFFRACTION | 1.41 | 27 | |
| 35 | 1JBS|1|D | Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog | X-RAY DIFFRACTION | 1.97 | 29 | |
| 36 | 1JBS|1|C | Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog | X-RAY DIFFRACTION | 1.97 | 29 | |
| 37 | 1JBR|1|D | Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor | X-RAY DIFFRACTION | 2.15 | 31 |
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.
Coloring options: