Equivalence class NR_2.5_60167.2 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Domain | Rfam | Title | Method | Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3C3Z|1|A+ 3C3Z|1|B (rep) | HIV-1 subtype F genomic RNA | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin | X-ray diffraction | 1.5 | 2008-05-06 | ||||
| 2 | 1Y99|1|A+ 1Y99|1|B | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 subtype A DIS RNA duplex | X-ray diffraction | 2.4 | 2004-12-21 | ||||
| 3 | 1NLC|1|B+ 1NLC|1|A | HIV-1 DIS(MAL) genomic RNA | HIV-1 DIS(Mal) duplex Zn-soaked | X-ray diffraction | 1.85 | 2003-05-13 | ||||
| 4 | 462D|1|B+ 462D|1|A | RNA (5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G) -3') | CRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITE | X-ray diffraction | 2.3 | 1999-12-02 | ||||
| 5 | 2OIJ|1|A+ 2OIJ|1|B | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3' | HIV-1 subtype B DIS RNA extended duplex AuCl3 soaked | X-ray diffraction | 2.31 | 2007-02-13 | ||||
| 6 | 2QEK|1|A+ 2QEK|1|B | HIV-1 subtype F DIS genomic RNA | HIV-1 subtype F DIS RNA extended duplex form | X-ray diffraction | 1.8 | 2008-05-06 | ||||
| 7 | 3FAR|1|A+ 3FAR|1|B | RNA (5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3') | Cation-dependent self-cleavage activity in the duplex form of the subtype-B HIV-1 RNA Dimerization Initiation Site | X-ray diffraction | 2.4 | 2009-11-24 | ||||
| 8 | 2OIY|1|A+ 2OIY|1|B | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3' | Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site | X-ray diffraction | 1.6 | 2007-12-25 | ||||
| 9 | 3C44|1|A+ 3C44|1|B | HIV-1 subtype F genomic RNA | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycin | X-ray diffraction | 2 | 2008-05-06 | ||||
| 10 | 3DVV|1|A+ 3DVV|1|B | HIV-1 genomic RNA | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe) | X-ray diffraction | 2 | 2008-08-12 | ||||
| 11 | 3C7R|1|A+ 3C7R|1|B | HIV-1 subtype F genomic RNA | Crystal Structure of HIV-1 subtype F DIS extended duplex RNA bound to neomycin | X-ray diffraction | 1.7 | 2008-05-06 | ||||
| 12 | 3C5D|1|A+ 3C5D|1|B | 'HIV-1 subtype F genomic RNA | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to lividomycin | X-ray diffraction | 1.8 | 2008-05-06 |
Release history
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_2.5_60167.2 | NR_2.5_60167.1 | 2.124 | (9) 2QEK|1|A+2QEK|1|B, 2OIY|1|A+2OIY|1|B, 2OIJ|1|A+2OIJ|1|B, 1Y99|1|A+1Y99|1|B, 1NLC|1|B+1NLC|1|A, 462D|1|B+462D|1|A, 3FAR|1|A+3FAR|1|B, 3DVV|1|A+3DVV|1|B, 3C44|1|A+3C44|1|B | (3) 3C3Z|1|A+3C3Z|1|B, 3C7R|1|A+3C7R|1|B, 3C5D|1|A+3C5D|1|B | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_2.5_60167.2 | NR_2.5_60167.3 | 2.132 | (9) 2OIJ|1|A+2OIJ|1|B, 3FAR|1|A+3FAR|1|B, 3C44|1|A+3C44|1|B, 462D|1|B+462D|1|A, 1NLC|1|B+1NLC|1|A, 2OIY|1|A+2OIY|1|B, 1Y99|1|A+1Y99|1|B, 3DVV|1|A+3DVV|1|B, 2QEK|1|A+2QEK|1|B | (3) 3C3Z|1|A+3C3Z|1|B, 3C5D|1|A+3C5D|1|B, 3C7R|1|A+3C7R|1|B | (0) |
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 | 3DVV|1|A+3DVV|1|B | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe) | X-RAY DIFFRACTION | 2 | 22 |
| 2 | 3C3Z|1|A+3C3Z|1|B | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin | X-RAY DIFFRACTION | 1.5 | 22 |
| 3 | 3C7R|1|A+3C7R|1|B | Crystal Structure of HIV-1 subtype F DIS extended duplex RNA bound to neomycin | X-RAY DIFFRACTION | 1.7 | 22 |
| 4 | 3C5D|1|A+3C5D|1|B | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to lividomycin | X-RAY DIFFRACTION | 1.8 | 22 |
| 5 | 3C44|1|A+3C44|1|B | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycin | X-RAY DIFFRACTION | 2 | 23 |
| 6 | 3FAR|1|A+3FAR|1|B | Cation-dependent self-cleavage activity in the duplex form of the subtype-B HIV-1 RNA Dimerization Initiation Site | X-RAY DIFFRACTION | 2.4 | 23 |
| 7 | 2OIY|1|A+2OIY|1|B | Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site | X-RAY DIFFRACTION | 1.6 | 23 |
| 8 | 2OIJ|1|A+2OIJ|1|B | HIV-1 subtype B DIS RNA extended duplex AuCl3 soaked | X-RAY DIFFRACTION | 2.31 | 23 |
| 9 | 1Y99|1|A+1Y99|1|B | HIV-1 subtype A DIS RNA duplex | X-RAY DIFFRACTION | 2.4 | 26 |
| 10 | 462D|1|B+462D|1|A | CRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITE | X-RAY DIFFRACTION | 2.3 | 26 |
| 11 | 1NLC|1|B+1NLC|1|A | HIV-1 DIS(Mal) duplex Zn-soaked | X-RAY DIFFRACTION | 1.85 | 26 |
| 12 | 2QEK|1|A+2QEK|1|B | HIV-1 subtype F DIS RNA extended duplex form | X-RAY DIFFRACTION | 1.8 | 23 |