Equivalence class NR_2.5_59443.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1XPE|1|A+ 1XPE|1|B (rep) | 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 genomic RNA Dimerization Initiation Site | X-ray diffraction | 1.94 | 2005-10-18 | ||||
| 2 | 1XPF|1|A+ 1XPF|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 genomic RNA Dimerization Initiation Site | X-ray diffraction | 2.3 | 2005-10-18 | ||||
| 3 | 1XP7|1|A+ 1XP7|1|B | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 subtype F genomic RNA Dimerization Initiation Site | X-ray diffraction | 2.5 | 2005-10-18 | ||||
| 4 | 2FCY|1|A+ 2FCY|1|B | HIV-1 DIS RNA | HIV-1 DIS kissing-loop in complex with Neomycin | X-ray diffraction | 2.2 | 2006-05-16 | ||||
| 5 | 1ZCI|1|A+ 1ZCI|1|B | 5'-R(*CP*(5BU)P*UP*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 DIS RNA subtype F- monoclinic form | X-ray diffraction | 1.65 | 2006-01-31 | ||||
| 6 | 2FCX|1|A+ 2FCX|1|B | HIV-1 DIS RNA | HIV-1 DIS kissing-loop in complex with neamine | X-ray diffraction | 2 | 2006-05-16 | ||||
| 7 | 1Y3S|1|A+ 1Y3S|1|B | 5'-R(*CP*UP*(5BU)P*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 DIS RNA subtype F- MPD form | X-ray diffraction | 2.25 | 2005-11-08 | ||||
| 8 | 2FCZ|1|A+ 2FCZ|1|B | HIV-1 DIS RNA | HIV-1 DIS kissing-loop in complex with ribostamycin | X-ray diffraction | 2.01 | 2006-05-16 | ||||
| 9 | 1YXP|1|A+ 1YXP|1|B | 5'-R(*CP*UP*(5BU)P*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 DIS RNA subtype F- Zn soaked | X-ray diffraction | 2.4 | 2006-01-31 | ||||
| 10 | 2FD0|1|A+ 2FD0|1|B | HIV-1 DIS RNA | HIV-1 DIS kissing-loop in complex with lividomycin | X-ray diffraction | 1.8 | 2006-05-16 | ||||
| 11 | 1ZCI|1|C+ 1ZCI|1|D | 5'-R(*CP*(5BU)P*UP*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 DIS RNA subtype F- monoclinic form | X-ray diffraction | 1.65 | 2006-01-31 | ||||
| 12 | 2FCZ|1|C+ 2FCZ|1|D | HIV-1 DIS RNA | HIV-1 DIS kissing-loop in complex with ribostamycin | X-ray diffraction | 2.01 | 2006-05-16 | ||||
| 13 | 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 | ||||
| 14 | 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 | ||||
| 15 | 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 | ||||
| 16 | 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 | ||||
| 17 | 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 | ||||
| 18 | 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 | ||||
| 19 | 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 | ||||
| 20 | 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 | ||||
| 21 | 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 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_2.5_59443.1 | NR_all_41479.1 | 3.0 | (12) 2FCZ|1|C+2FCZ|1|D, 1ZCI|1|A+1ZCI|1|B, 2FCZ|1|A+2FCZ|1|B, 1YXP|1|A+1YXP|1|B, 2FCX|1|A+2FCX|1|B, 1XPF|1|A+1XPF|1|B, 2FD0|1|A+2FD0|1|B, 1XP7|1|A+1XP7|1|B, 1Y3S|1|A+1Y3S|1|B, 2FCY|1|A+2FCY|1|B, 1ZCI|1|C+1ZCI|1|D, 1XPE|1|A+1XPE|1|B | (9) 462D|1|B+462D|1|A, 1Y99|1|A+1Y99|1|B, 2QEK|1|A+2QEK|1|B, 2OIY|1|A+2OIY|1|B, 3DVV|1|A+3DVV|1|B, 3C44|1|A+3C44|1|B, 3FAR|1|A+3FAR|1|B, 1NLC|1|B+1NLC|1|A, 2OIJ|1|A+2OIJ|1|B | (34) 1Y95|1|A, 1NLC|1|B, 2QEK|1|A, 1Y6T|1|A, 1K9W|1|B, 1Y99|1|A, 1WVD|1|B, 3DVV|1|A, 1Y90|1|A, 2OIY|1|A, 1K9W|1|D, 1Y6S|1|A, 1JTJ|1|A, 1O3Z|1|B, 1Y73|1|A, 2B8S|1|A+2B8S|1|B, 462D|1|A, 2B8R|1|A+2B8R|1|B, 1JU1|1|A, 1WVD|1|A, 3FAR|1|A, 3C44|1|A, 1Y73|1|B, 1NLC|1|A, 2OIJ|1|A, 1Y6S|1|B, 462D|1|B, 1Y95|1|B, 1O3Z|1|A, 1Y6T|1|B, 1K9W|1|C, 1Y3O|1|A+1Y3O|1|B, 1Y90|1|B, 2OJ0|1|A |
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 | NAKB_NA_annotation | NAKB_protein_annotation |
|---|---|---|---|---|---|---|---|
| 1 | 2FCZ|1|A+2FCZ|1|B | Title: HIV-1 DIS kissing-loop in complex with ribostamycin | X-RAY DIFFRACTION | 2.01 | 22 | ||
| 2 | 2FD0|1|A+2FD0|1|B | Title: HIV-1 DIS kissing-loop in complex with lividomycin | X-RAY DIFFRACTION | 1.8 | 22 | ||
| 3 | 2FCY|1|A+2FCY|1|B | Title: HIV-1 DIS kissing-loop in complex with Neomycin | X-RAY DIFFRACTION | 2.2 | 22 | ||
| 4 | 2FCZ|1|C+2FCZ|1|D | Title: HIV-1 DIS kissing-loop in complex with ribostamycin | X-RAY DIFFRACTION | 2.01 | 22 | ||
| 5 | 2FCX|1|A+2FCX|1|B | Title: HIV-1 DIS kissing-loop in complex with neamine | X-RAY DIFFRACTION | 2 | 22 | ||
| 6 | 1XPE|1|A+1XPE|1|B | Title: HIV-1 subtype B genomic RNA Dimerization Initiation Site | X-RAY DIFFRACTION | 1.94 | 23 | ||
| 7 | 1XPF|1|A+1XPF|1|B | Title: HIV-1 subtype A genomic RNA Dimerization Initiation Site | X-RAY DIFFRACTION | 2.3 | 23 | ||
| 8 | 1YXP|1|A+1YXP|1|B | Title: HIV-1 DIS RNA subtype F- Zn soaked | X-RAY DIFFRACTION | 2.4 | 22 | ||
| 9 | 1Y3S|1|A+1Y3S|1|B | Title: HIV-1 DIS RNA subtype F- MPD form | X-RAY DIFFRACTION | 2.25 | 22 | ||
| 10 | 1XP7|1|A+1XP7|1|B | Title: HIV-1 subtype F genomic RNA Dimerization Initiation Site | X-RAY DIFFRACTION | 2.5 | 23 | ||
| 11 | 1ZCI|1|C+1ZCI|1|D | Title: HIV-1 DIS RNA subtype F- monoclinic form | X-RAY DIFFRACTION | 1.65 | 22 | ||
| 12 | 1ZCI|1|A+1ZCI|1|B | Title: HIV-1 DIS RNA subtype F- monoclinic form | X-RAY DIFFRACTION | 1.65 | 22 | ||
| 13 | 3DVV|1|A+3DVV|1|B | Title: Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe) | X-RAY DIFFRACTION | 2 | 22 | ||
| 14 | 3C44|1|A+3C44|1|B | Title: Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycin | X-RAY DIFFRACTION | 2 | 23 | ||
| 15 | 3FAR|1|A+3FAR|1|B | Title: 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 | ||
| 16 | 2OIY|1|A+2OIY|1|B | Title: Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site | X-RAY DIFFRACTION | 1.6 | 23 | ||
| 17 | 2OIJ|1|A+2OIJ|1|B | Title: HIV-1 subtype B DIS RNA extended duplex AuCl3 soaked | X-RAY DIFFRACTION | 2.31 | 23 | ||
| 18 | 1Y99|1|A+1Y99|1|B | Title: HIV-1 subtype A DIS RNA duplex | X-RAY DIFFRACTION | 2.4 | 26 | ||
| 19 | 1NLC|1|B+1NLC|1|A | Title: HIV-1 DIS(Mal) duplex Zn-soaked | X-RAY DIFFRACTION | 1.85 | 26 | ||
| 20 | 462D|1|B+462D|1|A | Title: CRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITE | X-RAY DIFFRACTION | 2.3 | 26 | ||
| 21 | 2QEK|1|A+2QEK|1|B | Title: HIV-1 subtype F DIS RNA extended duplex form | X-RAY DIFFRACTION | 1.8 | 23 |
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