RNA 3D Hub //

Equivalence class NR_all_30081.2 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
13C3Z|1|A+ 3C3Z|1|B (rep)HIV-1 subtype F genomic RNACrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycinX-ray diffraction1.5462008-05-06
22OIY|1|A+ 2OIY|1|B5'-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 siteX-ray diffraction1.6462007-12-25
3462D|1|A+ 462D|1|BRNA (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 SITEX-ray diffraction2.3461999-12-02
41NLC|1|A+ 1NLC|1|BHIV-1 DIS(MAL) genomic RNAHIV-1 DIS(Mal) duplex Zn-soakedX-ray diffraction1.85462003-05-13
53C44|1|A+ 3C44|1|BHIV-1 subtype F genomic RNACrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycinX-ray diffraction2462008-05-06
61O3Z|1|A+ 1O3Z|1|BHIV-1 DIS(MAL) GENOMIC RNAHIV-1 DIS(MAL) DUPLEX RU HEXAMINE-SOAKEDX-ray diffraction2.65462003-05-27
73C5D|1|A+ 3C5D|1|B'HIV-1 subtype F genomic RNACrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to lividomycinX-ray diffraction1.8462008-05-06
81Y73|1|A+ 1Y73|1|B5'-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 Dis(Mal) Duplex Pt-SoakedX-ray diffraction2.9462004-12-21
93C7R|1|A+ 3C7R|1|BHIV-1 subtype F genomic RNACrystal Structure of HIV-1 subtype F DIS extended duplex RNA bound to neomycinX-ray diffraction1.7462008-05-06
101Y99|1|A+ 1Y99|1|B5'-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 duplexX-ray diffraction2.4462004-12-21
112OJ0|1|A+ 2OJ0|1|B5'-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 MN soakedX-ray diffraction2.6462007-12-25
123DVV|1|A+ 3DVV|1|BHIV-1 genomic RNACrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe)X-ray diffraction2462008-08-12
131Y90|1|A+ 1Y90|1|B5'-R(*CP*(5BU)P*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3'HIV-1 Dis(Mal) Duplex Mn-SoakedX-ray diffraction3.08462004-12-21
141WVD|1|A+ 1WVD|1|B5'-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 Dis(Mal) Duplex CoCl2-SoakedX-ray diffraction2.93462004-12-21
152OIJ|1|A+ 2OIJ|1|B5'-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 soakedX-ray diffraction2.31462007-02-13
161Y6T|1|A+ 1Y6T|1|B5'-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 Dis(Mal) Duplex Co Hexamine-SoakedX-ray diffraction2.6462004-12-21
171Y95|1|A+ 1Y95|1|B5'-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 Dis(Mal) Duplex Pb-SoakedX-ray diffraction2.8462004-12-21
183FAR|1|A+ 3FAR|1|BRNA (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 SiteX-ray diffraction2.4462009-11-24
191Y6S|1|A+ 1Y6S|1|B5'-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 DIS(Mal) duplex Ba-soakedX-ray diffraction2.9462004-12-21

Release history

Release4.0
Date2025-08-13

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

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.

#SViewPDBTitleMethodResolution#NTs
12OIJ|1|A+ 2OIJ|1|BHIV-1 subtype B DIS RNA extended duplex AuCl3 soakedX-RAY DIFFRACTION2.3146
22OIY|1|A+ 2OIY|1|BCrystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation siteX-RAY DIFFRACTION1.646
33FAR|1|A+ 3FAR|1|BCation-dependent self-cleavage activity in the duplex form of the subtype-B HIV-1 RNA Dimerization Initiation SiteX-RAY DIFFRACTION2.446
42OJ0|1|A+ 2OJ0|1|BCrystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soakedX-RAY DIFFRACTION2.646
51Y99|1|A+ 1Y99|1|BHIV-1 subtype A DIS RNA duplexX-RAY DIFFRACTION2.446
61Y90|1|A+ 1Y90|1|BHIV-1 Dis(Mal) Duplex Mn-SoakedX-RAY DIFFRACTION3.0846
71WVD|1|A+ 1WVD|1|BHIV-1 Dis(Mal) Duplex CoCl2-SoakedX-RAY DIFFRACTION2.9346
81NLC|1|A+ 1NLC|1|BHIV-1 DIS(Mal) duplex Zn-soakedX-RAY DIFFRACTION1.8546
9462D|1|A+ 462D|1|BCRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITEX-RAY DIFFRACTION2.346
101O3Z|1|A+ 1O3Z|1|BHIV-1 DIS(MAL) DUPLEX RU HEXAMINE-SOAKEDX-RAY DIFFRACTION2.6546
111Y95|1|A+ 1Y95|1|BHIV-1 Dis(Mal) Duplex Pb-SoakedX-RAY DIFFRACTION2.846
121Y73|1|A+ 1Y73|1|BHIV-1 Dis(Mal) Duplex Pt-SoakedX-RAY DIFFRACTION2.946
131Y6T|1|A+ 1Y6T|1|BHIV-1 Dis(Mal) Duplex Co Hexamine-SoakedX-RAY DIFFRACTION2.646
141Y6S|1|A+ 1Y6S|1|BHIV-1 DIS(Mal) duplex Ba-soakedX-RAY DIFFRACTION2.946
153C7R|1|A+ 3C7R|1|BCrystal Structure of HIV-1 subtype F DIS extended duplex RNA bound to neomycinX-RAY DIFFRACTION1.746
163C3Z|1|A+ 3C3Z|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycinX-RAY DIFFRACTION1.546
173DVV|1|A+ 3DVV|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe)X-RAY DIFFRACTION246
183C5D|1|A+ 3C5D|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to lividomycinX-RAY DIFFRACTION1.846
193C44|1|A+ 3C44|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycinX-RAY DIFFRACTION246

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.


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