RNA 3D Hub //

Equivalence class NR_4.0_01949.8 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
19OL3|1|A+ 9OL3|1|B (rep)RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructDNA-imidazolium-bridged dinucleotide intermediate complexX-ray diffraction1.557282025-10-22
29OL2|1|A+ 9OL2|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA-imidazolium-bridged dinucleotide intermediate complexX-ray diffraction1.528282025-10-22
37KUP|1|A+ 7KUP|1|B5'-R((LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(OMG))-3'synthetic construct2'-OMe modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')GX-ray diffraction1.44282021-09-08
47KUK|1|A+ 7KUK|1|BRNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructHigh resolution RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')GX-ray diffraction1.67282021-09-08
57KUM|1|A+ 7KUM|1|B5'-R((LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(LCG)-3'synthetic constructLNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')GX-ray diffraction1.714282021-09-08
65UED|1|A+ 5UED|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA primer-template complex with guanosine dinucleotide ligand G(5')pp(5')GX-ray diffraction1.5282017-07-05
76C8J|1|A+ 6C8J|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA-activated 2-AIpG monomer complex, 15 min soakingX-ray diffraction1.5282018-05-30
88SWG|1|A+ 8SWG|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(GA3))-3')synthetic constructRNA duplex bound with GpppA dinucleotide ligandX-ray diffraction1.5282023-05-31
97KUL|1|A+ 7KUL|1|BDNA/RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*C)-D(P*G)-3')synthetic constructDNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')GX-ray diffraction1.64282021-09-08
106C8D|1|A+ 6C8D|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA-dGMP complex with Mg ionX-ray diffraction1.92282018-05-30
116C8I|1|A+ 6C8I|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA-activated 2-AIpG monomer complex, 5 min soakingX-ray diffraction1.77282018-05-30
125UEE|1|A+ 5UEE|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')GX-ray diffraction1.9282017-07-05
137KUO|1|A+ 7KUO|1|BRNA (5'-R((LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(GFL))-3')synthetic constructFANA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')GX-ray diffraction2.281282021-09-08
146C8L|1|A+ 6C8L|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA-activated 2-AIpG monomer complex, 1h soakingX-ray diffraction2.25282018-05-30
156C8E|1|A+ 6C8E|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA-imidazolium-bridged intermediate complex, 4h soakingX-ray diffraction1.8282018-05-30
166U8U|1|A+ 6U8U|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA duplex bound with TNA 3'-3' imidazolium dimerX-ray diffraction2.4282020-12-09
176C8K|1|A+ 6C8K|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA-activated 2-AIpG monomer complex, 30 min soakingX-ray diffraction2.26282018-05-30
186CAB|1|A+ 6CAB|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA-dGMP complex with Sr ionX-ray diffraction2.5282018-05-30
195UEF|1|A+ 5UEF|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligandX-ray diffraction2.1282017-07-05
205UEG|1|C+ 5UEG|1|DRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA primer-template complex with guanosine dinucleotide G(5')pppp(5')G ligandX-ray diffraction2.6282017-07-05
215UEG|1|A+ 5UEG|1|BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')synthetic constructRNA primer-template complex with guanosine dinucleotide G(5')pppp(5')G ligandX-ray diffraction2.6282017-07-05
226OWL|1|ARNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*R)-3')synthetic constructRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-ray diffraction2142020-02-26

Release history

Release4.10
Date2025-10-22

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

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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
17KUO|1|A+ 7KUO|1|BFANA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')GX-RAY DIFFRACTION2.28128
26CAB|1|A+ 6CAB|1|BRNA-dGMP complex with Sr ionX-RAY DIFFRACTION2.528
36C8L|1|A+ 6C8L|1|BRNA-activated 2-AIpG monomer complex, 1h soakingX-RAY DIFFRACTION2.2528
49OL3|1|A+ 9OL3|1|BDNA-imidazolium-bridged dinucleotide intermediate complexX-RAY DIFFRACTION1.55728
59OL2|1|A+ 9OL2|1|BRNA-imidazolium-bridged dinucleotide intermediate complexX-RAY DIFFRACTION1.52828
66C8J|1|A+ 6C8J|1|BRNA-activated 2-AIpG monomer complex, 15 min soakingX-RAY DIFFRACTION1.528
76C8D|1|A+ 6C8D|1|BRNA-dGMP complex with Mg ionX-RAY DIFFRACTION1.9228
87KUL|1|A+ 7KUL|1|BDNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')GX-RAY DIFFRACTION1.6428
96C8E|1|A+ 6C8E|1|BRNA-imidazolium-bridged intermediate complex, 4h soakingX-RAY DIFFRACTION1.828
107KUP|1|A+ 7KUP|1|B2'-OMe modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')GX-RAY DIFFRACTION1.4428
117KUK|1|A+ 7KUK|1|BHigh resolution RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')GX-RAY DIFFRACTION1.6728
125UEE|1|A+ 5UEE|1|BRNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')GX-RAY DIFFRACTION1.928
137KUM|1|A+ 7KUM|1|BLNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')GX-RAY DIFFRACTION1.71428
146C8K|1|A+ 6C8K|1|BRNA-activated 2-AIpG monomer complex, 30 min soakingX-RAY DIFFRACTION2.2628
155UEG|1|C+ 5UEG|1|DRNA primer-template complex with guanosine dinucleotide G(5')pppp(5')G ligandX-RAY DIFFRACTION2.628
165UEG|1|A+ 5UEG|1|BRNA primer-template complex with guanosine dinucleotide G(5')pppp(5')G ligandX-RAY DIFFRACTION2.628
175UEF|1|A+ 5UEF|1|BRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligandX-RAY DIFFRACTION2.128
185UED|1|A+ 5UED|1|BRNA primer-template complex with guanosine dinucleotide ligand G(5')pp(5')GX-RAY DIFFRACTION1.528
196C8I|1|A+ 6C8I|1|BRNA-activated 2-AIpG monomer complex, 5 min soakingX-RAY DIFFRACTION1.7728
208SWG|1|A+ 8SWG|1|BRNA duplex bound with GpppA dinucleotide ligandX-RAY DIFFRACTION1.528
216U8U|1|A+ 6U8U|1|BRNA duplex bound with TNA 3'-3' imidazolium dimerX-RAY DIFFRACTION2.428
226OWL|1|ARNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-RAY DIFFRACTION214

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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