RNA 3D Hub //

Equivalence class NR_3.5_78372.6 Current

Showing 1 to 13 of 13 entries
#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
16X1B|1|D (rep)DNA (5'-R(*GP*U)-3')synthetic constructCrystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU.X-ray diffraction1.9722020-05-27
26X1B|1|FDNA (5'-R(*GP*U)-3')synthetic constructCrystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU.X-ray diffraction1.9722020-05-27
35K77|1|xbrnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'Saccharomyces cerevisiaeDbr1 in complex with 7-mer branched RNAX-ray diffraction2.1722016-12-07
45K77|1|zbrnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'Saccharomyces cerevisiaeDbr1 in complex with 7-mer branched RNAX-ray diffraction2.1722016-12-07
55K77|1|vbrnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'Saccharomyces cerevisiaeDbr1 in complex with 7-mer branched RNAX-ray diffraction2.1722016-12-07
65K77|1|ybrnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'Saccharomyces cerevisiaeDbr1 in complex with 7-mer branched RNAX-ray diffraction2.1722016-12-07
75K77|1|wbrnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'Saccharomyces cerevisiaeDbr1 in complex with 7-mer branched RNAX-ray diffraction2.1722016-12-07
87VA6|1|CRNA (5'-R(P*GP*U)-3')synthetic constructPaOrn Oligoribonuclease D11A mutant with RNA GU complex structureX-ray diffraction2.122022-09-07
95F6C|1|CRNA (5'-R(P*GP*U)-3')Escherichia coliThe structure of E. coli RNase E catalytically inactive mutant with RNA boundX-ray diffraction322016-12-14
106I0T|1|BRNA (5'-R(*GP*U)-3')Drosophila melanogasterCrystal structure of DmTailor in complex with GpUX-ray diffraction222018-12-05
111B2M|1|C5'-R(*GP*(U34))-3'THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.X-ray diffraction221999-03-25
121B2M|1|D5'-R(*GP*(U34))-3'THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.X-ray diffraction221999-03-25
131B2M|1|E5'-R(*GP*(U34))-3'THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.X-ray diffraction221999-03-25

Release history

Release3.3783.3793.3803.3813.3823.3833.3843.3853.3863.3873.3883.3893.3903.3913.3923.393
Date2025-03-132025-03-192025-03-262025-04-022025-04-092025-04-162025-04-232025-04-302025-05-072025-05-142025-05-212025-05-282025-06-042025-06-112025-06-182025-06-25

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.

Showing 1 to 13 of 13 entries
#SViewPDBTitleMethodResolution#NTs
16X1B|1|DCrystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU.X-RAY DIFFRACTION1.972
21B2M|1|DTHREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.X-RAY DIFFRACTION22
31B2M|1|ETHREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.X-RAY DIFFRACTION22
41B2M|1|CTHREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.X-RAY DIFFRACTION22
55K77|1|vDbr1 in complex with 7-mer branched RNAX-RAY DIFFRACTION2.172
67VA6|1|CPaOrn Oligoribonuclease D11A mutant with RNA GU complex structureX-RAY DIFFRACTION2.12
76X1B|1|FCrystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU.X-RAY DIFFRACTION1.972
85K77|1|xDbr1 in complex with 7-mer branched RNAX-RAY DIFFRACTION2.172
95K77|1|zDbr1 in complex with 7-mer branched RNAX-RAY DIFFRACTION2.172
106I0T|1|BCrystal structure of DmTailor in complex with GpUX-RAY DIFFRACTION22
115K77|1|yDbr1 in complex with 7-mer branched RNAX-RAY DIFFRACTION2.172
125F6C|1|CThe structure of E. coli RNase E catalytically inactive mutant with RNA boundX-RAY DIFFRACTION32
135K77|1|wDbr1 in complex with 7-mer branched RNAX-RAY DIFFRACTION2.172

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.

6X1B|1|D:6X1B|1|D = 06X1B|1|D:1B2M|1|D not available6X1B|1|D:1B2M|1|E not available6X1B|1|D:1B2M|1|C not available6X1B|1|D:5K77|1|v not available6X1B|1|D:7VA6|1|C not available6X1B|1|D:6X1B|1|F not available6X1B|1|D:5K77|1|x not available6X1B|1|D:5K77|1|z not available6X1B|1|D:6I0T|1|B not available6X1B|1|D:5K77|1|y not available6X1B|1|D:5F6C|1|C not available6X1B|1|D:5K77|1|w not available1B2M|1|D:6X1B|1|D not available1B2M|1|D:1B2M|1|D = 01B2M|1|D:1B2M|1|E = 2.06241B2M|1|D:1B2M|1|C = 2.78011B2M|1|D:5K77|1|v not available1B2M|1|D:7VA6|1|C not available1B2M|1|D:6X1B|1|F not available1B2M|1|D:5K77|1|x not available1B2M|1|D:5K77|1|z not available1B2M|1|D:6I0T|1|B not available1B2M|1|D:5K77|1|y not available1B2M|1|D:5F6C|1|C not available1B2M|1|D:5K77|1|w not available1B2M|1|E:6X1B|1|D not available1B2M|1|E:1B2M|1|D = 2.06241B2M|1|E:1B2M|1|E = 01B2M|1|E:1B2M|1|C = 2.11071B2M|1|E:5K77|1|v not available1B2M|1|E:7VA6|1|C not available1B2M|1|E:6X1B|1|F not available1B2M|1|E:5K77|1|x not available1B2M|1|E:5K77|1|z not available1B2M|1|E:6I0T|1|B not available1B2M|1|E:5K77|1|y not available1B2M|1|E:5F6C|1|C not available1B2M|1|E:5K77|1|w not available1B2M|1|C:6X1B|1|D not available1B2M|1|C:1B2M|1|D = 2.78011B2M|1|C:1B2M|1|E = 2.11071B2M|1|C:1B2M|1|C = 01B2M|1|C:5K77|1|v not available1B2M|1|C:7VA6|1|C not available1B2M|1|C:6X1B|1|F not available1B2M|1|C:5K77|1|x not available1B2M|1|C:5K77|1|z not available1B2M|1|C:6I0T|1|B not available1B2M|1|C:5K77|1|y not available1B2M|1|C:5F6C|1|C not available1B2M|1|C:5K77|1|w not available5K77|1|v:6X1B|1|D not available5K77|1|v:1B2M|1|D not available5K77|1|v:1B2M|1|E not available5K77|1|v:1B2M|1|C not available5K77|1|v:5K77|1|v = 05K77|1|v:7VA6|1|C not available5K77|1|v:6X1B|1|F not available5K77|1|v:5K77|1|x not available5K77|1|v:5K77|1|z not available5K77|1|v:6I0T|1|B not available5K77|1|v:5K77|1|y not available5K77|1|v:5F6C|1|C not available5K77|1|v:5K77|1|w not available7VA6|1|C:6X1B|1|D not available7VA6|1|C:1B2M|1|D not available7VA6|1|C:1B2M|1|E not available7VA6|1|C:1B2M|1|C not available7VA6|1|C:5K77|1|v not available7VA6|1|C:7VA6|1|C = 07VA6|1|C:6X1B|1|F not available7VA6|1|C:5K77|1|x not available7VA6|1|C:5K77|1|z not available7VA6|1|C:6I0T|1|B not available7VA6|1|C:5K77|1|y not available7VA6|1|C:5F6C|1|C not available7VA6|1|C:5K77|1|w not available6X1B|1|F:6X1B|1|D not available6X1B|1|F:1B2M|1|D not available6X1B|1|F:1B2M|1|E not available6X1B|1|F:1B2M|1|C not available6X1B|1|F:5K77|1|v not available6X1B|1|F:7VA6|1|C not available6X1B|1|F:6X1B|1|F = 06X1B|1|F:5K77|1|x not available6X1B|1|F:5K77|1|z not available6X1B|1|F:6I0T|1|B not available6X1B|1|F:5K77|1|y not available6X1B|1|F:5F6C|1|C not available6X1B|1|F:5K77|1|w not available5K77|1|x:6X1B|1|D not available5K77|1|x:1B2M|1|D not available5K77|1|x:1B2M|1|E not available5K77|1|x:1B2M|1|C not available5K77|1|x:5K77|1|v not available5K77|1|x:7VA6|1|C not available5K77|1|x:6X1B|1|F not available5K77|1|x:5K77|1|x = 05K77|1|x:5K77|1|z not available5K77|1|x:6I0T|1|B not available5K77|1|x:5K77|1|y not available5K77|1|x:5F6C|1|C not available5K77|1|x:5K77|1|w not available5K77|1|z:6X1B|1|D not available5K77|1|z:1B2M|1|D not available5K77|1|z:1B2M|1|E not available5K77|1|z:1B2M|1|C not available5K77|1|z:5K77|1|v not available5K77|1|z:7VA6|1|C not available5K77|1|z:6X1B|1|F not available5K77|1|z:5K77|1|x not available5K77|1|z:5K77|1|z = 05K77|1|z:6I0T|1|B not available5K77|1|z:5K77|1|y not available5K77|1|z:5F6C|1|C not available5K77|1|z:5K77|1|w not available6I0T|1|B:6X1B|1|D not available6I0T|1|B:1B2M|1|D not available6I0T|1|B:1B2M|1|E not available6I0T|1|B:1B2M|1|C not available6I0T|1|B:5K77|1|v not available6I0T|1|B:7VA6|1|C not available6I0T|1|B:6X1B|1|F not available6I0T|1|B:5K77|1|x not available6I0T|1|B:5K77|1|z not available6I0T|1|B:6I0T|1|B = 06I0T|1|B:5K77|1|y not available6I0T|1|B:5F6C|1|C not available6I0T|1|B:5K77|1|w not available5K77|1|y:6X1B|1|D not available5K77|1|y:1B2M|1|D not available5K77|1|y:1B2M|1|E not available5K77|1|y:1B2M|1|C not available5K77|1|y:5K77|1|v not available5K77|1|y:7VA6|1|C not available5K77|1|y:6X1B|1|F not available5K77|1|y:5K77|1|x not available5K77|1|y:5K77|1|z not available5K77|1|y:6I0T|1|B not available5K77|1|y:5K77|1|y = 05K77|1|y:5F6C|1|C not available5K77|1|y:5K77|1|w not available5F6C|1|C:6X1B|1|D not available5F6C|1|C:1B2M|1|D not available5F6C|1|C:1B2M|1|E not available5F6C|1|C:1B2M|1|C not available5F6C|1|C:5K77|1|v not available5F6C|1|C:7VA6|1|C not available5F6C|1|C:6X1B|1|F not available5F6C|1|C:5K77|1|x not available5F6C|1|C:5K77|1|z not available5F6C|1|C:6I0T|1|B not available5F6C|1|C:5K77|1|y not available5F6C|1|C:5F6C|1|C = 05F6C|1|C:5K77|1|w not available5K77|1|w:6X1B|1|D not available5K77|1|w:1B2M|1|D not available5K77|1|w:1B2M|1|E not available5K77|1|w:1B2M|1|C not available5K77|1|w:5K77|1|v not available5K77|1|w:7VA6|1|C not available5K77|1|w:6X1B|1|F not available5K77|1|w:5K77|1|x not available5K77|1|w:5K77|1|z not available5K77|1|w:6I0T|1|B not available5K77|1|w:5K77|1|y not available5K77|1|w:5F6C|1|C not available5K77|1|w:5K77|1|w = 06X1B|1|D1B2M|1|D1B2M|1|E1B2M|1|C5K77|1|v7VA6|1|C6X1B|1|F5K77|1|x5K77|1|z6I0T|1|B5K77|1|y5F6C|1|C5K77|1|wDiscrepancy0.000.501.001.502.002.50

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