RNA 3D Hub //

Equivalence class NR_4.0_65789.3 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
16N6F|1|D (rep)RNA (5'-R(P*GP*C)-3')synthetic constructVibrio cholerae Oligoribonuclease bound to pGCX-ray diffraction1.7422019-06-12
27MPN|1|B5'-phosphorylated GCsynthetic constructBartonella henselae NrnC bound to pGCX-ray diffraction1.9422021-09-15
37MPN|1|N5'-phosphorylated GCsynthetic constructBartonella henselae NrnC bound to pGCX-ray diffraction1.9422021-09-15
47MPN|1|J5'-phosphorylated GCsynthetic constructBartonella henselae NrnC bound to pGCX-ray diffraction1.9422021-09-15
54OHY|1|BRNA (5'-R(*GP*C)-3')C. Elegans Clp1 bound to ssRNA dinucleotide GC, AMP-PNP, and Mg2+(inhibited substrate bound state)X-ray diffraction222014-05-14
67MPN|1|P5'-phosphorylated GCsynthetic constructBartonella henselae NrnC bound to pGCX-ray diffraction1.9422021-09-15
77MPN|1|H5'-phosphorylated GCsynthetic constructBartonella henselae NrnC bound to pGCX-ray diffraction1.9422021-09-15
87MPN|1|L5'-phosphorylated GCsynthetic constructBartonella henselae NrnC bound to pGCX-ray diffraction1.9422021-09-15
97MPN|1|D5'-phosphorylated GCsynthetic constructBartonella henselae NrnC bound to pGCX-ray diffraction1.9422021-09-15
107MPN|1|F5'-phosphorylated GCsynthetic constructBartonella henselae NrnC bound to pGCX-ray diffraction1.9422021-09-15
114OI1|1|BRNA (5'-R(*GP*C)-3')Clp1 bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set II)X-ray diffraction2.322014-05-14
124OI0|1|BRNA (5'-R(*GP*C)-3')bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set I)X-ray diffraction2.222014-05-14

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.

#SViewPDBTitleMethodResolution#NTs
14OI0|1|Bbound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set I)X-RAY DIFFRACTION2.22
24OI1|1|BClp1 bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set II)X-RAY DIFFRACTION2.32
34OHY|1|BC. Elegans Clp1 bound to ssRNA dinucleotide GC, AMP-PNP, and Mg2+(inhibited substrate bound state)X-RAY DIFFRACTION22
47MPN|1|DBartonella henselae NrnC bound to pGCX-RAY DIFFRACTION1.942
56N6F|1|DVibrio cholerae Oligoribonuclease bound to pGCX-RAY DIFFRACTION1.742
67MPN|1|PBartonella henselae NrnC bound to pGCX-RAY DIFFRACTION1.942
77MPN|1|HBartonella henselae NrnC bound to pGCX-RAY DIFFRACTION1.942
87MPN|1|JBartonella henselae NrnC bound to pGCX-RAY DIFFRACTION1.942
97MPN|1|FBartonella henselae NrnC bound to pGCX-RAY DIFFRACTION1.942
107MPN|1|LBartonella henselae NrnC bound to pGCX-RAY DIFFRACTION1.942
117MPN|1|BBartonella henselae NrnC bound to pGCX-RAY DIFFRACTION1.942
127MPN|1|NBartonella henselae NrnC bound to pGCX-RAY DIFFRACTION1.942

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.

4OI0|1|B:4OI0|1|B = 04OI0|1|B:4OI1|1|B = 0.94114OI0|1|B:4OHY|1|B = 0.38684OI0|1|B:7MPN|1|D not available4OI0|1|B:6N6F|1|D not available4OI0|1|B:7MPN|1|P not available4OI0|1|B:7MPN|1|H not available4OI0|1|B:7MPN|1|J not available4OI0|1|B:7MPN|1|F not available4OI0|1|B:7MPN|1|L not available4OI0|1|B:7MPN|1|B not available4OI0|1|B:7MPN|1|N not available4OI1|1|B:4OI0|1|B = 0.94114OI1|1|B:4OI1|1|B = 04OI1|1|B:4OHY|1|B = 1.55534OI1|1|B:7MPN|1|D not available4OI1|1|B:6N6F|1|D not available4OI1|1|B:7MPN|1|P not available4OI1|1|B:7MPN|1|H not available4OI1|1|B:7MPN|1|J not available4OI1|1|B:7MPN|1|F not available4OI1|1|B:7MPN|1|L not available4OI1|1|B:7MPN|1|B not available4OI1|1|B:7MPN|1|N not available4OHY|1|B:4OI0|1|B = 0.38684OHY|1|B:4OI1|1|B = 1.55534OHY|1|B:4OHY|1|B = 04OHY|1|B:7MPN|1|D not available4OHY|1|B:6N6F|1|D not available4OHY|1|B:7MPN|1|P not available4OHY|1|B:7MPN|1|H not available4OHY|1|B:7MPN|1|J not available4OHY|1|B:7MPN|1|F not available4OHY|1|B:7MPN|1|L not available4OHY|1|B:7MPN|1|B not available4OHY|1|B:7MPN|1|N not available7MPN|1|D:4OI0|1|B not available7MPN|1|D:4OI1|1|B not available7MPN|1|D:4OHY|1|B not available7MPN|1|D:7MPN|1|D = 07MPN|1|D:6N6F|1|D not available7MPN|1|D:7MPN|1|P not available7MPN|1|D:7MPN|1|H not available7MPN|1|D:7MPN|1|J not available7MPN|1|D:7MPN|1|F not available7MPN|1|D:7MPN|1|L not available7MPN|1|D:7MPN|1|B not available7MPN|1|D:7MPN|1|N not available6N6F|1|D:4OI0|1|B not available6N6F|1|D:4OI1|1|B not available6N6F|1|D:4OHY|1|B not available6N6F|1|D:7MPN|1|D not available6N6F|1|D:6N6F|1|D = 06N6F|1|D:7MPN|1|P not available6N6F|1|D:7MPN|1|H not available6N6F|1|D:7MPN|1|J not available6N6F|1|D:7MPN|1|F not available6N6F|1|D:7MPN|1|L not available6N6F|1|D:7MPN|1|B not available6N6F|1|D:7MPN|1|N not available7MPN|1|P:4OI0|1|B not available7MPN|1|P:4OI1|1|B not available7MPN|1|P:4OHY|1|B not available7MPN|1|P:7MPN|1|D not available7MPN|1|P:6N6F|1|D not available7MPN|1|P:7MPN|1|P = 07MPN|1|P:7MPN|1|H not available7MPN|1|P:7MPN|1|J not available7MPN|1|P:7MPN|1|F not available7MPN|1|P:7MPN|1|L not available7MPN|1|P:7MPN|1|B not available7MPN|1|P:7MPN|1|N not available7MPN|1|H:4OI0|1|B not available7MPN|1|H:4OI1|1|B not available7MPN|1|H:4OHY|1|B not available7MPN|1|H:7MPN|1|D not available7MPN|1|H:6N6F|1|D not available7MPN|1|H:7MPN|1|P not available7MPN|1|H:7MPN|1|H = 07MPN|1|H:7MPN|1|J not available7MPN|1|H:7MPN|1|F not available7MPN|1|H:7MPN|1|L not available7MPN|1|H:7MPN|1|B not available7MPN|1|H:7MPN|1|N not available7MPN|1|J:4OI0|1|B not available7MPN|1|J:4OI1|1|B not available7MPN|1|J:4OHY|1|B not available7MPN|1|J:7MPN|1|D not available7MPN|1|J:6N6F|1|D not available7MPN|1|J:7MPN|1|P not available7MPN|1|J:7MPN|1|H not available7MPN|1|J:7MPN|1|J = 07MPN|1|J:7MPN|1|F not available7MPN|1|J:7MPN|1|L not available7MPN|1|J:7MPN|1|B not available7MPN|1|J:7MPN|1|N not available7MPN|1|F:4OI0|1|B not available7MPN|1|F:4OI1|1|B not available7MPN|1|F:4OHY|1|B not available7MPN|1|F:7MPN|1|D not available7MPN|1|F:6N6F|1|D not available7MPN|1|F:7MPN|1|P not available7MPN|1|F:7MPN|1|H not available7MPN|1|F:7MPN|1|J not available7MPN|1|F:7MPN|1|F = 07MPN|1|F:7MPN|1|L not available7MPN|1|F:7MPN|1|B not available7MPN|1|F:7MPN|1|N not available7MPN|1|L:4OI0|1|B not available7MPN|1|L:4OI1|1|B not available7MPN|1|L:4OHY|1|B not available7MPN|1|L:7MPN|1|D not available7MPN|1|L:6N6F|1|D not available7MPN|1|L:7MPN|1|P not available7MPN|1|L:7MPN|1|H not available7MPN|1|L:7MPN|1|J not available7MPN|1|L:7MPN|1|F not available7MPN|1|L:7MPN|1|L = 07MPN|1|L:7MPN|1|B not available7MPN|1|L:7MPN|1|N not available7MPN|1|B:4OI0|1|B not available7MPN|1|B:4OI1|1|B not available7MPN|1|B:4OHY|1|B not available7MPN|1|B:7MPN|1|D not available7MPN|1|B:6N6F|1|D not available7MPN|1|B:7MPN|1|P not available7MPN|1|B:7MPN|1|H not available7MPN|1|B:7MPN|1|J not available7MPN|1|B:7MPN|1|F not available7MPN|1|B:7MPN|1|L not available7MPN|1|B:7MPN|1|B = 07MPN|1|B:7MPN|1|N not available7MPN|1|N:4OI0|1|B not available7MPN|1|N:4OI1|1|B not available7MPN|1|N:4OHY|1|B not available7MPN|1|N:7MPN|1|D not available7MPN|1|N:6N6F|1|D not available7MPN|1|N:7MPN|1|P not available7MPN|1|N:7MPN|1|H not available7MPN|1|N:7MPN|1|J not available7MPN|1|N:7MPN|1|F not available7MPN|1|N:7MPN|1|L not available7MPN|1|N:7MPN|1|B not available7MPN|1|N:7MPN|1|N = 04OI0|1|B4OI1|1|B4OHY|1|B7MPN|1|D6N6F|1|D7MPN|1|P7MPN|1|H7MPN|1|J7MPN|1|F7MPN|1|L7MPN|1|B7MPN|1|NDiscrepancy0.000.200.400.600.801.001.201.40

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