RNA 3D Hub //

Equivalence class NR_3.0_53003.3 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
16N6C|1|D (rep)RNA (5'-R(P*AP*A)-3')synthetic constructVibrio cholerae Oligoribonuclease bound to pAAX-ray diffraction1.6222019-06-12
26N6J|1|CRNA (5'-R(P*AP*A)-3')synthetic constructHuman REXO2 bound to pAAX-ray diffraction1.3222019-06-12
36N6J|1|DRNA (5'-R(P*AP*A)-3')synthetic constructHuman REXO2 bound to pAAX-ray diffraction1.3222019-06-12
47MPM|1|B5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
57MPM|1|H5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
67MPM|1|L5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
77MPM|1|F5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
87MPM|1|J5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
97MPM|1|D5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
107MPM|1|P5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
117MPM|1|N5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
126P7Q|1|ERNA (5'-R(P*AP*A)-3')Escherichia coliStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-ray diffraction1.6622019-12-25
136P7Q|1|FRNA (5'-R(P*AP*A)-3')Escherichia coliStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-ray diffraction1.6622019-12-25
146P7Q|1|DRNA (5'-R(P*AP*A)-3')Escherichia coliStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-ray diffraction1.6622019-12-25
156RCL|1|CRNA (5'-R(P*AP*A)-3')synthetic constructCrystal structure of REXO2-D199A-AAX-ray diffraction1.9722019-10-09
168JBB|1|DRNA (5'-R(*AP*(A23))-3')synthetic constructCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-ray diffraction1.8122023-12-13
178JBB|1|CRNA (5'-R(*AP*(A23))-3')synthetic constructCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-ray diffraction1.8122023-12-13
185JJU|1|CRNA (5'-R(P*AP*A)-3')synthetic constructCrystal structure of Rv2837c complexed with 5'-pApA and 5'-AMPX-ray diffraction2.3122016-05-04
194EJT|1|G5'-R(*AP*A)-3'Staphylococcus epidermidis TcaR in complex with RNAX-ray diffraction322013-06-05

Release history

Release3.3443.3453.3463.3473.3483.3493.3503.3513.3523.3533.3543.3553.3563.3573.3583.3593.3603.3613.3623.3633.3643.3653.3663.3673.3683.3693.3703.3713.3723.3733.3743.3753.3763.377
Date2024-07-172024-07-252024-07-312024-08-072024-08-142024-08-212024-08-282024-09-042024-09-112024-09-182024-09-252024-10-022024-10-092024-10-162024-10-232024-10-302024-11-062024-11-132024-11-202024-11-272024-12-042024-12-112024-12-182024-12-252025-01-012025-01-082025-01-152025-01-222025-01-292025-02-052025-02-122025-02-192025-02-262025-03-05

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
16RCL|1|CCrystal structure of REXO2-D199A-AAX-RAY DIFFRACTION1.972
25JJU|1|CCrystal structure of Rv2837c complexed with 5'-pApA and 5'-AMPX-RAY DIFFRACTION2.312
34EJT|1|GStaphylococcus epidermidis TcaR in complex with RNAX-RAY DIFFRACTION32
48JBB|1|DCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
58JBB|1|CCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
67MPM|1|LBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
76N6J|1|DHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
86N6C|1|DVibrio cholerae Oligoribonuclease bound to pAAX-RAY DIFFRACTION1.622
97MPM|1|FBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
107MPM|1|HBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
117MPM|1|BBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
126N6J|1|CHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
137MPM|1|DBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
147MPM|1|JBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
156P7Q|1|EStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
166P7Q|1|DStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
177MPM|1|PBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
187MPM|1|NBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
196P7Q|1|FStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662

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.

6RCL|1|C:6RCL|1|C = 06RCL|1|C:5JJU|1|C not available6RCL|1|C:4EJT|1|G not available6RCL|1|C:8JBB|1|D not available6RCL|1|C:8JBB|1|C not available6RCL|1|C:7MPM|1|L not available6RCL|1|C:6N6J|1|D not available6RCL|1|C:6N6C|1|D not available6RCL|1|C:7MPM|1|F not available6RCL|1|C:7MPM|1|H not available6RCL|1|C:7MPM|1|B not available6RCL|1|C:6N6J|1|C not available6RCL|1|C:7MPM|1|D not available6RCL|1|C:7MPM|1|J not available6RCL|1|C:6P7Q|1|E not available6RCL|1|C:6P7Q|1|D not available6RCL|1|C:7MPM|1|P not available6RCL|1|C:7MPM|1|N not available6RCL|1|C:6P7Q|1|F not available5JJU|1|C:6RCL|1|C not available5JJU|1|C:5JJU|1|C = 05JJU|1|C:4EJT|1|G = 2.95005JJU|1|C:8JBB|1|D not available5JJU|1|C:8JBB|1|C not available5JJU|1|C:7MPM|1|L not available5JJU|1|C:6N6J|1|D not available5JJU|1|C:6N6C|1|D not available5JJU|1|C:7MPM|1|F not available5JJU|1|C:7MPM|1|H not available5JJU|1|C:7MPM|1|B not available5JJU|1|C:6N6J|1|C not available5JJU|1|C:7MPM|1|D not available5JJU|1|C:7MPM|1|J not available5JJU|1|C:6P7Q|1|E not available5JJU|1|C:6P7Q|1|D not available5JJU|1|C:7MPM|1|P not available5JJU|1|C:7MPM|1|N not available5JJU|1|C:6P7Q|1|F not available4EJT|1|G:6RCL|1|C not available4EJT|1|G:5JJU|1|C = 2.95004EJT|1|G:4EJT|1|G = 04EJT|1|G:8JBB|1|D not available4EJT|1|G:8JBB|1|C not available4EJT|1|G:7MPM|1|L not available4EJT|1|G:6N6J|1|D not available4EJT|1|G:6N6C|1|D not available4EJT|1|G:7MPM|1|F not available4EJT|1|G:7MPM|1|H not available4EJT|1|G:7MPM|1|B not available4EJT|1|G:6N6J|1|C not available4EJT|1|G:7MPM|1|D not available4EJT|1|G:7MPM|1|J not available4EJT|1|G:6P7Q|1|E not available4EJT|1|G:6P7Q|1|D not available4EJT|1|G:7MPM|1|P not available4EJT|1|G:7MPM|1|N not available4EJT|1|G:6P7Q|1|F not available8JBB|1|D:6RCL|1|C not available8JBB|1|D:5JJU|1|C not available8JBB|1|D:4EJT|1|G not available8JBB|1|D:8JBB|1|D = 08JBB|1|D:8JBB|1|C not available8JBB|1|D:7MPM|1|L not available8JBB|1|D:6N6J|1|D not available8JBB|1|D:6N6C|1|D not available8JBB|1|D:7MPM|1|F not available8JBB|1|D:7MPM|1|H not available8JBB|1|D:7MPM|1|B not available8JBB|1|D:6N6J|1|C not available8JBB|1|D:7MPM|1|D not available8JBB|1|D:7MPM|1|J not available8JBB|1|D:6P7Q|1|E not available8JBB|1|D:6P7Q|1|D not available8JBB|1|D:7MPM|1|P not available8JBB|1|D:7MPM|1|N not available8JBB|1|D:6P7Q|1|F not available8JBB|1|C:6RCL|1|C not available8JBB|1|C:5JJU|1|C not available8JBB|1|C:4EJT|1|G not available8JBB|1|C:8JBB|1|D not available8JBB|1|C:8JBB|1|C = 08JBB|1|C:7MPM|1|L not available8JBB|1|C:6N6J|1|D not available8JBB|1|C:6N6C|1|D not available8JBB|1|C:7MPM|1|F not available8JBB|1|C:7MPM|1|H not available8JBB|1|C:7MPM|1|B not available8JBB|1|C:6N6J|1|C not available8JBB|1|C:7MPM|1|D not available8JBB|1|C:7MPM|1|J not available8JBB|1|C:6P7Q|1|E not available8JBB|1|C:6P7Q|1|D not available8JBB|1|C:7MPM|1|P not available8JBB|1|C:7MPM|1|N not available8JBB|1|C:6P7Q|1|F not available7MPM|1|L:6RCL|1|C not available7MPM|1|L:5JJU|1|C not available7MPM|1|L:4EJT|1|G not available7MPM|1|L:8JBB|1|D not available7MPM|1|L:8JBB|1|C not available7MPM|1|L:7MPM|1|L = 07MPM|1|L:6N6J|1|D not available7MPM|1|L:6N6C|1|D not available7MPM|1|L:7MPM|1|F not available7MPM|1|L:7MPM|1|H not available7MPM|1|L:7MPM|1|B not available7MPM|1|L:6N6J|1|C not available7MPM|1|L:7MPM|1|D not available7MPM|1|L:7MPM|1|J not available7MPM|1|L:6P7Q|1|E not available7MPM|1|L:6P7Q|1|D not available7MPM|1|L:7MPM|1|P not available7MPM|1|L:7MPM|1|N not available7MPM|1|L:6P7Q|1|F not available6N6J|1|D:6RCL|1|C not available6N6J|1|D:5JJU|1|C not available6N6J|1|D:4EJT|1|G not available6N6J|1|D:8JBB|1|D not available6N6J|1|D:8JBB|1|C not available6N6J|1|D:7MPM|1|L not available6N6J|1|D:6N6J|1|D = 06N6J|1|D:6N6C|1|D not available6N6J|1|D:7MPM|1|F not available6N6J|1|D:7MPM|1|H not available6N6J|1|D:7MPM|1|B not available6N6J|1|D:6N6J|1|C not available6N6J|1|D:7MPM|1|D not available6N6J|1|D:7MPM|1|J not available6N6J|1|D:6P7Q|1|E not available6N6J|1|D:6P7Q|1|D not available6N6J|1|D:7MPM|1|P not available6N6J|1|D:7MPM|1|N not available6N6J|1|D:6P7Q|1|F not available6N6C|1|D:6RCL|1|C not available6N6C|1|D:5JJU|1|C not available6N6C|1|D:4EJT|1|G not available6N6C|1|D:8JBB|1|D not available6N6C|1|D:8JBB|1|C not available6N6C|1|D:7MPM|1|L not available6N6C|1|D:6N6J|1|D not available6N6C|1|D:6N6C|1|D = 06N6C|1|D:7MPM|1|F not available6N6C|1|D:7MPM|1|H not available6N6C|1|D:7MPM|1|B not available6N6C|1|D:6N6J|1|C not available6N6C|1|D:7MPM|1|D not available6N6C|1|D:7MPM|1|J not available6N6C|1|D:6P7Q|1|E not available6N6C|1|D:6P7Q|1|D not available6N6C|1|D:7MPM|1|P not available6N6C|1|D:7MPM|1|N not available6N6C|1|D:6P7Q|1|F not available7MPM|1|F:6RCL|1|C not available7MPM|1|F:5JJU|1|C not available7MPM|1|F:4EJT|1|G not available7MPM|1|F:8JBB|1|D not available7MPM|1|F:8JBB|1|C not available7MPM|1|F:7MPM|1|L not available7MPM|1|F:6N6J|1|D not available7MPM|1|F:6N6C|1|D not available7MPM|1|F:7MPM|1|F = 07MPM|1|F:7MPM|1|H not available7MPM|1|F:7MPM|1|B not available7MPM|1|F:6N6J|1|C not available7MPM|1|F:7MPM|1|D not available7MPM|1|F:7MPM|1|J not available7MPM|1|F:6P7Q|1|E not available7MPM|1|F:6P7Q|1|D not available7MPM|1|F:7MPM|1|P not available7MPM|1|F:7MPM|1|N not available7MPM|1|F:6P7Q|1|F not available7MPM|1|H:6RCL|1|C not available7MPM|1|H:5JJU|1|C not available7MPM|1|H:4EJT|1|G not available7MPM|1|H:8JBB|1|D not available7MPM|1|H:8JBB|1|C not available7MPM|1|H:7MPM|1|L not available7MPM|1|H:6N6J|1|D not available7MPM|1|H:6N6C|1|D not available7MPM|1|H:7MPM|1|F not available7MPM|1|H:7MPM|1|H = 07MPM|1|H:7MPM|1|B not available7MPM|1|H:6N6J|1|C not available7MPM|1|H:7MPM|1|D not available7MPM|1|H:7MPM|1|J not available7MPM|1|H:6P7Q|1|E not available7MPM|1|H:6P7Q|1|D not available7MPM|1|H:7MPM|1|P not available7MPM|1|H:7MPM|1|N not available7MPM|1|H:6P7Q|1|F not available7MPM|1|B:6RCL|1|C not available7MPM|1|B:5JJU|1|C not available7MPM|1|B:4EJT|1|G not available7MPM|1|B:8JBB|1|D not available7MPM|1|B:8JBB|1|C not available7MPM|1|B:7MPM|1|L not available7MPM|1|B:6N6J|1|D not available7MPM|1|B:6N6C|1|D not available7MPM|1|B:7MPM|1|F not available7MPM|1|B:7MPM|1|H not available7MPM|1|B:7MPM|1|B = 07MPM|1|B:6N6J|1|C not available7MPM|1|B:7MPM|1|D not available7MPM|1|B:7MPM|1|J not available7MPM|1|B:6P7Q|1|E not available7MPM|1|B:6P7Q|1|D not available7MPM|1|B:7MPM|1|P not available7MPM|1|B:7MPM|1|N not available7MPM|1|B:6P7Q|1|F not available6N6J|1|C:6RCL|1|C not available6N6J|1|C:5JJU|1|C not available6N6J|1|C:4EJT|1|G not available6N6J|1|C:8JBB|1|D not available6N6J|1|C:8JBB|1|C not available6N6J|1|C:7MPM|1|L not available6N6J|1|C:6N6J|1|D not available6N6J|1|C:6N6C|1|D not available6N6J|1|C:7MPM|1|F not available6N6J|1|C:7MPM|1|H not available6N6J|1|C:7MPM|1|B not available6N6J|1|C:6N6J|1|C = 06N6J|1|C:7MPM|1|D not available6N6J|1|C:7MPM|1|J not available6N6J|1|C:6P7Q|1|E not available6N6J|1|C:6P7Q|1|D not available6N6J|1|C:7MPM|1|P not available6N6J|1|C:7MPM|1|N not available6N6J|1|C:6P7Q|1|F not available7MPM|1|D:6RCL|1|C not available7MPM|1|D:5JJU|1|C not available7MPM|1|D:4EJT|1|G not available7MPM|1|D:8JBB|1|D not available7MPM|1|D:8JBB|1|C not available7MPM|1|D:7MPM|1|L not available7MPM|1|D:6N6J|1|D not available7MPM|1|D:6N6C|1|D not available7MPM|1|D:7MPM|1|F not available7MPM|1|D:7MPM|1|H not available7MPM|1|D:7MPM|1|B not available7MPM|1|D:6N6J|1|C not available7MPM|1|D:7MPM|1|D = 07MPM|1|D:7MPM|1|J not available7MPM|1|D:6P7Q|1|E not available7MPM|1|D:6P7Q|1|D not available7MPM|1|D:7MPM|1|P not available7MPM|1|D:7MPM|1|N not available7MPM|1|D:6P7Q|1|F not available7MPM|1|J:6RCL|1|C not available7MPM|1|J:5JJU|1|C not available7MPM|1|J:4EJT|1|G not available7MPM|1|J:8JBB|1|D not available7MPM|1|J:8JBB|1|C not available7MPM|1|J:7MPM|1|L not available7MPM|1|J:6N6J|1|D not available7MPM|1|J:6N6C|1|D not available7MPM|1|J:7MPM|1|F not available7MPM|1|J:7MPM|1|H not available7MPM|1|J:7MPM|1|B not available7MPM|1|J:6N6J|1|C not available7MPM|1|J:7MPM|1|D not available7MPM|1|J:7MPM|1|J = 07MPM|1|J:6P7Q|1|E not available7MPM|1|J:6P7Q|1|D not available7MPM|1|J:7MPM|1|P not available7MPM|1|J:7MPM|1|N not available7MPM|1|J:6P7Q|1|F not available6P7Q|1|E:6RCL|1|C not available6P7Q|1|E:5JJU|1|C not available6P7Q|1|E:4EJT|1|G not available6P7Q|1|E:8JBB|1|D not available6P7Q|1|E:8JBB|1|C not available6P7Q|1|E:7MPM|1|L not available6P7Q|1|E:6N6J|1|D not available6P7Q|1|E:6N6C|1|D not available6P7Q|1|E:7MPM|1|F not available6P7Q|1|E:7MPM|1|H not available6P7Q|1|E:7MPM|1|B not available6P7Q|1|E:6N6J|1|C not available6P7Q|1|E:7MPM|1|D not available6P7Q|1|E:7MPM|1|J not available6P7Q|1|E:6P7Q|1|E = 06P7Q|1|E:6P7Q|1|D not available6P7Q|1|E:7MPM|1|P not available6P7Q|1|E:7MPM|1|N not available6P7Q|1|E:6P7Q|1|F not available6P7Q|1|D:6RCL|1|C not available6P7Q|1|D:5JJU|1|C not available6P7Q|1|D:4EJT|1|G not available6P7Q|1|D:8JBB|1|D not available6P7Q|1|D:8JBB|1|C not available6P7Q|1|D:7MPM|1|L not available6P7Q|1|D:6N6J|1|D not available6P7Q|1|D:6N6C|1|D not available6P7Q|1|D:7MPM|1|F not available6P7Q|1|D:7MPM|1|H not available6P7Q|1|D:7MPM|1|B not available6P7Q|1|D:6N6J|1|C not available6P7Q|1|D:7MPM|1|D not available6P7Q|1|D:7MPM|1|J not available6P7Q|1|D:6P7Q|1|E not available6P7Q|1|D:6P7Q|1|D = 06P7Q|1|D:7MPM|1|P not available6P7Q|1|D:7MPM|1|N not available6P7Q|1|D:6P7Q|1|F not available7MPM|1|P:6RCL|1|C not available7MPM|1|P:5JJU|1|C not available7MPM|1|P:4EJT|1|G not available7MPM|1|P:8JBB|1|D not available7MPM|1|P:8JBB|1|C not available7MPM|1|P:7MPM|1|L not available7MPM|1|P:6N6J|1|D not available7MPM|1|P:6N6C|1|D not available7MPM|1|P:7MPM|1|F not available7MPM|1|P:7MPM|1|H not available7MPM|1|P:7MPM|1|B not available7MPM|1|P:6N6J|1|C not available7MPM|1|P:7MPM|1|D not available7MPM|1|P:7MPM|1|J not available7MPM|1|P:6P7Q|1|E not available7MPM|1|P:6P7Q|1|D not available7MPM|1|P:7MPM|1|P = 07MPM|1|P:7MPM|1|N not available7MPM|1|P:6P7Q|1|F not available7MPM|1|N:6RCL|1|C not available7MPM|1|N:5JJU|1|C not available7MPM|1|N:4EJT|1|G not available7MPM|1|N:8JBB|1|D not available7MPM|1|N:8JBB|1|C not available7MPM|1|N:7MPM|1|L not available7MPM|1|N:6N6J|1|D not available7MPM|1|N:6N6C|1|D not available7MPM|1|N:7MPM|1|F not available7MPM|1|N:7MPM|1|H not available7MPM|1|N:7MPM|1|B not available7MPM|1|N:6N6J|1|C not available7MPM|1|N:7MPM|1|D not available7MPM|1|N:7MPM|1|J not available7MPM|1|N:6P7Q|1|E not available7MPM|1|N:6P7Q|1|D not available7MPM|1|N:7MPM|1|P not available7MPM|1|N:7MPM|1|N = 07MPM|1|N:6P7Q|1|F not available6P7Q|1|F:6RCL|1|C not available6P7Q|1|F:5JJU|1|C not available6P7Q|1|F:4EJT|1|G not available6P7Q|1|F:8JBB|1|D not available6P7Q|1|F:8JBB|1|C not available6P7Q|1|F:7MPM|1|L not available6P7Q|1|F:6N6J|1|D not available6P7Q|1|F:6N6C|1|D not available6P7Q|1|F:7MPM|1|F not available6P7Q|1|F:7MPM|1|H not available6P7Q|1|F:7MPM|1|B not available6P7Q|1|F:6N6J|1|C not available6P7Q|1|F:7MPM|1|D not available6P7Q|1|F:7MPM|1|J not available6P7Q|1|F:6P7Q|1|E not available6P7Q|1|F:6P7Q|1|D not available6P7Q|1|F:7MPM|1|P not available6P7Q|1|F:7MPM|1|N not available6P7Q|1|F:6P7Q|1|F = 06RCL|1|C5JJU|1|C4EJT|1|G8JBB|1|D8JBB|1|C7MPM|1|L6N6J|1|D6N6C|1|D7MPM|1|F7MPM|1|H7MPM|1|B6N6J|1|C7MPM|1|D7MPM|1|J6P7Q|1|E6P7Q|1|D7MPM|1|P7MPM|1|N6P7Q|1|FDiscrepancy0.000.501.001.502.002.50

Coloring options:

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