RNA 3D Hub //

Equivalence class NR_2.5_52978.5 Current

#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
115O4Z|1|BRNA 5'-pApAsynthetic constructStructure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with substrate 5'-pApAX-ray diffraction1.722017-10-25
127MPM|1|N5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
136P7Q|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
146P7Q|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
156P7Q|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
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
175XSP|1|CDNA (5'-R(P*AP*A)-3')synthetic constructThe catalytic domain of GdpP with 5'-pApAX-ray diffraction2.14622018-01-31
185XSP|1|DDNA (5'-R(P*AP*A)-3')synthetic constructThe catalytic domain of GdpP with 5'-pApAX-ray diffraction2.14622018-01-31
196RCL|1|CRNA (5'-R(P*AP*A)-3')synthetic constructCrystal structure of REXO2-D199A-AAX-ray diffraction1.9722019-10-09
208JBB|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
219EBT|1|CTetra-adenylateThermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, refined against a composite mapElectron microscopy2.3622026-01-07
229EBT|1|DTetra-adenylateThermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, refined against a composite mapElectron microscopy2.3622026-01-07
235JJU|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
249MMW|1|QRNA (5'-R(*AP*(A23))-3')Thermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapElectron microscopy2.3622025-11-12
259MMW|1|DRNA (5'-R(*AP*(A23))-3')Thermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapElectron microscopy2.3622025-11-12
269MMW|1|CRNA (5'-R(*AP*(A23))-3')Thermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapElectron microscopy2.3622025-11-12
279MMW|1|TRNA (5'-R(*AP*(A23))-3')Thermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapElectron microscopy2.3622025-11-12
289MMW|1|IRNA (5'-R(*AP*(A23))-3')Thermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapElectron microscopy2.3622025-11-12
299MMW|1|JRNA (5'-R(*AP*(A23))-3')Thermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapElectron microscopy2.3622025-11-12

Release history

Release4.404.414.424.434.44
Date2026-05-202026-05-272026-06-032026-06-102026-06-17

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
17MPM|1|DBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
25JJU|1|CCrystal structure of Rv2837c complexed with 5'-pApA and 5'-AMPX-RAY DIFFRACTION2.312
39EBT|1|DCRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, refined against a composite mapELECTRON MICROSCOPY2.362
49MMW|1|DCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
57MPM|1|PBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
66N6J|1|CHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
77MPM|1|NBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
87MPM|1|BBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
98JBB|1|CCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
108JBB|1|DCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
119MMW|1|ICRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
126N6J|1|DHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
139MMW|1|CCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
146RCL|1|CCrystal structure of REXO2-D199A-AAX-RAY DIFFRACTION1.972
156P7Q|1|EStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
165XSP|1|DThe catalytic domain of GdpP with 5'-pApAX-RAY DIFFRACTION2.1462
177MPM|1|FBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
187MPM|1|JBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
196N6C|1|DVibrio cholerae Oligoribonuclease bound to pAAX-RAY DIFFRACTION1.622
209MMW|1|TCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
215XSP|1|CThe catalytic domain of GdpP with 5'-pApAX-RAY DIFFRACTION2.1462
229MMW|1|QCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
235O4Z|1|BStructure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with substrate 5'-pApAX-RAY DIFFRACTION1.72
246P7Q|1|DStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
257MPM|1|HBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
267MPM|1|LBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
276P7Q|1|FStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
289EBT|1|CCRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, refined against a composite mapELECTRON MICROSCOPY2.362
299MMW|1|JCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362

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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