RNA 3D Hub //

Equivalence class NR_3.0_52978.3 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
215JJU|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
229MMW|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
239MMW|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
249MMW|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
259MMW|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
269MMW|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
279MMW|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
289OFE|1|JcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
299OFD|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerElectron microscopy2.8622025-08-20
309OFE|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
319OFB|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapElectron microscopy2.6822025-08-20
329OFD|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerElectron microscopy2.8622025-08-20
339OFB|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapElectron microscopy2.6822025-08-20
349OFE|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
359OFE|1|IcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
364EJT|1|G5'-R(*AP*A)-3'Staphylococcus epidermidis TcaR in complex with RNAX-ray diffraction322013-06-05

Release history

Release4.18
Date2025-12-17

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
19MMW|1|TCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
27MPM|1|BBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
39OFD|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerELECTRON MICROSCOPY2.862
46RCL|1|CCrystal structure of REXO2-D199A-AAX-RAY DIFFRACTION1.972
57MPM|1|LBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
69MMW|1|DCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
76N6J|1|DHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
86N6J|1|CHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
98JBB|1|DCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
107MPM|1|JBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
115XSP|1|DThe catalytic domain of GdpP with 5'-pApAX-RAY DIFFRACTION2.1462
129OFE|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
139OFE|1|JCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
146P7Q|1|EStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
159OFB|1|DCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapELECTRON MICROSCOPY2.682
169OFB|1|CCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapELECTRON MICROSCOPY2.682
176P7Q|1|DStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
188JBB|1|CCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
199OFE|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
207MPM|1|FBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
215O4Z|1|BStructure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with substrate 5'-pApAX-RAY DIFFRACTION1.72
229MMW|1|JCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
239OFD|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerELECTRON MICROSCOPY2.862
249OFE|1|ICryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
257MPM|1|NBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
269MMW|1|CCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
279MMW|1|QCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
284EJT|1|GStaphylococcus epidermidis TcaR in complex with RNAX-RAY DIFFRACTION32
296P7Q|1|FStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
307MPM|1|HBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
315XSP|1|CThe catalytic domain of GdpP with 5'-pApAX-RAY DIFFRACTION2.1462
326N6C|1|DVibrio cholerae Oligoribonuclease bound to pAAX-RAY DIFFRACTION1.622
335JJU|1|CCrystal structure of Rv2837c complexed with 5'-pApA and 5'-AMPX-RAY DIFFRACTION2.312
349MMW|1|ICRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
357MPM|1|PBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
367MPM|1|DBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952

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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