RNA 3D Hub //

Equivalence class NR_3.0_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
309OFE|1|JcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
319OFD|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerElectron microscopy2.8622025-08-20
329OFE|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
339OFB|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
349OFD|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerElectron microscopy2.8622025-08-20
359OFB|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
369OFE|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
379OFE|1|IcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
384EJT|1|G5'-R(*AP*A)-3'Staphylococcus epidermidis TcaR in complex with RNAX-ray diffraction322013-06-05

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
14EJT|1|GStaphylococcus epidermidis TcaR in complex with RNAX-RAY DIFFRACTION32
29OFB|1|DCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapELECTRON MICROSCOPY2.682
37MPM|1|FBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
46RCL|1|CCrystal structure of REXO2-D199A-AAX-RAY DIFFRACTION1.972
56P7Q|1|DStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
68JBB|1|CCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
77MPM|1|NBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
89OFB|1|CCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapELECTRON MICROSCOPY2.682
99MMW|1|JCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
109MMW|1|ICRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
119OFD|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerELECTRON MICROSCOPY2.862
125XSP|1|CThe catalytic domain of GdpP with 5'-pApAX-RAY DIFFRACTION2.1462
139OFE|1|ICryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
147MPM|1|HBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
155O4Z|1|BStructure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with substrate 5'-pApAX-RAY DIFFRACTION1.72
169OFE|1|JCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
179MMW|1|DCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
189OFE|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
199EBT|1|CCRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, refined against a composite mapELECTRON MICROSCOPY2.362
205XSP|1|DThe catalytic domain of GdpP with 5'-pApAX-RAY DIFFRACTION2.1462
217MPM|1|BBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
229OFE|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
236P7Q|1|FStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
249EBT|1|DCRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, refined against a composite mapELECTRON MICROSCOPY2.362
259OFD|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerELECTRON MICROSCOPY2.862
267MPM|1|DBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
277MPM|1|JBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
286N6J|1|DHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
297MPM|1|LBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
309MMW|1|QCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
315JJU|1|CCrystal structure of Rv2837c complexed with 5'-pApA and 5'-AMPX-RAY DIFFRACTION2.312
326P7Q|1|EStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
336N6J|1|CHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
349MMW|1|CCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
358JBB|1|DCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
366N6C|1|DVibrio cholerae Oligoribonuclease bound to pAAX-RAY DIFFRACTION1.622
377MPM|1|PBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
389MMW|1|TCRISPR-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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