#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
16N6I|1|C (rep)RNA (5'-R(P*GP*G)-3')synthetic constructHuman REXO2 bound to pGGX-ray diffraction1.4322019-06-12
26N6I|1|DRNA (5'-R(P*GP*G)-3')synthetic constructHuman REXO2 bound to pGGX-ray diffraction1.4322019-06-12
36N6A|1|DRNA (5'-R(P*GP*G)-3')Pseudomonas aeruginosaVibrio cholerae Oligoribonuclease bound to pGGX-ray diffraction1.522019-06-12
47MPL|1|D5'-phosphorylated GGsynthetic constructBartonella henselae NrnC bound to pGGX-ray diffraction1.822021-09-15
57MPL|1|H5'-phosphorylated GGsynthetic constructBartonella henselae NrnC bound to pGGX-ray diffraction1.822021-09-15
67MPL|1|B5'-phosphorylated GGsynthetic constructBartonella henselae NrnC bound to pGGX-ray diffraction1.822021-09-15
77MPL|1|J5'-phosphorylated GGsynthetic constructBartonella henselae NrnC bound to pGGX-ray diffraction1.822021-09-15
87MPL|1|F5'-phosphorylated GGsynthetic constructBartonella henselae NrnC bound to pGGX-ray diffraction1.822021-09-15
97MPL|1|N5'-phosphorylated GGsynthetic constructBartonella henselae NrnC bound to pGGX-ray diffraction1.822021-09-15
107MPL|1|L5'-phosphorylated GGsynthetic constructBartonella henselae NrnC bound to pGGX-ray diffraction1.822021-09-15
117MPL|1|P5'-phosphorylated GGsynthetic constructBartonella henselae NrnC bound to pGGX-ray diffraction1.822021-09-15
129F7M|1|JRNA (5'-R(P*GP*G)-3')Blastococcus aggregatusBlastococcus Orn bound to pGGX-ray diffraction1.6522024-12-04
139F7M|1|IRNA (5'-R(P*GP*G)-3')Blastococcus aggregatusBlastococcus Orn bound to pGGX-ray diffraction1.6522024-12-04
149F7M|1|MRNA (5'-R(P*GP*G)-3')Blastococcus aggregatusBlastococcus Orn bound to pGGX-ray diffraction1.6522024-12-04
159F7M|1|KRNA (5'-R(P*GP*G)-3')Blastococcus aggregatusBlastococcus Orn bound to pGGX-ray diffraction1.6522024-12-04
169F7M|1|LRNA (5'-R(P*GP*G)-3')Blastococcus aggregatusBlastococcus Orn bound to pGGX-ray diffraction1.6522024-12-04
179F7M|1|ORNA (5'-R(P*GP*G)-3')Blastococcus aggregatusBlastococcus Orn bound to pGGX-ray diffraction1.6522024-12-04
189F7M|1|NRNA (5'-R(P*GP*G)-3')Blastococcus aggregatusBlastococcus Orn bound to pGGX-ray diffraction1.6522024-12-04
199F7M|1|PRNA (5'-R(P*GP*G)-3')Blastococcus aggregatusBlastococcus Orn bound to pGGX-ray diffraction1.6522024-12-04
207VA3|1|CRNA (5'-R(P*GP*G)-3')synthetic constructPaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structureX-ray diffraction1.822022-09-07
217MPU|1|D5'-phosphorylated GGsynthetic constructBrucella melitensis NrnC bound to pGGX-ray diffraction1.7222021-09-15
226IJ2|1|FRNA (5'-R(P*GP*G)-3')synthetic constructCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-ray diffraction1.722019-10-09
236IJ2|1|GRNA (5'-R(P*GP*G)-3')synthetic constructCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-ray diffraction1.722019-10-09
246IJ2|1|HRNA (5'-R(P*GP*G)-3')synthetic constructCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-ray diffraction1.722019-10-09
256IJ2|1|ERNA (5'-R(P*GP*G)-3')synthetic constructCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-ray diffraction1.722019-10-09
263U2E|1|DRNA (5'-R(P*GP*G)-3')EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++X-ray diffraction2.3222011-10-12
273U2E|1|CRNA (5'-R(P*GP*G)-3')EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++X-ray diffraction2.3222011-10-12
287PVK|1|GpGpGsynthetic constructX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-ray diffraction2.422022-12-14
297PVK|1|EpGpGsynthetic constructX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-ray diffraction2.422022-12-14
307MPQ|1|R5'-phosphorylated GGsynthetic constructBartonella henselae NrnC cleaving pGG in the presence of Mn2+X-ray diffraction2.3522021-09-15
317PVK|1|HpGpGsynthetic constructX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-ray diffraction2.422022-12-14
327MQB|1|BRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
337MQB|1|HRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
347MQB|1|JRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
357MQB|1|FRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
367MQB|1|LRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
377MQB|1|DRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
387MQB|1|NRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
397MQB|1|PRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
407EH1|1|IRNA (5'-R(*GP*G)-3')synthetic constructThermus thermophilus transcription initiation complex containing a template-strand purine at position TSS-2, GpG RNA primer, and CMPcPPX-ray diffraction2.922021-07-14
417PVK|1|FpGpGsynthetic constructX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-ray diffraction2.422022-12-14
425UEF|1|CRNA (5'-R(P*GP*G)-3')synthetic constructRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligandX-ray diffraction2.122017-07-05
437MQC|1|PRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
446OY5|1|IRNA (5'-D(*(GTP))-R(P*G)-3')Thermus thermophilusX-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter at 3 minX-ray diffraction3.122019-06-05
457MQC|1|BRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
465UEF|1|DRNA (5'-R(P*GP*G)-3')synthetic constructRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligandX-ray diffraction2.122017-07-05
477MQC|1|NRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
487MQC|1|FRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
497EH2|1|RRNA (5'-R(*GP*G)-3')synthetic constructThermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primerX-ray diffraction3.3422021-07-14
507EH2|1|IRNA (5'-R(*GP*G)-3')synthetic constructThermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primerX-ray diffraction3.3422021-07-14
517MQC|1|LRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
527MQC|1|JRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
537MQC|1|HRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
547MQC|1|DRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
554X4T|1|IRNA (5'-D(P*GP*G)-3')Homo sapiensCrystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in CCACCAX-ray diffraction2.522015-02-11
563UCZ|1|DRNA (5'-R(*GP*G)-3')The c-di-GMP-I riboswitch bound to GpGX-ray diffraction2.822012-01-04
574X4U|1|HRNA (5'-D(*GP*G)-3')Homo sapiensCrystal structure of the A.fulgidus CCA-adding enzyme in complex with a human MenBeta minihelix ending in CCACCX-ray diffraction2.722015-02-11
584AFY|1|D5'-R(*GP*GP)-3'synthetic constructCrystal structure of the FimX EAL domain in complex with reaction product pGpGX-ray diffraction2.0122013-01-09
596YMW|1|CRNA (pppGpG)synthetic constructCryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complexElectron microscopy3.7122020-12-09
606OWL|1|BRNA (5'-R(P*G)-3')synthetic constructRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-ray diffraction212020-02-26
614AFY|1|C5'-R(*GP*GP)-3'synthetic constructCrystal structure of the FimX EAL domain in complex with reaction product pGpGX-ray diffraction2.0122013-01-09
626OWL|1|CRNA (5'-R(P*G)-3')synthetic constructRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-ray diffraction212020-02-26
636S0M|1|CRNA (5'-R(P*G)-3')Escherichia coliStructural and dynamic studies provide insights into specificity and allosteric regulation of Ribonuclease AS, a key enzyme in mycobacterial virulenceX-ray diffraction212019-08-28
644LQ3|1|R5'-R(P*GP*G)-3'Crystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDSX-ray diffraction2.622014-02-12
653UCU|1|Adiguanosine monophosphateThe c-di-GMP-I riboswitch bound to pGpGX-ray diffraction2.822012-01-04

Release history

Release4.0
Date2025-08-13

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
17MPL|1|JBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
27MPL|1|DBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
37MPL|1|FBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
46N6I|1|DHuman REXO2 bound to pGGX-RAY DIFFRACTION1.432
57MPL|1|BBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
67MPL|1|HBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
76N6A|1|DVibrio cholerae Oligoribonuclease bound to pGGX-RAY DIFFRACTION1.52
86N6I|1|CHuman REXO2 bound to pGGX-RAY DIFFRACTION1.432
97MPL|1|NBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
103U2E|1|CEAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++X-RAY DIFFRACTION2.322
114AFY|1|CCrystal structure of the FimX EAL domain in complex with reaction product pGpGX-RAY DIFFRACTION2.012
124AFY|1|DCrystal structure of the FimX EAL domain in complex with reaction product pGpGX-RAY DIFFRACTION2.012
133U2E|1|DEAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++X-RAY DIFFRACTION2.322
143UCU|1|AThe c-di-GMP-I riboswitch bound to pGpGX-RAY DIFFRACTION2.82
154X4U|1|HCrystal structure of the A.fulgidus CCA-adding enzyme in complex with a human MenBeta minihelix ending in CCACCX-RAY DIFFRACTION2.72
164X4T|1|ICrystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in CCACCAX-RAY DIFFRACTION2.52
174LQ3|1|RCrystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDSX-RAY DIFFRACTION2.62
186OWL|1|CRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-RAY DIFFRACTION21
196S0M|1|CStructural and dynamic studies provide insights into specificity and allosteric regulation of Ribonuclease AS, a key enzyme in mycobacterial virulenceX-RAY DIFFRACTION21
206OWL|1|BRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-RAY DIFFRACTION21
217MQB|1|BBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
227MQB|1|HBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
237MQB|1|NBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
247PVK|1|HX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
257MQB|1|JBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
267MQB|1|LBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
277MQB|1|DBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
287MPQ|1|RBartonella henselae NrnC cleaving pGG in the presence of Mn2+X-RAY DIFFRACTION2.352
297MQB|1|FBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
307MQC|1|JBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
317MQC|1|HBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
327MQC|1|FBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
337EH2|1|IThermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primerX-RAY DIFFRACTION3.342
347MQC|1|LBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
353UCZ|1|DThe c-di-GMP-I riboswitch bound to GpGX-RAY DIFFRACTION2.82
366YMW|1|CCryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complexELECTRON MICROSCOPY3.712
377MQC|1|DBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
387EH2|1|RThermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primerX-RAY DIFFRACTION3.342
399F7M|1|NBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
409F7M|1|LBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
419F7M|1|IBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
427MPL|1|LBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
439F7M|1|MBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
449F7M|1|OBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
457MPL|1|PBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
469F7M|1|KBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
479F7M|1|JBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
486IJ2|1|FCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
496IJ2|1|GCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
509F7M|1|PBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
517MPU|1|DBrucella melitensis NrnC bound to pGGX-RAY DIFFRACTION1.722
526IJ2|1|ECrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
536IJ2|1|HCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
547PVK|1|GX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
557PVK|1|EX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
567VA3|1|CPaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structureX-RAY DIFFRACTION1.82
575UEF|1|DRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligandX-RAY DIFFRACTION2.12
586OY5|1|IX-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter at 3 minX-RAY DIFFRACTION3.12
597MQC|1|NBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
607MQB|1|PBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
617EH1|1|IThermus thermophilus transcription initiation complex containing a template-strand purine at position TSS-2, GpG RNA primer, and CMPcPPX-RAY DIFFRACTION2.92
627MQC|1|PBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
635UEF|1|CRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligandX-RAY DIFFRACTION2.12
647MQC|1|BBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
657PVK|1|FX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42

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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