#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
285MFU|1|BRNA (pGpG)synthetic constructPA3825-EAL Mn-pGpG StructureX-ray diffraction2.1522017-03-01
297PVK|1|GpGpGsynthetic constructX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-ray diffraction2.422022-12-14
307PVK|1|EpGpGsynthetic constructX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-ray diffraction2.422022-12-14
317MPQ|1|R5'-phosphorylated GGsynthetic constructBartonella henselae NrnC cleaving pGG in the presence of Mn2+X-ray diffraction2.3522021-09-15
327PVK|1|HpGpGsynthetic constructX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-ray diffraction2.422022-12-14
337MQB|1|BRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
347MQB|1|HRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
357MQB|1|JRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
367MQB|1|FRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
377MQB|1|LRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
387MQB|1|DRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
397MQB|1|NRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
407MQB|1|PRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
417EH1|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
427PVK|1|FpGpGsynthetic constructX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-ray diffraction2.422022-12-14
435UEF|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
447MQC|1|PRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
456OY5|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
467MQC|1|BRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
475UEF|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
487MQC|1|NRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
497MQC|1|FRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
509RTC|1|bbRNA (5'-R(P*GP*G)-3')Escherichia coliOkeania NrnC bound to pGGX-ray diffraction322026-07-15
517EH2|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
527EH2|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
539RTC|1|ffRNA (5'-R(P*GP*G)-3')Escherichia coliOkeania NrnC bound to pGGX-ray diffraction322026-07-15
547MQC|1|LRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
557MQC|1|JRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
567MQC|1|HRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
577MQC|1|DRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
584X4T|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
593UCZ|1|DRNA (5'-R(*GP*G)-3')The c-di-GMP-I riboswitch bound to GpGX-ray diffraction2.822012-01-04
609RTC|1|ccRNA (5'-R(P*GP*G)-3')Escherichia coliOkeania NrnC bound to pGGX-ray diffraction322026-07-15
614X4U|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
624AFY|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
636YMW|1|CRNA (pppGpG)synthetic constructCryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complexElectron microscopy3.7122020-12-09
646OWL|1|BRNA (5'-R(P*G)-3')synthetic constructRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-ray diffraction212020-02-26
654AFY|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
666OWL|1|CRNA (5'-R(P*G)-3')synthetic constructRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-ray diffraction212020-02-26
676S0M|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
684LQ3|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
693UCU|1|Adiguanosine monophosphateThe c-di-GMP-I riboswitch bound to pGpGX-ray diffraction2.822012-01-04
701UVK|1|F5'-D(*GP*GP)-3'The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end complexX-ray diffraction2.4512004-02-19
711UVK|1|D5'-D(*GP*GP)-3'The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end complexX-ray diffraction2.4512004-02-19
721UVK|1|B5'-D(*GP*GP)-3'The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end complexX-ray diffraction2.4512004-02-19

Release history

Release4.48
Date2026-07-15

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
16OY5|1|IX-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter at 3 minX-RAY DIFFRACTION3.12
27MQC|1|PBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
35UEF|1|DRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligandX-RAY DIFFRACTION2.12
47MQC|1|NBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
57EH2|1|IThermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primerX-RAY DIFFRACTION3.342
67MQC|1|BBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
79RTC|1|ffOkeania NrnC bound to pGGX-RAY DIFFRACTION32
87MQC|1|LBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
97MQC|1|FBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
107EH2|1|RThermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primerX-RAY DIFFRACTION3.342
119RTC|1|bbOkeania NrnC bound to pGGX-RAY DIFFRACTION32
127MQC|1|JBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
131UVK|1|FThe structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end complexX-RAY DIFFRACTION2.451
143U2E|1|DEAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++X-RAY DIFFRACTION2.322
154AFY|1|DCrystal structure of the FimX EAL domain in complex with reaction product pGpGX-RAY DIFFRACTION2.012
164AFY|1|CCrystal structure of the FimX EAL domain in complex with reaction product pGpGX-RAY DIFFRACTION2.012
173U2E|1|CEAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++X-RAY DIFFRACTION2.322
181UVK|1|DThe structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end complexX-RAY DIFFRACTION2.451
193UCU|1|AThe c-di-GMP-I riboswitch bound to pGpGX-RAY DIFFRACTION2.82
204LQ3|1|RCrystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDSX-RAY DIFFRACTION2.62
214X4T|1|ICrystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in CCACCAX-RAY DIFFRACTION2.52
224X4U|1|HCrystal structure of the A.fulgidus CCA-adding enzyme in complex with a human MenBeta minihelix ending in CCACCX-RAY DIFFRACTION2.72
231UVK|1|BThe structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end complexX-RAY DIFFRACTION2.451
246OWL|1|CRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-RAY DIFFRACTION21
256YMW|1|CCryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complexELECTRON MICROSCOPY3.712
266S0M|1|CStructural and dynamic studies provide insights into specificity and allosteric regulation of Ribonuclease AS, a key enzyme in mycobacterial virulenceX-RAY DIFFRACTION21
276OWL|1|BRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-RAY DIFFRACTION21
289RTC|1|ccOkeania NrnC bound to pGGX-RAY DIFFRACTION32
297MQC|1|DBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
307MQC|1|HBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
313UCZ|1|DThe c-di-GMP-I riboswitch bound to GpGX-RAY DIFFRACTION2.82
326IJ2|1|FCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
336N6I|1|DHuman REXO2 bound to pGGX-RAY DIFFRACTION1.432
347MPL|1|LBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
357MPL|1|FBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
367MQB|1|DBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
377MPL|1|HBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
389F7M|1|KBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
396IJ2|1|ECrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
407PVK|1|HX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
417MPQ|1|RBartonella henselae NrnC cleaving pGG in the presence of Mn2+X-RAY DIFFRACTION2.352
427MPL|1|BBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
437PVK|1|EX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
446IJ2|1|HCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
457MPL|1|DBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
467MQB|1|FBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
477EH1|1|IThermus thermophilus transcription initiation complex containing a template-strand purine at position TSS-2, GpG RNA primer, and CMPcPPX-RAY DIFFRACTION2.92
489F7M|1|LBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
495MFU|1|BPA3825-EAL Mn-pGpG StructureX-RAY DIFFRACTION2.152
507PVK|1|GX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
519F7M|1|OBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
527VA3|1|CPaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structureX-RAY DIFFRACTION1.82
539F7M|1|IBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
549F7M|1|MBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
557MPL|1|NBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
567MQB|1|LBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
577MPL|1|PBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
587MQB|1|BBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
596IJ2|1|GCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
607MQB|1|HBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
617MPU|1|DBrucella melitensis NrnC bound to pGGX-RAY DIFFRACTION1.722
629F7M|1|PBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
639F7M|1|JBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
647MPL|1|JBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
656N6I|1|CHuman REXO2 bound to pGGX-RAY DIFFRACTION1.432
667PVK|1|FX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
675UEF|1|CRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligandX-RAY DIFFRACTION2.12
689F7M|1|NBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
697MQB|1|JBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
706N6A|1|DVibrio cholerae Oligoribonuclease bound to pGGX-RAY DIFFRACTION1.52
717MQB|1|NBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
727MQB|1|PBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252

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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