#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
119F7M|1|JRNA (5'-R(P*GP*G)-3')Blastococcus aggregatusBlastococcus Orn bound to pGGX-ray diffraction1.6522024-12-04
129F7M|1|IRNA (5'-R(P*GP*G)-3')Blastococcus aggregatusBlastococcus Orn bound to pGGX-ray diffraction1.6522024-12-04
139F7M|1|MRNA (5'-R(P*GP*G)-3')Blastococcus aggregatusBlastococcus Orn bound to pGGX-ray diffraction1.6522024-12-04
149F7M|1|KRNA (5'-R(P*GP*G)-3')Blastococcus aggregatusBlastococcus Orn bound to pGGX-ray diffraction1.6522024-12-04
157MPL|1|P5'-phosphorylated GGsynthetic constructBartonella henselae NrnC bound to pGGX-ray diffraction1.822021-09-15
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
216IJ2|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
226IJ2|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
236IJ2|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
246IJ2|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
253U2E|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
263U2E|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
277EH1|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
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
307PVK|1|HpGpGsynthetic 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
325UEF|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
337PVK|1|FpGpGsynthetic constructX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-ray diffraction2.422022-12-14
345UEF|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
357EH2|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
367EH2|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
374X4U|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
384AFY|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
396OY5|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
406OWL|1|BRNA (5'-R(P*G)-3')synthetic constructRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-ray diffraction212020-02-26
416OWL|1|CRNA (5'-R(P*G)-3')synthetic constructRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-ray diffraction212020-02-26
424AFY|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
434LQ3|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
446S0M|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
457MPU|1|D5'-phosphorylated GGsynthetic constructBrucella melitensis NrnC bound to pGGX-ray diffraction1.7222021-09-15
467MQB|1|BRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
477MQB|1|DRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
487MQB|1|FRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
497MQB|1|HRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
507MQB|1|JRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
517MQB|1|LRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
527MQB|1|NRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
537MQB|1|PRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. D4 SymmetryElectron microscopy3.2522021-09-15
547MQC|1|BRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
557MQC|1|DRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
567MQC|1|FRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
577MQC|1|HRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
587MQC|1|JRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
597MQC|1|LRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
607MQC|1|NRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
617MQC|1|PRNA (5'-R(P*GP*G)-3')synthetic constructBartonella henselae NrnC bound to pGG. C1 reconstruction.Electron microscopy3.6422021-09-15
626YMW|1|CRNA (pppGpG)synthetic constructCryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complexElectron microscopy3.7122020-12-09

Release history

Release3.3643.3653.3663.3673.3683.3693.3703.3713.3723.3733.3743.3753.3763.377
Date2024-12-042024-12-112024-12-182024-12-252025-01-012025-01-082025-01-152025-01-222025-01-292025-02-052025-02-122025-02-192025-02-262025-03-05

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
13U2E|1|DEAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++X-RAY DIFFRACTION2.322
23U2E|1|CEAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++X-RAY DIFFRACTION2.322
34AFY|1|CCrystal structure of the FimX EAL domain in complex with reaction product pGpGX-RAY DIFFRACTION2.012
44AFY|1|DCrystal structure of the FimX EAL domain in complex with reaction product pGpGX-RAY DIFFRACTION2.012
54X4U|1|HCrystal structure of the A.fulgidus CCA-adding enzyme in complex with a human MenBeta minihelix ending in CCACCX-RAY DIFFRACTION2.72
64LQ3|1|RCrystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDSX-RAY DIFFRACTION2.62
76S0M|1|CStructural and dynamic studies provide insights into specificity and allosteric regulation of Ribonuclease AS, a key enzyme in mycobacterial virulenceX-RAY DIFFRACTION21
87MPU|1|DBrucella melitensis NrnC bound to pGGX-RAY DIFFRACTION1.722
96OWL|1|CRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-RAY DIFFRACTION21
107MPL|1|NBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
117MPL|1|BBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
127MPL|1|DBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
137MPL|1|FBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
146N6A|1|DVibrio cholerae Oligoribonuclease bound to pGGX-RAY DIFFRACTION1.52
156N6I|1|CHuman REXO2 bound to pGGX-RAY DIFFRACTION1.432
167MPL|1|HBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
176N6I|1|DHuman REXO2 bound to pGGX-RAY DIFFRACTION1.432
187MPL|1|JBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
197MQC|1|JBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
207MQC|1|NBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
217MQC|1|HBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
227MQC|1|LBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
237MQC|1|PBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
247MQC|1|DBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
256YMW|1|CCryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complexELECTRON MICROSCOPY3.712
267MQC|1|FBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
277PVK|1|EX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
286IJ2|1|FCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
296IJ2|1|ECrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
307VA3|1|CPaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structureX-RAY DIFFRACTION1.82
317PVK|1|GX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
329F7M|1|PBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
336IJ2|1|HCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
347EH1|1|IThermus thermophilus transcription initiation complex containing a template-strand purine at position TSS-2, GpG RNA primer, and CMPcPPX-RAY DIFFRACTION2.92
356IJ2|1|GCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
367MPL|1|LBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
379F7M|1|OBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
389F7M|1|JBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
397MPL|1|PBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
409F7M|1|MBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
419F7M|1|KBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
429F7M|1|LBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
439F7M|1|IBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
449F7M|1|NBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
455UEF|1|DRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligandX-RAY DIFFRACTION2.12
467EH2|1|RThermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primerX-RAY DIFFRACTION3.342
476OWL|1|BRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-RAY DIFFRACTION21
487PVK|1|HX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
497EH2|1|IThermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primerX-RAY DIFFRACTION3.342
506OY5|1|IX-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter at 3 minX-RAY DIFFRACTION3.12
517PVK|1|FX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
525UEF|1|CRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligandX-RAY DIFFRACTION2.12
537MPQ|1|RBartonella henselae NrnC cleaving pGG in the presence of Mn2+X-RAY DIFFRACTION2.352
547MQC|1|BBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
557MQB|1|PBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
567MQB|1|BBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
577MQB|1|FBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
587MQB|1|LBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
597MQB|1|DBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
607MQB|1|HBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
617MQB|1|NBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
627MQB|1|JBartonella 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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