#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
17EH2|1|IThermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primerX-RAY DIFFRACTION3.342
27PVK|1|FX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
36OWL|1|BRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-RAY DIFFRACTION21
46OY5|1|IX-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter at 3 minX-RAY DIFFRACTION3.12
57PVK|1|HX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
67EH2|1|RThermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primerX-RAY DIFFRACTION3.342
77MPQ|1|RBartonella henselae NrnC cleaving pGG in the presence of Mn2+X-RAY DIFFRACTION2.352
85UEF|1|CRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligandX-RAY DIFFRACTION2.12
95UEF|1|DRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligandX-RAY DIFFRACTION2.12
107PVK|1|GX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
116IJ2|1|HCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
127VA3|1|CPaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structureX-RAY DIFFRACTION1.82
139F7M|1|PBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
146IJ2|1|FCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
157EH1|1|IThermus thermophilus transcription initiation complex containing a template-strand purine at position TSS-2, GpG RNA primer, and CMPcPPX-RAY DIFFRACTION2.92
166IJ2|1|ECrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
177PVK|1|EX-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.X-RAY DIFFRACTION2.42
186IJ2|1|GCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound formX-RAY DIFFRACTION1.72
197MPL|1|JBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
207MPL|1|HBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
217MPL|1|NBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
227MPL|1|DBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
237MPL|1|BBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
246N6I|1|DHuman REXO2 bound to pGGX-RAY DIFFRACTION1.432
257MPL|1|FBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
266N6I|1|CHuman REXO2 bound to pGGX-RAY DIFFRACTION1.432
276N6A|1|DVibrio cholerae Oligoribonuclease bound to pGGX-RAY DIFFRACTION1.52
287MPU|1|DBrucella melitensis NrnC bound to pGGX-RAY DIFFRACTION1.722
296OWL|1|CRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMPX-RAY DIFFRACTION21
304LQ3|1|RCrystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDSX-RAY DIFFRACTION2.62
314X4U|1|HCrystal structure of the A.fulgidus CCA-adding enzyme in complex with a human MenBeta minihelix ending in CCACCX-RAY DIFFRACTION2.72
324AFY|1|DCrystal structure of the FimX EAL domain in complex with reaction product pGpGX-RAY DIFFRACTION2.012
334AFY|1|CCrystal structure of the FimX EAL domain in complex with reaction product pGpGX-RAY DIFFRACTION2.012
343U2E|1|CEAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++X-RAY DIFFRACTION2.322
353U2E|1|DEAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++X-RAY DIFFRACTION2.322
366S0M|1|CStructural and dynamic studies provide insights into specificity and allosteric regulation of Ribonuclease AS, a key enzyme in mycobacterial virulenceX-RAY DIFFRACTION21
377MQB|1|PBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
387MQB|1|LBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
397MQB|1|BBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
407MQB|1|JBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
417MQB|1|FBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
427MQB|1|DBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
437MQB|1|NBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
447MQC|1|BBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
457MQB|1|HBartonella henselae NrnC bound to pGG. D4 SymmetryELECTRON MICROSCOPY3.252
467MQC|1|PBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
477MQC|1|LBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
487MQC|1|DBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
497MQC|1|NBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
506YMW|1|CCryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complexELECTRON MICROSCOPY3.712
517MQC|1|JBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
527MQC|1|FBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
537MQC|1|HBartonella henselae NrnC bound to pGG. C1 reconstruction.ELECTRON MICROSCOPY3.642
547MPL|1|LBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
559F7M|1|LBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
567MPL|1|PBartonella henselae NrnC bound to pGGX-RAY DIFFRACTION1.82
579F7M|1|JBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
589F7M|1|IBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
599F7M|1|MBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
609F7M|1|KBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
619F7M|1|NBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652
629F7M|1|OBlastococcus Orn bound to pGGX-RAY DIFFRACTION1.652

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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