Equivalence class NR_3.0_98428.6 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 6N6I|1|C (rep) | RNA (5'-R(P*GP*G)-3') | synthetic construct | Human REXO2 bound to pGG | X-ray diffraction | 1.43 | 2 | 2019-06-12 | |||
| 2 | 6N6I|1|D | RNA (5'-R(P*GP*G)-3') | synthetic construct | Human REXO2 bound to pGG | X-ray diffraction | 1.43 | 2 | 2019-06-12 | |||
| 3 | 6N6A|1|D | RNA (5'-R(P*GP*G)-3') | Pseudomonas aeruginosa | Vibrio cholerae Oligoribonuclease bound to pGG | X-ray diffraction | 1.5 | 2 | 2019-06-12 | |||
| 4 | 7MPL|1|D | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2 | 2021-09-15 | |||
| 5 | 7MPL|1|H | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2 | 2021-09-15 | |||
| 6 | 7MPL|1|B | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2 | 2021-09-15 | |||
| 7 | 7MPL|1|J | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2 | 2021-09-15 | |||
| 8 | 7MPL|1|F | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2 | 2021-09-15 | |||
| 9 | 7MPL|1|N | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2 | 2021-09-15 | |||
| 10 | 7MPL|1|L | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2 | 2021-09-15 | |||
| 11 | 7MPL|1|P | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2 | 2021-09-15 | |||
| 12 | 9F7M|1|J | RNA (5'-R(P*GP*G)-3') | Blastococcus aggregatus | Blastococcus Orn bound to pGG | X-ray diffraction | 1.65 | 2 | 2024-12-04 | |||
| 13 | 9F7M|1|I | RNA (5'-R(P*GP*G)-3') | Blastococcus aggregatus | Blastococcus Orn bound to pGG | X-ray diffraction | 1.65 | 2 | 2024-12-04 | |||
| 14 | 9F7M|1|M | RNA (5'-R(P*GP*G)-3') | Blastococcus aggregatus | Blastococcus Orn bound to pGG | X-ray diffraction | 1.65 | 2 | 2024-12-04 | |||
| 15 | 9F7M|1|K | RNA (5'-R(P*GP*G)-3') | Blastococcus aggregatus | Blastococcus Orn bound to pGG | X-ray diffraction | 1.65 | 2 | 2024-12-04 | |||
| 16 | 9F7M|1|L | RNA (5'-R(P*GP*G)-3') | Blastococcus aggregatus | Blastococcus Orn bound to pGG | X-ray diffraction | 1.65 | 2 | 2024-12-04 | |||
| 17 | 9F7M|1|O | RNA (5'-R(P*GP*G)-3') | Blastococcus aggregatus | Blastococcus Orn bound to pGG | X-ray diffraction | 1.65 | 2 | 2024-12-04 | |||
| 18 | 9F7M|1|N | RNA (5'-R(P*GP*G)-3') | Blastococcus aggregatus | Blastococcus Orn bound to pGG | X-ray diffraction | 1.65 | 2 | 2024-12-04 | |||
| 19 | 9F7M|1|P | RNA (5'-R(P*GP*G)-3') | Blastococcus aggregatus | Blastococcus Orn bound to pGG | X-ray diffraction | 1.65 | 2 | 2024-12-04 | |||
| 20 | 7VA3|1|C | RNA (5'-R(P*GP*G)-3') | synthetic construct | PaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structure | X-ray diffraction | 1.8 | 2 | 2022-09-07 | |||
| 21 | 7MPU|1|D | 5'-phosphorylated GG | synthetic construct | Brucella melitensis NrnC bound to pGG | X-ray diffraction | 1.72 | 2 | 2021-09-15 | |||
| 22 | 6IJ2|1|F | RNA (5'-R(P*GP*G)-3') | synthetic construct | Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound form | X-ray diffraction | 1.7 | 2 | 2019-10-09 | |||
| 23 | 6IJ2|1|G | RNA (5'-R(P*GP*G)-3') | synthetic construct | Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound form | X-ray diffraction | 1.7 | 2 | 2019-10-09 | |||
| 24 | 6IJ2|1|H | RNA (5'-R(P*GP*G)-3') | synthetic construct | Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound form | X-ray diffraction | 1.7 | 2 | 2019-10-09 | |||
| 25 | 6IJ2|1|E | RNA (5'-R(P*GP*G)-3') | synthetic construct | Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound form | X-ray diffraction | 1.7 | 2 | 2019-10-09 | |||
| 26 | 3U2E|1|D | RNA (5'-R(P*GP*G)-3') | EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ | X-ray diffraction | 2.32 | 2 | 2011-10-12 | ||||
| 27 | 3U2E|1|C | RNA (5'-R(P*GP*G)-3') | EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ | X-ray diffraction | 2.32 | 2 | 2011-10-12 | ||||
| 28 | 7PVK|1|G | pGpG | synthetic construct | X-ray structure of dimeric PorX (T272A mutant), in complex with pGpG. | X-ray diffraction | 2.4 | 2 | 2022-12-14 | |||
| 29 | 7PVK|1|E | pGpG | synthetic construct | X-ray structure of dimeric PorX (T272A mutant), in complex with pGpG. | X-ray diffraction | 2.4 | 2 | 2022-12-14 | |||
| 30 | 7MPQ|1|R | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC cleaving pGG in the presence of Mn2+ | X-ray diffraction | 2.35 | 2 | 2021-09-15 | |||
| 31 | 7PVK|1|H | pGpG | synthetic construct | X-ray structure of dimeric PorX (T272A mutant), in complex with pGpG. | X-ray diffraction | 2.4 | 2 | 2022-12-14 | |||
| 32 | 7EH1|1|I | RNA (5'-R(*GP*G)-3') | synthetic construct | Thermus thermophilus transcription initiation complex containing a template-strand purine at position TSS-2, GpG RNA primer, and CMPcPP | X-ray diffraction | 2.9 | 2 | 2021-07-14 | |||
| 33 | 7PVK|1|F | pGpG | synthetic construct | X-ray structure of dimeric PorX (T272A mutant), in complex with pGpG. | X-ray diffraction | 2.4 | 2 | 2022-12-14 | |||
| 34 | 5UEF|1|C | RNA (5'-R(P*GP*G)-3') | synthetic construct | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-ray diffraction | 2.1 | 2 | 2017-07-05 | |||
| 35 | 5UEF|1|D | RNA (5'-R(P*GP*G)-3') | synthetic construct | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-ray diffraction | 2.1 | 2 | 2017-07-05 | |||
| 36 | 4X4T|1|I | RNA (5'-D(P*GP*G)-3') | Homo sapiens | Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in CCACCA | X-ray diffraction | 2.5 | 2 | 2015-02-11 | |||
| 37 | 3UCZ|1|D | RNA (5'-R(*GP*G)-3') | The c-di-GMP-I riboswitch bound to GpG | X-ray diffraction | 2.8 | 2 | 2012-01-04 | ||||
| 38 | 4X4U|1|H | RNA (5'-D(*GP*G)-3') | Homo sapiens | Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a human MenBeta minihelix ending in CCACC | X-ray diffraction | 2.7 | 2 | 2015-02-11 | |||
| 39 | 4AFY|1|D | 5'-R(*GP*GP)-3' | synthetic construct | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-ray diffraction | 2.01 | 2 | 2013-01-09 | |||
| 40 | 6OWL|1|B | RNA (5'-R(P*G)-3') | synthetic construct | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-ray diffraction | 2 | 1 | 2020-02-26 | |||
| 41 | 4AFY|1|C | 5'-R(*GP*GP)-3' | synthetic construct | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-ray diffraction | 2.01 | 2 | 2013-01-09 | |||
| 42 | 6OWL|1|C | RNA (5'-R(P*G)-3') | synthetic construct | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-ray diffraction | 2 | 1 | 2020-02-26 | |||
| 43 | 6S0M|1|C | RNA (5'-R(P*G)-3') | Escherichia coli | Structural and dynamic studies provide insights into specificity and allosteric regulation of Ribonuclease AS, a key enzyme in mycobacterial virulence | X-ray diffraction | 2 | 1 | 2019-08-28 | |||
| 44 | 4LQ3|1|R | 5'-R(P*GP*G)-3' | Crystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDS | X-ray diffraction | 2.6 | 2 | 2014-02-12 | ||||
| 45 | 3UCU|1|A | diguanosine monophosphate | The c-di-GMP-I riboswitch bound to pGpG | X-ray diffraction | 2.8 | 2 | 2012-01-04 |
Release history
| Release | 4.0 |
|---|---|
| Date | 2025-08-13 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
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Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
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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.
| #S | View | PDB | Title | Method | Resolution | #NTs |
|---|---|---|---|---|---|---|
| 1 | 7MPQ|1|R | Bartonella henselae NrnC cleaving pGG in the presence of Mn2+ | X-RAY DIFFRACTION | 2.35 | 2 | |
| 2 | 5UEF|1|D | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-RAY DIFFRACTION | 2.1 | 2 | |
| 3 | 7PVK|1|H | X-ray structure of dimeric PorX (T272A mutant), in complex with pGpG. | X-RAY DIFFRACTION | 2.4 | 2 | |
| 4 | 6OWL|1|C | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-RAY DIFFRACTION | 2 | 1 | |
| 5 | 3UCZ|1|D | The c-di-GMP-I riboswitch bound to GpG | X-RAY DIFFRACTION | 2.8 | 2 | |
| 6 | 7PVK|1|F | X-ray structure of dimeric PorX (T272A mutant), in complex with pGpG. | X-RAY DIFFRACTION | 2.4 | 2 | |
| 7 | 6OWL|1|B | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-RAY DIFFRACTION | 2 | 1 | |
| 8 | 7EH1|1|I | Thermus thermophilus transcription initiation complex containing a template-strand purine at position TSS-2, GpG RNA primer, and CMPcPP | X-RAY DIFFRACTION | 2.9 | 2 | |
| 9 | 5UEF|1|C | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-RAY DIFFRACTION | 2.1 | 2 | |
| 10 | 6IJ2|1|F | Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound form | X-RAY DIFFRACTION | 1.7 | 2 | |
| 11 | 7PVK|1|E | X-ray structure of dimeric PorX (T272A mutant), in complex with pGpG. | X-RAY DIFFRACTION | 2.4 | 2 | |
| 12 | 6IJ2|1|G | Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound form | X-RAY DIFFRACTION | 1.7 | 2 | |
| 13 | 7MPU|1|D | Brucella melitensis NrnC bound to pGG | X-RAY DIFFRACTION | 1.72 | 2 | |
| 14 | 7VA3|1|C | PaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structure | X-RAY DIFFRACTION | 1.8 | 2 | |
| 15 | 9F7M|1|P | Blastococcus Orn bound to pGG | X-RAY DIFFRACTION | 1.65 | 2 | |
| 16 | 6IJ2|1|H | Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound form | X-RAY DIFFRACTION | 1.7 | 2 | |
| 17 | 6IJ2|1|E | Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound form | X-RAY DIFFRACTION | 1.7 | 2 | |
| 18 | 7PVK|1|G | X-ray structure of dimeric PorX (T272A mutant), in complex with pGpG. | X-RAY DIFFRACTION | 2.4 | 2 | |
| 19 | 6S0M|1|C | Structural and dynamic studies provide insights into specificity and allosteric regulation of Ribonuclease AS, a key enzyme in mycobacterial virulence | X-RAY DIFFRACTION | 2 | 1 | |
| 20 | 4LQ3|1|R | Crystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDS | X-RAY DIFFRACTION | 2.6 | 2 | |
| 21 | 4X4T|1|I | Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in CCACCA | X-RAY DIFFRACTION | 2.5 | 2 | |
| 22 | 4X4U|1|H | Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a human MenBeta minihelix ending in CCACC | X-RAY DIFFRACTION | 2.7 | 2 | |
| 23 | 3UCU|1|A | The c-di-GMP-I riboswitch bound to pGpG | X-RAY DIFFRACTION | 2.8 | 2 | |
| 24 | 3U2E|1|D | EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ | X-RAY DIFFRACTION | 2.32 | 2 | |
| 25 | 4AFY|1|D | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-RAY DIFFRACTION | 2.01 | 2 | |
| 26 | 4AFY|1|C | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-RAY DIFFRACTION | 2.01 | 2 | |
| 27 | 3U2E|1|C | EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ | X-RAY DIFFRACTION | 2.32 | 2 | |
| 28 | 6N6A|1|D | Vibrio cholerae Oligoribonuclease bound to pGG | X-RAY DIFFRACTION | 1.5 | 2 | |
| 29 | 7MPL|1|B | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 30 | 7MPL|1|F | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 31 | 7MPL|1|J | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 32 | 6N6I|1|D | Human REXO2 bound to pGG | X-RAY DIFFRACTION | 1.43 | 2 | |
| 33 | 6N6I|1|C | Human REXO2 bound to pGG | X-RAY DIFFRACTION | 1.43 | 2 | |
| 34 | 7MPL|1|H | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 35 | 7MPL|1|N | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 36 | 7MPL|1|D | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 37 | 9F7M|1|L | Blastococcus Orn bound to pGG | X-RAY DIFFRACTION | 1.65 | 2 | |
| 38 | 7MPL|1|P | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 39 | 9F7M|1|O | Blastococcus Orn bound to pGG | X-RAY DIFFRACTION | 1.65 | 2 | |
| 40 | 9F7M|1|I | Blastococcus Orn bound to pGG | X-RAY DIFFRACTION | 1.65 | 2 | |
| 41 | 7MPL|1|L | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 42 | 9F7M|1|J | Blastococcus Orn bound to pGG | X-RAY DIFFRACTION | 1.65 | 2 | |
| 43 | 9F7M|1|M | Blastococcus Orn bound to pGG | X-RAY DIFFRACTION | 1.65 | 2 | |
| 44 | 9F7M|1|N | Blastococcus Orn bound to pGG | X-RAY DIFFRACTION | 1.65 | 2 | |
| 45 | 9F7M|1|K | Blastococcus Orn bound to pGG | X-RAY DIFFRACTION | 1.65 | 2 |
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.
Coloring options: