Equivalence class NR_2.5_98428.2 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | 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 | 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 | 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 | 2019-06-12 | |||
| 4 | 7MPL|1|D | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | |||
| 5 | 7MPL|1|H | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | |||
| 6 | 7MPL|1|B | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | |||
| 7 | 7MPL|1|J | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | |||
| 8 | 7MPL|1|F | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | |||
| 9 | 7MPL|1|N | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | |||
| 10 | 7MPL|1|L | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | |||
| 11 | 7MPL|1|P | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | |||
| 12 | 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 | 2022-09-07 | |||
| 13 | 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 | 2019-10-09 | |||
| 14 | 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 | 2019-10-09 | |||
| 15 | 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 | 2019-10-09 | |||
| 16 | 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 | 2019-10-09 | |||
| 17 | 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 | 2011-10-12 | ||||
| 18 | 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 | 2011-10-12 | ||||
| 19 | 7MPQ|1|R | 5'-phosphorylated GG | synthetic construct | Bartonella henselae NrnC cleaving pGG in the presence of Mn2+ | X-ray diffraction | 2.35 | 2021-09-15 | |||
| 20 | 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 | 2017-07-05 | |||
| 21 | 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 | 2017-07-05 | |||
| 22 | 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 | 2013-01-09 | |||
| 23 | 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 | 2020-02-26 | |||
| 24 | 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 | 2020-02-26 | |||
| 25 | 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 | 2013-01-09 | |||
| 26 | 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 | 2019-08-28 | |||
| 27 | 7MPU|1|D | 5'-phosphorylated GG | synthetic construct | Brucella melitensis NrnC bound to pGG | X-ray diffraction | 1.72 | 2021-09-15 |
Release history
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_2.5_98428.2 | NR_2.5_98428.1 | 3.247 | (26) 7MPL|1|F, 7MPL|1|D, 7MPL|1|B, 6S0M|1|C, 6OWL|1|C, 6OWL|1|B, 6N6I|1|D, 6N6I|1|C, 6N6A|1|D, 6IJ2|1|H, 6IJ2|1|G, 6IJ2|1|F, 6IJ2|1|E, 5UEF|1|D, 5UEF|1|C, 4AFY|1|D, 4AFY|1|C, 3U2E|1|D, 3U2E|1|C, 7MPU|1|D, 7MPQ|1|R, 7MPL|1|P, 7MPL|1|N, 7MPL|1|L, 7MPL|1|J, 7MPL|1|H | (1) 7VA3|1|C | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_2.5_98428.2 | NR_2.5_98428.3 | 3.264 | (27) 5UEF|1|C, 6IJ2|1|G, 6N6I|1|D, 7MPL|1|B, 7MPL|1|J, 3U2E|1|C, 7MPQ|1|R, 6IJ2|1|F, 6N6I|1|C, 6S0M|1|C, 7MPL|1|H, 7MPL|1|P, 4AFY|1|D, 7VA3|1|C, 6IJ2|1|E, 6N6A|1|D, 6OWL|1|C, 7MPL|1|F, 7MPL|1|N, 4AFY|1|C, 5UEF|1|D, 6IJ2|1|H, 6OWL|1|B, 7MPL|1|D, 7MPL|1|L, 3U2E|1|D, 7MPU|1|D | (0) | (4) 7PVK|1|F, 7PVK|1|E, 7PVK|1|H, 7PVK|1|G |
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5
#S - ordering by similarity (same as in the heat map).| #S | PDB | Title | Method | Resolution | Length |
|---|---|---|---|---|---|
| 1 | 6N6I|1|D | Human REXO2 bound to pGG | X-RAY DIFFRACTION | 1.43 | 2 |
| 2 | 6N6A|1|D | Vibrio cholerae Oligoribonuclease bound to pGG | X-RAY DIFFRACTION | 1.5 | 2 |
| 3 | 7MPL|1|D | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 4 | 7MPL|1|F | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 5 | 7MPL|1|H | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 6 | 6N6I|1|C | Human REXO2 bound to pGG | X-RAY DIFFRACTION | 1.43 | 2 |
| 7 | 7MPL|1|B | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 8 | 7MPL|1|J | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 9 | 7MPL|1|P | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 10 | 7MPQ|1|R | Bartonella henselae NrnC cleaving pGG in the presence of Mn2+ | X-RAY DIFFRACTION | 2.35 | 2 |
| 11 | 5UEF|1|C | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-RAY DIFFRACTION | 2.1 | 2 |
| 12 | 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 |
| 13 | 3U2E|1|C | EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ | X-RAY DIFFRACTION | 2.32 | 2 |
| 14 | 4AFY|1|C | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-RAY DIFFRACTION | 2.01 | 2 |
| 15 | 4AFY|1|D | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-RAY DIFFRACTION | 2.01 | 2 |
| 16 | 3U2E|1|D | EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ | X-RAY DIFFRACTION | 2.32 | 2 |
| 17 | 5UEF|1|D | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-RAY DIFFRACTION | 2.1 | 2 |
| 18 | 6OWL|1|C | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-RAY DIFFRACTION | 2 | 1 |
| 19 | 7MPU|1|D | Brucella melitensis NrnC bound to pGG | X-RAY DIFFRACTION | 1.72 | 2 |
| 20 | 7VA3|1|C | PaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structure | X-RAY DIFFRACTION | 1.8 | 2 |
| 21 | 6OWL|1|B | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-RAY DIFFRACTION | 2 | 1 |
| 22 | 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 |
| 23 | 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 |
| 24 | 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 |
| 25 | 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 |
| 26 | 7MPL|1|L | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 27 | 7MPL|1|N | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |