Equivalence class NR_3.0_98428.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 6N6I|1|C (rep) | RNA (5'-R(P*GP*G)-3') | synthetic construct | Synthetic | 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 | Synthetic | 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 | Bacteria | Vibrio cholerae Oligoribonuclease bound to pGG | X-ray diffraction | 1.5 | 2019-06-12 | ||
| 4 | 7MPL|1|D | 5'-phosphorylated GG | synthetic construct | Synthetic | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | ||
| 5 | 7MPL|1|H | 5'-phosphorylated GG | synthetic construct | Synthetic | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | ||
| 6 | 7MPL|1|B | 5'-phosphorylated GG | synthetic construct | Synthetic | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | ||
| 7 | 7MPL|1|J | 5'-phosphorylated GG | synthetic construct | Synthetic | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | ||
| 8 | 7MPL|1|F | 5'-phosphorylated GG | synthetic construct | Synthetic | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | ||
| 9 | 7MPL|1|N | 5'-phosphorylated GG | synthetic construct | Synthetic | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | ||
| 10 | 7MPL|1|L | 5'-phosphorylated GG | synthetic construct | Synthetic | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | ||
| 11 | 7MPL|1|P | 5'-phosphorylated GG | synthetic construct | Synthetic | Bartonella henselae NrnC bound to pGG | X-ray diffraction | 1.8 | 2021-09-15 | ||
| 12 | 6IJ2|1|F | RNA (5'-R(P*GP*G)-3') | synthetic construct | Synthetic | Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound form | X-ray diffraction | 1.7 | 2019-10-09 | ||
| 13 | 6IJ2|1|G | RNA (5'-R(P*GP*G)-3') | synthetic construct | Synthetic | 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|H | RNA (5'-R(P*GP*G)-3') | synthetic construct | Synthetic | 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|E | RNA (5'-R(P*GP*G)-3') | synthetic construct | Synthetic | 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 | 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 | ||||
| 17 | 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 | ||||
| 18 | 7EH1|1|I | RNA (5'-R(*GP*G)-3') | synthetic construct | Synthetic | Thermus thermophilus transcription initiation complex containing a template-strand purine at position TSS-2, GpG RNA primer, and CMPcPP | X-ray diffraction | 2.9 | 2021-07-14 | ||
| 19 | 7MPQ|1|R | 5'-phosphorylated GG | synthetic construct | Synthetic | 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 | Synthetic | 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 | Synthetic | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-ray diffraction | 2.1 | 2017-07-05 | ||
| 22 | 4X4U|1|H | RNA (5'-D(*GP*G)-3') | Homo sapiens | Eukarya | Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a human MenBeta minihelix ending in CCACC | X-ray diffraction | 2.7 | 2015-02-11 | ||
| 23 | 4AFY|1|D | 5'-R(*GP*GP)-3' | synthetic construct | Synthetic | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-ray diffraction | 2.01 | 2013-01-09 | ||
| 24 | 6OWL|1|B | RNA (5'-R(P*G)-3') | synthetic construct | Synthetic | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-ray diffraction | 2 | 2020-02-26 | ||
| 25 | 6OWL|1|C | RNA (5'-R(P*G)-3') | synthetic construct | Synthetic | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-ray diffraction | 2 | 2020-02-26 | ||
| 26 | 4AFY|1|C | 5'-R(*GP*GP)-3' | synthetic construct | Synthetic | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-ray diffraction | 2.01 | 2013-01-09 | ||
| 27 | 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 | 2014-02-12 | ||||
| 28 | 6S0M|1|C | RNA (5'-R(P*G)-3') | Escherichia coli | Bacteria | 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 | ||
| 29 | 7MPU|1|D | 5'-phosphorylated GG | synthetic construct | Synthetic | Brucella melitensis NrnC bound to pGG | X-ray diffraction | 1.72 | 2021-09-15 |
Release history
| Release | 3.196 | 3.197 | 3.198 | 3.199 | 3.200 | 3.201 | 3.202 | 3.203 | 3.204 | 3.205 | 3.206 | 3.207 | 3.208 | 3.209 | 3.210 | 3.211 | 3.212 | 3.213 | 3.214 | 3.215 | 3.216 | 3.217 | 3.218 | 3.219 | 3.220 | 3.221 | 3.222 | 3.223 | 3.224 | 3.225 | 3.226 | 3.227 | 3.228 | 3.229 | 3.230 | 3.231 | 3.232 | 3.233 | 3.234 | 3.235 | 3.236 | 3.237 | 3.238 | 3.239 | 3.240 | 3.241 | 3.242 | 3.243 | 3.244 | 3.245 | 3.246 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2021-09-15 | 2021-09-22 | 2021-09-29 | 2021-10-06 | 2021-10-13 | 2021-10-20 | 2021-10-27 | 2021-11-03 | 2021-11-10 | 2021-11-17 | 2021-11-24 | 2021-12-01 | 2021-12-08 | 2021-12-15 | 2021-12-22 | 2021-12-29 | 2022-01-05 | 2022-01-12 | 2022-01-19 | 2022-01-26 | 2022-02-02 | 2022-02-09 | 2022-02-16 | 2022-02-23 | 2022-03-02 | 2022-03-09 | 2022-03-16 | 2022-03-23 | 2022-03-30 | 2022-04-06 | 2022-04-13 | 2022-04-20 | 2022-04-27 | 2022-05-04 | 2022-05-11 | 2022-05-18 | 2022-05-25 | 2022-06-01 | 2022-06-08 | 2022-06-15 | 2022-06-22 | 2022-06-29 | 2022-07-06 | 2022-07-13 | 2022-07-20 | 2022-07-27 | 2022-08-03 | 2022-08-10 | 2022-08-17 | 2022-08-24 | 2022-08-31 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.0_98428.1 | NR_3.0_89612.10 | 3.196 | (19) 6OWL|1|B, 6IJ2|1|E, 7EH1|1|I, 4AFY|1|C, 6IJ2|1|H, 4X4U|1|H, 6N6I|1|D, 3U2E|1|D, 6S0M|1|C, 4LQ3|1|R, 5UEF|1|D, 6IJ2|1|G, 6N6I|1|C, 3U2E|1|C, 6OWL|1|C, 4AFY|1|D, 5UEF|1|C, 6IJ2|1|F, 6N6A|1|D | (10) 7MPL|1|B, 7MPL|1|N, 7MPL|1|J, 7MPL|1|F, 7MPQ|1|R, 7MPU|1|D, 7MPL|1|L, 7MPL|1|H, 7MPL|1|D, 7MPL|1|P | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.0_98428.1 | NR_3.0_98428.2 | 3.247 | (29) 7MPL|1|N, 6IJ2|1|F, 7MPL|1|L, 6IJ2|1|E, 7MPL|1|J, 5UEF|1|D, 7MPL|1|H, 5UEF|1|C, 7MPL|1|F, 4X4U|1|H, 7MPL|1|D, 4LQ3|1|R, 7MPL|1|B, 4AFY|1|D, 4AFY|1|C, 7EH1|1|I, 3U2E|1|D, 6S0M|1|C, 3U2E|1|C, 6OWL|1|C, 6OWL|1|B, 6N6I|1|D, 6N6I|1|C, 7MPU|1|D, 6N6A|1|D, 7MPQ|1|R, 6IJ2|1|H, 7MPL|1|P, 6IJ2|1|G | (0) | (1) 7VA3|1|C |
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|C | 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 | 6N6I|1|D | Human REXO2 bound to pGG | X-RAY DIFFRACTION | 1.43 | 2 |
| 4 | 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 |
| 5 | 5UEF|1|C | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-RAY DIFFRACTION | 2.1 | 2 |
| 6 | 7MPL|1|D | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 7 | 4LQ3|1|R | Crystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDS | X-RAY DIFFRACTION | 2.6 | 2 |
| 8 | 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 |
| 9 | 4AFY|1|D | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-RAY DIFFRACTION | 2.01 | 2 |
| 10 | 4AFY|1|C | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-RAY DIFFRACTION | 2.01 | 2 |
| 11 | 3U2E|1|D | EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ | X-RAY DIFFRACTION | 2.32 | 2 |
| 12 | 3U2E|1|C | EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ | X-RAY DIFFRACTION | 2.32 | 2 |
| 13 | 6OWL|1|C | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-RAY DIFFRACTION | 2 | 1 |
| 14 | 7MPL|1|L | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 15 | 5UEF|1|D | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-RAY DIFFRACTION | 2.1 | 2 |
| 16 | 7MPQ|1|R | Bartonella henselae NrnC cleaving pGG in the presence of Mn2+ | X-RAY DIFFRACTION | 2.35 | 2 |
| 17 | 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 |
| 18 | 6OWL|1|B | 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 | 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 |
| 21 | 7MPL|1|P | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 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 | 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 |
| 24 | 7MPL|1|F | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 25 | 7MPL|1|N | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 26 | 7MPL|1|B | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 27 | 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 |
| 28 | 7MPL|1|H | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 29 | 7MPL|1|J | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |