Equivalence class NR_3.5_98428.1 Obsolete
| # | 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 | 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 | |||
| 13 | 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 | |||
| 14 | 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 | |||
| 15 | 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 | |||
| 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 | 2 | 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 | 2 | 2011-10-12 | ||||
| 18 | 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 | |||
| 19 | 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 | |||
| 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 | 2 | 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 | 2 | 2017-07-05 | |||
| 22 | 7EH2|1|R | RNA (5'-R(*GP*G)-3') | synthetic construct | Thermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primer | X-ray diffraction | 3.34 | 2 | 2021-07-14 | |||
| 23 | 7EH2|1|I | RNA (5'-R(*GP*G)-3') | synthetic construct | Thermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primer | X-ray diffraction | 3.34 | 2 | 2021-07-14 | |||
| 24 | 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 | |||
| 25 | 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 | |||
| 26 | 6OY5|1|I | RNA (5'-D(*(GTP))-R(P*G)-3') | Thermus thermophilus | X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter at 3 min | X-ray diffraction | 3.1 | 2 | 2019-06-05 | |||
| 27 | 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 | |||
| 28 | 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 | |||
| 29 | 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 | |||
| 30 | 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 | ||||
| 31 | 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 | |||
| 32 | 7MPU|1|D | 5'-phosphorylated GG | synthetic construct | Brucella melitensis NrnC bound to pGG | X-ray diffraction | 1.72 | 2 | 2021-09-15 | |||
| 33 | 7MQB|1|B | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2 | 2021-09-15 | |||
| 34 | 7MQB|1|D | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2 | 2021-09-15 | |||
| 35 | 7MQB|1|F | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2 | 2021-09-15 | |||
| 36 | 7MQB|1|H | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2 | 2021-09-15 | |||
| 37 | 7MQB|1|J | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2 | 2021-09-15 | |||
| 38 | 7MQB|1|L | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2 | 2021-09-15 | |||
| 39 | 7MQB|1|N | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2 | 2021-09-15 | |||
| 40 | 7MQB|1|P | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2 | 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_3.5_98428.1 | NR_3.5_89612.10 | 3.196 | (22) 3U2E|1|C, 3U2E|1|D, 4AFY|1|C, 4AFY|1|D, 4LQ3|1|R, 4X4U|1|H, 5UEF|1|C, 5UEF|1|D, 6IJ2|1|E, 6IJ2|1|F, 6IJ2|1|G, 6IJ2|1|H, 6N6A|1|D, 6N6I|1|C, 6N6I|1|D, 6OWL|1|B, 6OWL|1|C, 6OY5|1|I, 6S0M|1|C, 7EH1|1|I, 7EH2|1|I, 7EH2|1|R | (18) 7MPL|1|B, 7MPL|1|D, 7MPL|1|F, 7MPL|1|H, 7MPL|1|J, 7MPL|1|L, 7MPL|1|N, 7MPL|1|P, 7MPQ|1|R, 7MPU|1|D, 7MQB|1|B, 7MQB|1|D, 7MQB|1|F, 7MQB|1|H, 7MQB|1|J, 7MQB|1|L, 7MQB|1|N, 7MQB|1|P | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.5_98428.1 | NR_3.5_98428.2 | 3.247 | (40) 3U2E|1|C, 3U2E|1|D, 4AFY|1|C, 4AFY|1|D, 4LQ3|1|R, 4X4U|1|H, 5UEF|1|C, 5UEF|1|D, 6IJ2|1|E, 6IJ2|1|F, 6IJ2|1|G, 6IJ2|1|H, 6N6A|1|D, 6N6I|1|C, 6N6I|1|D, 6OWL|1|B, 6OWL|1|C, 6OY5|1|I, 6S0M|1|C, 7EH1|1|I, 7EH2|1|I, 7EH2|1|R, 7MPL|1|B, 7MPL|1|D, 7MPL|1|F, 7MPL|1|H, 7MPL|1|J, 7MPL|1|L, 7MPL|1|N, 7MPL|1|P, 7MPQ|1|R, 7MPU|1|D, 7MQB|1|B, 7MQB|1|D, 7MQB|1|F, 7MQB|1|H, 7MQB|1|J, 7MQB|1|L, 7MQB|1|N, 7MQB|1|P | (0) | (1) 7VA3|1|C |
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 | 3U2E|1|D | EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ | X-RAY DIFFRACTION | 2.32 | 2 | |
| 2 | 3U2E|1|C | EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ | X-RAY DIFFRACTION | 2.32 | 2 | |
| 3 | 4AFY|1|C | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-RAY DIFFRACTION | 2.01 | 2 | |
| 4 | 4AFY|1|D | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-RAY DIFFRACTION | 2.01 | 2 | |
| 5 | 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 | |
| 6 | 4LQ3|1|R | Crystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDS | X-RAY DIFFRACTION | 2.6 | 2 | |
| 7 | 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 | |
| 8 | 7MPL|1|F | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 9 | 7MPL|1|N | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 10 | 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 | |
| 11 | 5UEF|1|D | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-RAY DIFFRACTION | 2.1 | 2 | |
| 12 | 6OWL|1|B | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-RAY DIFFRACTION | 2 | 1 | |
| 13 | 7MQB|1|B | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 | |
| 14 | 7EH2|1|R | Thermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primer | X-RAY DIFFRACTION | 3.34 | 2 | |
| 15 | 6OWL|1|C | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-RAY DIFFRACTION | 2 | 1 | |
| 16 | 7EH2|1|I | Thermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primer | X-RAY DIFFRACTION | 3.34 | 2 | |
| 17 | 7MQB|1|N | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 | |
| 18 | 7MPL|1|L | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 19 | 7MPL|1|P | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 20 | 7MPU|1|D | Brucella melitensis NrnC bound to pGG | X-RAY DIFFRACTION | 1.72 | 2 | |
| 21 | 7MPL|1|J | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 22 | 7MPL|1|H | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 23 | 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 | |
| 24 | 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 | |
| 25 | 7MPQ|1|R | Bartonella henselae NrnC cleaving pGG in the presence of Mn2+ | X-RAY DIFFRACTION | 2.35 | 2 | |
| 26 | 7MQB|1|H | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 | |
| 27 | 5UEF|1|C | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-RAY DIFFRACTION | 2.1 | 2 | |
| 28 | 7MQB|1|F | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 | |
| 29 | 7MQB|1|D | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 | |
| 30 | 7MPL|1|B | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 31 | 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 | |
| 32 | 6OY5|1|I | X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter at 3 min | X-RAY DIFFRACTION | 3.1 | 2 | |
| 33 | 7MQB|1|J | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 | |
| 34 | 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 | |
| 35 | 7MQB|1|L | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 | |
| 36 | 7MQB|1|P | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 | |
| 37 | 6N6A|1|D | Vibrio cholerae Oligoribonuclease bound to pGG | X-RAY DIFFRACTION | 1.5 | 2 | |
| 38 | 7MPL|1|D | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 | |
| 39 | 6N6I|1|C | Human REXO2 bound to pGG | X-RAY DIFFRACTION | 1.43 | 2 | |
| 40 | 6N6I|1|D | Human REXO2 bound to pGG | X-RAY DIFFRACTION | 1.43 | 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: