Equivalence class NR_all_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 | 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 | 2021-07-14 | |||
| 20 | 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 | |||
| 21 | 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 | |||
| 22 | 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 | |||
| 23 | 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 | 2021-07-14 | |||
| 24 | 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 | 2021-07-14 | |||
| 25 | 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 | 2015-02-11 | |||
| 26 | 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 | |||
| 27 | 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 | 2019-06-05 | |||
| 28 | 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 | |||
| 29 | 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 | |||
| 30 | 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 | |||
| 31 | 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 | ||||
| 32 | 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 | |||
| 33 | 7MPU|1|D | 5'-phosphorylated GG | synthetic construct | Brucella melitensis NrnC bound to pGG | X-ray diffraction | 1.72 | 2021-09-15 | |||
| 34 | 7MQB|1|B | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2021-09-15 | |||
| 35 | 7MQB|1|D | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2021-09-15 | |||
| 36 | 7MQB|1|F | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2021-09-15 | |||
| 37 | 7MQB|1|H | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2021-09-15 | |||
| 38 | 7MQB|1|J | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2021-09-15 | |||
| 39 | 7MQB|1|L | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2021-09-15 | |||
| 40 | 7MQB|1|N | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2021-09-15 | |||
| 41 | 7MQB|1|P | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. D4 Symmetry | Electron microscopy | 3.25 | 2021-09-15 | |||
| 42 | 7MQC|1|B | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | Electron microscopy | 3.64 | 2021-09-15 | |||
| 43 | 7MQC|1|D | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | Electron microscopy | 3.64 | 2021-09-15 | |||
| 44 | 7MQC|1|F | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | Electron microscopy | 3.64 | 2021-09-15 | |||
| 45 | 7MQC|1|H | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | Electron microscopy | 3.64 | 2021-09-15 | |||
| 46 | 7MQC|1|J | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | Electron microscopy | 3.64 | 2021-09-15 | |||
| 47 | 7MQC|1|L | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | Electron microscopy | 3.64 | 2021-09-15 | |||
| 48 | 7MQC|1|N | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | Electron microscopy | 3.64 | 2021-09-15 | |||
| 49 | 7MQC|1|P | RNA (5'-R(P*GP*G)-3') | synthetic construct | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | Electron microscopy | 3.64 | 2021-09-15 | |||
| 50 | 6YMW|1|C | RNA (pppGpG) | synthetic construct | Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex | Electron microscopy | 3.71 | 2020-12-09 |
Release history
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_all_98428.2 | NR_all_98428.1 | 3.247 | (49) 6N6I|1|D, 7MQC|1|L, 6N6I|1|C, 7MQC|1|J, 6N6A|1|D, 7MQC|1|H, 6IJ2|1|H, 7MQC|1|F, 6IJ2|1|G, 7MQC|1|D, 6IJ2|1|F, 7MQC|1|B, 6IJ2|1|E, 7MQB|1|P, 5UEF|1|D, 7MQB|1|N, 5UEF|1|C, 7MQB|1|L, 4X4U|1|H, 7MQB|1|J, 4LQ3|1|R, 7MQB|1|H, 4AFY|1|D, 7MQB|1|F, 4AFY|1|C, 7MQB|1|D, 3U2E|1|D, 7MQB|1|B, 3U2E|1|C, 7MPU|1|D, 7MPQ|1|R, 7MPL|1|P, 7MPL|1|N, 7MPL|1|L, 7MPL|1|J, 7MPL|1|H, 7MPL|1|F, 7MPL|1|D, 7MPL|1|B, 7EH2|1|R, 7EH2|1|I, 7EH1|1|I, 6YMW|1|C, 6S0M|1|C, 6OY5|1|I, 6OWL|1|C, 7MQC|1|P, 6OWL|1|B, 7MQC|1|N | (1) 7VA3|1|C | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_all_98428.2 | NR_all_98428.3 | 3.264 | (50) 7MQC|1|L, 7MPL|1|F, 4X4U|1|H, 7MPL|1|N, 6IJ2|1|F, 7MQB|1|B, 6N6I|1|C, 7MQB|1|J, 6OY5|1|I, 7MQC|1|B, 7EH2|1|I, 3U2E|1|D, 7MQC|1|J, 7VA3|1|C, 7MPL|1|D, 4LQ3|1|R, 7MPL|1|L, 6IJ2|1|E, 7MPU|1|D, 6N6A|1|D, 7MQB|1|H, 6OWL|1|C, 7MQB|1|P, 7EH1|1|I, 3U2E|1|C, 7MQC|1|P, 7MQC|1|H, 4AFY|1|D, 7MPL|1|J, 5UEF|1|D, 7MPQ|1|R, 6IJ2|1|H, 7MQB|1|F, 6OWL|1|B, 7MQB|1|N, 6YMW|1|C, 7MPL|1|B, 7MQC|1|N, 7MQC|1|F, 4AFY|1|C, 7MPL|1|H, 5UEF|1|C, 7MPL|1|P, 6IJ2|1|G, 7MQB|1|D, 6N6I|1|D, 7MQB|1|L, 6S0M|1|C, 7EH2|1|R, 7MQC|1|D | (0) | (4) 7PVK|1|E, 7PVK|1|H, 7PVK|1|G, 7PVK|1|F |
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 | 7MPL|1|L | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 2 | 7MQB|1|N | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 |
| 3 | 7MPU|1|D | Brucella melitensis NrnC bound to pGG | X-RAY DIFFRACTION | 1.72 | 2 |
| 4 | 7MQC|1|B | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | ELECTRON MICROSCOPY | 3.64 | 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 | 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 |
| 7 | 6OY5|1|I | X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter at 3 min | X-RAY DIFFRACTION | 3.1 | 1 |
| 8 | 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 |
| 9 | 6YMW|1|C | Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex | ELECTRON MICROSCOPY | 3.71 | 1 |
| 10 | 7MQC|1|L | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | ELECTRON MICROSCOPY | 3.64 | 2 |
| 11 | 7MQC|1|N | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | ELECTRON MICROSCOPY | 3.64 | 2 |
| 12 | 7MQB|1|J | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 |
| 13 | 7MQB|1|P | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 |
| 14 | 6N6I|1|C | Human REXO2 bound to pGG | X-RAY DIFFRACTION | 1.43 | 2 |
| 15 | 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 |
| 16 | 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 |
| 17 | 7MQB|1|B | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 |
| 18 | 6N6A|1|D | Vibrio cholerae Oligoribonuclease bound to pGG | X-RAY DIFFRACTION | 1.5 | 2 |
| 19 | 6N6I|1|D | Human REXO2 bound to pGG | X-RAY DIFFRACTION | 1.43 | 2 |
| 20 | 7MPL|1|N | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 21 | 7MPL|1|H | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 22 | 7MPL|1|P | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 23 | 7MPL|1|F | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 24 | 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 |
| 25 | 7MPL|1|J | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 26 | 7VA3|1|C | PaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structure | X-RAY DIFFRACTION | 1.8 | 2 |
| 27 | 7MPL|1|B | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 28 | 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 |
| 29 | 4LQ3|1|R | Crystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDS | X-RAY DIFFRACTION | 2.6 | 2 |
| 30 | 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 |
| 31 | 4AFY|1|D | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-RAY DIFFRACTION | 2.01 | 2 |
| 32 | 4AFY|1|C | Crystal structure of the FimX EAL domain in complex with reaction product pGpG | X-RAY DIFFRACTION | 2.01 | 2 |
| 33 | 3U2E|1|D | EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ | X-RAY DIFFRACTION | 2.32 | 2 |
| 34 | 3U2E|1|C | EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ | X-RAY DIFFRACTION | 2.32 | 2 |
| 35 | 6OWL|1|C | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-RAY DIFFRACTION | 2 | 1 |
| 36 | 7MQB|1|F | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 |
| 37 | 7MPQ|1|R | Bartonella henselae NrnC cleaving pGG in the presence of Mn2+ | X-RAY DIFFRACTION | 2.35 | 2 |
| 38 | 7MPL|1|D | Bartonella henselae NrnC bound to pGG | X-RAY DIFFRACTION | 1.8 | 2 |
| 39 | 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 |
| 40 | 5UEF|1|D | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-RAY DIFFRACTION | 2.1 | 2 |
| 41 | 6OWL|1|B | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-RAY DIFFRACTION | 2 | 1 |
| 42 | 7MQC|1|D | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | ELECTRON MICROSCOPY | 3.64 | 2 |
| 43 | 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 |
| 44 | 7MQB|1|L | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 |
| 45 | 7MQB|1|D | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 |
| 46 | 7MQC|1|H | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | ELECTRON MICROSCOPY | 3.64 | 2 |
| 47 | 7MQC|1|F | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | ELECTRON MICROSCOPY | 3.64 | 2 |
| 48 | 7MQC|1|J | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | ELECTRON MICROSCOPY | 3.64 | 2 |
| 49 | 7MQB|1|H | Bartonella henselae NrnC bound to pGG. D4 Symmetry | ELECTRON MICROSCOPY | 3.25 | 2 |
| 50 | 7MQC|1|P | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | ELECTRON MICROSCOPY | 3.64 | 2 |