Equivalence class NR_3.5_01949.4 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 5UED|1|A+ 5UED|1|B (rep) | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | RNA primer-template complex with guanosine dinucleotide ligand G(5')pp(5')G | X-ray diffraction | 1.5 | 2017-07-05 | |||
| 2 | 6C8J|1|A+ 6C8J|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | RNA-activated 2-AIpG monomer complex, 15 min soaking | X-ray diffraction | 1.5 | 2018-05-30 | |||
| 3 | 7KUP|1|A+ 7KUP|1|B | 5'-R((LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(OMG))-3' | synthetic construct | 2'-OMe modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | X-ray diffraction | 1.44 | 2021-09-08 | |||
| 4 | 7KUK|1|A+ 7KUK|1|B | RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | High resolution RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | X-ray diffraction | 1.67 | 2021-09-08 | |||
| 5 | 7KUM|1|A+ 7KUM|1|B | 5'-R((LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(LCG)-3' | synthetic construct | LNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | X-ray diffraction | 1.714 | 2021-09-08 | |||
| 6 | 7KUL|1|A+ 7KUL|1|B | DNA/RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*C)-D(P*G)-3') | synthetic construct | DNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | X-ray diffraction | 1.64 | 2021-09-08 | |||
| 7 | 6C8D|1|A+ 6C8D|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | RNA-dGMP complex with Mg ion | X-ray diffraction | 1.92 | 2018-05-30 | |||
| 8 | 6C8I|1|A+ 6C8I|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | RNA-activated 2-AIpG monomer complex, 5 min soaking | X-ray diffraction | 1.77 | 2018-05-30 | |||
| 9 | 5UEE|1|A+ 5UEE|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | RNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')G | X-ray diffraction | 1.9 | 2017-07-05 | |||
| 10 | 6C8L|1|A+ 6C8L|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | RNA-activated 2-AIpG monomer complex, 1h soaking | X-ray diffraction | 2.25 | 2018-05-30 | |||
| 11 | 6C8E|1|A+ 6C8E|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | RNA-imidazolium-bridged intermediate complex, 4h soaking | X-ray diffraction | 1.8 | 2018-05-30 | |||
| 12 | 6U8U|1|A+ 6U8U|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | RNA duplex bound with TNA 3'-3' imidazolium dimer | X-ray diffraction | 2.4 | 2020-12-09 | |||
| 13 | 5UEF|1|A+ 5UEF|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*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 | |||
| 14 | 7KUO|1|A+ 7KUO|1|B | RNA (5'-R((LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(GFL))-3') | synthetic construct | FANA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | X-ray diffraction | 2.281 | 2021-09-08 | |||
| 15 | 6C8K|1|A+ 6C8K|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | RNA-activated 2-AIpG monomer complex, 30 min soaking | X-ray diffraction | 2.26 | 2018-05-30 | |||
| 16 | 6CAB|1|A+ 6CAB|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | RNA-dGMP complex with Sr ion | X-ray diffraction | 2.5 | 2018-05-30 | |||
| 17 | 6OWL|1|A | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*R)-3') | synthetic construct | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-ray diffraction | 2 | 2020-02-26 | |||
| 18 | 5UEG|1|A+ 5UEG|1|B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | RNA primer-template complex with guanosine dinucleotide G(5')pppp(5')G ligand | X-ray diffraction | 2.6 | 2017-07-05 | |||
| 19 | 5UEG|1|C+ 5UEG|1|D | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | synthetic construct | RNA primer-template complex with guanosine dinucleotide G(5')pppp(5')G ligand | X-ray diffraction | 2.6 | 2017-07-05 |
Release history
| Release | 3.195 | 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 | 3.247 | 3.248 | 3.249 | 3.250 | 3.251 | 3.252 | 3.253 | 3.254 | 3.255 | 3.256 | 3.257 | 3.258 | 3.259 | 3.260 | 3.261 | 3.262 | 3.263 | 3.264 | 3.265 | 3.266 | 3.267 | 3.268 | 3.269 | 3.270 | 3.271 | 3.272 | 3.273 | 3.274 | 3.275 | 3.276 | 3.277 | 3.278 | 3.279 | 3.280 | 3.281 | 3.282 | 3.283 | 3.284 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2021-09-08 | 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 | 2022-09-07 | 2022-09-14 | 2022-09-21 | 2022-09-28 | 2022-10-05 | 2022-10-12 | 2022-10-19 | 2022-10-26 | 2022-11-02 | 2022-11-09 | 2022-11-16 | 2022-11-23 | 2022-11-30 | 2022-12-07 | 2022-12-14 | 2022-12-21 | 2022-12-28 | 2023-01-04 | 2023-01-11 | 2023-01-18 | 2023-01-25 | 2023-02-01 | 2023-02-08 | 2023-02-15 | 2023-02-22 | 2023-03-01 | 2023-03-08 | 2023-03-15 | 2023-03-22 | 2023-03-29 | 2023-04-05 | 2023-04-12 | 2023-04-19 | 2023-04-26 | 2023-05-03 | 2023-05-10 | 2023-05-17 | 2023-05-24 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.5_01949.4 | NR_3.5_01949.3 | 3.195 | (14) 5UED|1|A+5UED|1|B, 5UEE|1|A+5UEE|1|B, 5UEF|1|A+5UEF|1|B, 5UEG|1|A+5UEG|1|B, 5UEG|1|C+5UEG|1|D, 6C8D|1|A+6C8D|1|B, 6C8E|1|A+6C8E|1|B, 6C8I|1|A+6C8I|1|B, 6C8J|1|A+6C8J|1|B, 6C8K|1|A+6C8K|1|B, 6C8L|1|A+6C8L|1|B, 6CAB|1|A+6CAB|1|B, 6OWL|1|A, 6U8U|1|A+6U8U|1|B | (5) 7KUK|1|A+7KUK|1|B, 7KUL|1|A+7KUL|1|B, 7KUM|1|A+7KUM|1|B, 7KUO|1|A+7KUO|1|B, 7KUP|1|A+7KUP|1|B | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.5_01949.4 | NR_3.5_01949.5 | 3.285 | (19) 5UED|1|A+5UED|1|B, 5UEE|1|A+5UEE|1|B, 5UEF|1|A+5UEF|1|B, 5UEG|1|A+5UEG|1|B, 5UEG|1|C+5UEG|1|D, 6C8D|1|A+6C8D|1|B, 6C8E|1|A+6C8E|1|B, 6C8I|1|A+6C8I|1|B, 6C8J|1|A+6C8J|1|B, 6C8K|1|A+6C8K|1|B, 6C8L|1|A+6C8L|1|B, 6CAB|1|A+6CAB|1|B, 6OWL|1|A, 6U8U|1|A+6U8U|1|B, 7KUK|1|A+7KUK|1|B, 7KUL|1|A+7KUL|1|B, 7KUM|1|A+7KUM|1|B, 7KUO|1|A+7KUO|1|B, 7KUP|1|A+7KUP|1|B | (0) | (1) 8SWG|1|A+8SWG|1|B |
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.
| #S | PDB | Title | Method | Resolution | Length |
|---|---|---|---|---|---|
| 1 | 7KUO|1|A+7KUO|1|B | FANA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | X-RAY DIFFRACTION | 2.281 | 9 |
| 2 | 6CAB|1|A+6CAB|1|B | RNA-dGMP complex with Sr ion | X-RAY DIFFRACTION | 2.5 | 12 |
| 3 | 6C8L|1|A+6C8L|1|B | RNA-activated 2-AIpG monomer complex, 1h soaking | X-RAY DIFFRACTION | 2.25 | 10 |
| 4 | 6C8K|1|A+6C8K|1|B | RNA-activated 2-AIpG monomer complex, 30 min soaking | X-RAY DIFFRACTION | 2.26 | 10 |
| 5 | 7KUM|1|A+7KUM|1|B | LNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | X-RAY DIFFRACTION | 1.714 | 9 |
| 6 | 5UEE|1|A+5UEE|1|B | RNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')G | X-RAY DIFFRACTION | 1.9 | 11 |
| 7 | 7KUK|1|A+7KUK|1|B | High resolution RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | X-RAY DIFFRACTION | 1.67 | 10 |
| 8 | 7KUP|1|A+7KUP|1|B | 2'-OMe modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | X-RAY DIFFRACTION | 1.44 | 9 |
| 9 | 6C8E|1|A+6C8E|1|B | RNA-imidazolium-bridged intermediate complex, 4h soaking | X-RAY DIFFRACTION | 1.8 | 10 |
| 10 | 7KUL|1|A+7KUL|1|B | DNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | X-RAY DIFFRACTION | 1.64 | 9 |
| 11 | 6C8J|1|A+6C8J|1|B | RNA-activated 2-AIpG monomer complex, 15 min soaking | X-RAY DIFFRACTION | 1.5 | 10 |
| 12 | 6C8D|1|A+6C8D|1|B | RNA-dGMP complex with Mg ion | X-RAY DIFFRACTION | 1.92 | 10 |
| 13 | 5UEG|1|A+5UEG|1|B | RNA primer-template complex with guanosine dinucleotide G(5')pppp(5')G ligand | X-RAY DIFFRACTION | 2.6 | 11 |
| 14 | 5UEG|1|C+5UEG|1|D | RNA primer-template complex with guanosine dinucleotide G(5')pppp(5')G ligand | X-RAY DIFFRACTION | 2.6 | 11 |
| 15 | 5UEF|1|A+5UEF|1|B | RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand | X-RAY DIFFRACTION | 2.1 | 11 |
| 16 | 5UED|1|A+5UED|1|B | RNA primer-template complex with guanosine dinucleotide ligand G(5')pp(5')G | X-RAY DIFFRACTION | 1.5 | 11 |
| 17 | 6C8I|1|A+6C8I|1|B | RNA-activated 2-AIpG monomer complex, 5 min soaking | X-RAY DIFFRACTION | 1.77 | 10 |
| 18 | 6U8U|1|A+6U8U|1|B | RNA duplex bound with TNA 3'-3' imidazolium dimer | X-RAY DIFFRACTION | 2.4 | 10 |
| 19 | 6OWL|1|A | RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP | X-RAY DIFFRACTION | 2 | 9 |
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: