Equivalence class NR_3.5_88157.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 4CS1|1|A (rep) | 5'-(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP *GP*AP*GP*CP*CP)-3' | Haloarcula marismortui | Crystal structure of a simple duplex kink turn, HmKt-7 with 2 Mg bound. | X-ray diffraction | 2 | 2014-11-19 | |||
| 2 | 6Q8U|1|A+ 6Q8U|1|B | RNA (5'-R(*CP*GP*GP*CP*GP*AP*AP*GP*(6MZ)P*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*CP*G)-3') | Haloarcula marismortui | Structure of the standard kink turn HmKt-7 variant A2bm6A bound with AfL7Ae protein | X-ray diffraction | 1.99 | 2019-07-03 | |||
| 3 | 4C40|1|A | 5'-(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP *GP*AP*GP*CP*C)-3' | Haloarcula marismortui | The molecular recognition of kink turn structure by the L7Ae class of proteins | X-ray diffraction | 2.2 | 2013-11-06 | |||
| 4 | 5FJ0|1|C | HMKT-7 | Haloarcula marismortui | Structure of the standard kink turn HmKt-7 as simple duplex in P4222 space group | X-ray diffraction | 2.2 | 2016-09-28 | |||
| 5 | 5FJ0|1|A+ 5FJ0|1|B | HMKT-7 | Haloarcula marismortui | Structure of the standard kink turn HmKt-7 as simple duplex in P4222 space group | X-ray diffraction | 2.2 | 2016-09-28 | |||
| 6 | 7EI9|1|A+ 7EI9|1|B | RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | synthetic construct | RNA kink-turn motif with pyrrolo cytosine | X-ray diffraction | 2.7 | 2022-03-30 | |||
| 7 | 7EFI|1|A | DNA/RNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*(OMG)P*(OMG)P*(OMG))-D(P*GP*A)-R(P*GP*(OMC)P*(OMC))-3') | synthetic construct | RNA kink-turn motif composed of RNA, DNA and 2'-O-methyl RNA | X-ray diffraction | 2.9 | 2022-03-30 | |||
| 8 | 7EFH|1|A | RNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | synthetic construct | RNA kink-turn motif | X-ray diffraction | 2.7 | 2022-03-23 | |||
| 9 | 7EIA|1|G+ 7EIA|1|H | RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | synthetic construct | RNA kink-turn motif with pyrrolo cytosine | X-ray diffraction | 3 | 2022-03-30 | |||
| 10 | 7EIA|1|A+ 7EIA|1|B | RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | synthetic construct | RNA kink-turn motif with pyrrolo cytosine | X-ray diffraction | 3 | 2022-03-30 | |||
| 11 | 7EI8|1|C+ 7EI8|1|D | RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))-R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | synthetic construct | RNA kink-turn motif with 2-aminopurine | X-ray diffraction | 3.1 | 2022-03-30 | |||
| 12 | 7EIA|1|C+ 7EIA|1|D | RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | synthetic construct | RNA kink-turn motif with pyrrolo cytosine | X-ray diffraction | 3 | 2022-03-30 | |||
| 13 | 7EIA|1|E+ 7EIA|1|F | RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | synthetic construct | RNA kink-turn motif with pyrrolo cytosine | X-ray diffraction | 3 | 2022-03-30 | |||
| 14 | 7EI8|1|A+ 7EI8|1|B | RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))-R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | synthetic construct | RNA kink-turn motif with 2-aminopurine | X-ray diffraction | 3.1 | 2022-03-30 | |||
| 15 | 7EI7|1|A+ 7EI7|1|B | RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | synthetic construct | RNA kink-turn motif with 2-aminopurine | X-ray diffraction | 3.2 | 2022-03-30 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.5_88157.1 | NR_3.5_53984.1 | 3.224 | (1) 7EFH|1|A | (14) 7EIA|1|G+7EIA|1|H, 7EIA|1|E+7EIA|1|F, 7EIA|1|C+7EIA|1|D, 7EIA|1|A+7EIA|1|B, 7EI9|1|A+7EI9|1|B, 7EI8|1|C+7EI8|1|D, 7EI8|1|A+7EI8|1|B, 7EI7|1|A+7EI7|1|B, 7EFI|1|A, 6Q8U|1|A+6Q8U|1|B, 5FJ0|1|C, 5FJ0|1|A+5FJ0|1|B, 4CS1|1|A, 4C40|1|A | (0) |
| NR_3.5_88157.1 | NR_3.5_67355.2 | 3.224 | (3) 4C40|1|A, 6Q8U|1|A+6Q8U|1|B, 4CS1|1|A | (12) 7EFH|1|A, 7EIA|1|E+7EIA|1|F, 5FJ0|1|C, 7EIA|1|C+7EIA|1|D, 5FJ0|1|A+5FJ0|1|B, 7EIA|1|A+7EIA|1|B, 7EI9|1|A+7EI9|1|B, 7EI8|1|C+7EI8|1|D, 7EI8|1|A+7EI8|1|B, 7EI7|1|A+7EI7|1|B, 7EFI|1|A, 7EIA|1|G+7EIA|1|H | (0) |
| NR_3.5_88157.1 | NR_3.5_86832.1 | 3.224 | (2) 5FJ0|1|C, 5FJ0|1|A+5FJ0|1|B | (13) 7EIA|1|G+7EIA|1|H, 7EIA|1|E+7EIA|1|F, 7EIA|1|C+7EIA|1|D, 7EIA|1|A+7EIA|1|B, 7EI9|1|A+7EI9|1|B, 7EI8|1|C+7EI8|1|D, 7EI8|1|A+7EI8|1|B, 7EI7|1|A+7EI7|1|B, 7EFI|1|A, 7EFH|1|A, 6Q8U|1|A+6Q8U|1|B, 4CS1|1|A, 4C40|1|A | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.5_88157.1 | NR_3.5_88157.2 | 3.226 | (15) 7EI8|1|C+7EI8|1|D, 7EI8|1|A+7EI8|1|B, 7EI7|1|A+7EI7|1|B, 7EFI|1|A, 7EFH|1|A, 6Q8U|1|A+6Q8U|1|B, 5FJ0|1|C, 5FJ0|1|A+5FJ0|1|B, 4CS1|1|A, 4C40|1|A, 7EIA|1|G+7EIA|1|H, 7EIA|1|E+7EIA|1|F, 7EIA|1|C+7EIA|1|D, 7EIA|1|A+7EIA|1|B, 7EI9|1|A+7EI9|1|B | (0) | (1) 7EFG|1|A |
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 | 7EFI|1|A | RNA kink-turn motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 2.9 | 12 |
| 2 | 4CS1|1|A | Crystal structure of a simple duplex kink turn, HmKt-7 with 2 Mg bound. | X-RAY DIFFRACTION | 2 | 19 |
| 3 | 4C40|1|A | The molecular recognition of kink turn structure by the L7Ae class of proteins | X-RAY DIFFRACTION | 2.2 | 19 |
| 4 | 6Q8U|1|A+6Q8U|1|B | Structure of the standard kink turn HmKt-7 variant A2bm6A bound with AfL7Ae protein | X-RAY DIFFRACTION | 1.99 | 20 |
| 5 | 7EI8|1|A+7EI8|1|B | RNA kink-turn motif with 2-aminopurine | X-RAY DIFFRACTION | 3.1 | 15 |
| 6 | 7EI8|1|C+7EI8|1|D | RNA kink-turn motif with 2-aminopurine | X-RAY DIFFRACTION | 3.1 | 15 |
| 7 | 7EIA|1|A+7EIA|1|B | RNA kink-turn motif with pyrrolo cytosine | X-RAY DIFFRACTION | 3 | 18 |
| 8 | 7EIA|1|E+7EIA|1|F | RNA kink-turn motif with pyrrolo cytosine | X-RAY DIFFRACTION | 3 | 18 |
| 9 | 7EIA|1|G+7EIA|1|H | RNA kink-turn motif with pyrrolo cytosine | X-RAY DIFFRACTION | 3 | 18 |
| 10 | 5FJ0|1|A+5FJ0|1|B | Structure of the standard kink turn HmKt-7 as simple duplex in P4222 space group | X-RAY DIFFRACTION | 2.2 | 19 |
| 11 | 7EIA|1|C+7EIA|1|D | RNA kink-turn motif with pyrrolo cytosine | X-RAY DIFFRACTION | 3 | 18 |
| 12 | 5FJ0|1|C | Structure of the standard kink turn HmKt-7 as simple duplex in P4222 space group | X-RAY DIFFRACTION | 2.2 | 19 |
| 13 | 7EI9|1|A+7EI9|1|B | RNA kink-turn motif with pyrrolo cytosine | X-RAY DIFFRACTION | 2.7 | 18 |
| 14 | 7EI7|1|A+7EI7|1|B | RNA kink-turn motif with 2-aminopurine | X-RAY DIFFRACTION | 3.2 | 18 |
| 15 | 7EFH|1|A | RNA kink-turn motif | X-RAY DIFFRACTION | 2.7 | 19 |