Research workbench
RNA kink-turn motif with 2-aminopurine
Analyse RNA kink-turn motif with 2-aminopurine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F8Z
- Type
- RNA
- Length
- 190 nucleotides
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 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')
- Ligands
- K
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | 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') | rna | 19 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains A, C, G, F, H, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.63 | 0.75 | 33 | empty |
| 2 | 672 | 0.62 | 0.74 | 33 | K |
| 3 | 633 | 0.62 | 0.75 | 33 | empty |
| 4 | 559 | 0.60 | 0.75 | 30 | K |
| 5 | 493 | 0.57 | 0.74 | 32 | K |
Interfaces
15 interfaces between chains.
- E–F · 1358 Ų buried · 139 hydrogen bonds · nucleic-nucleic
- G–H · 1338 Ų buried · 128 hydrogen bonds · nucleic-nucleic
- C–D · 1334 Ų buried · 129 hydrogen bonds · nucleic-nucleic
- I–J · 1333 Ų buried · 123 hydrogen bonds · nucleic-nucleic
- A–B · 1333 Ų buried · 134 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 10 modified (nucleotide modification).
Compared structures
- 7F8Z · RNA kink-turn motif with 2-aminopurine · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7F8Z · PDBe 7F8Z
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