Research workbench
RNA hairpin structure containing 2-meimp-oligo analogue
Analyse RNA hairpin structure containing 2-meimp-oligo analogue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UZ6
- Type
- RNA
- Length
- 96 nucleotides
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (25-mer); RNA (5'-D(*(8OS))-R(P*CP*AP*CP*CP*UP*CP*A)-3')
- Ligands
- 8OS
- Pockets
- 4 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | RNA (25-mer) | rna | 25 | — | — |
| B, D, F | RNA (5'-D(*(8OS))-R(P*CP*AP*CP*CP*UP*CP*A)-3') | rna | 7 | — | — |
Ligands and binding sites
- 8OS · 5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl) phosphoryl]guanosine · ligand · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.38 | 0.75 | 12 | empty |
| 2 | 138 | 0.33 | 0.72 | 13 | empty |
| 3 | 73 | 0.26 | 0.72 | 10 | empty |
| 4 | 50 | 0.22 | 0.72 | 11 | empty |
Interfaces
5 interfaces between chains.
- C–D · 307 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- A–B · 306 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- E–F · 304 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- C–E · 108 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- C–F · 73 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 6 modified, 3 covalent (nucleotide modification, covalent ligand).
Compared structures
- 5UZ6 · RNA hairpin structure containing 2-MeImp-oligo analogue · 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 5UZ6 · PDBe 5UZ6
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