Research workbench
RNA octamer containing (S)-5' methyl, 2'-F U.
Analyse RNA octamer containing (S)-5' methyl, 2'-F U. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D8T
- Type
- RNA
- Length
- 16 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA oligonucleotide containing (S)-C5'-me-2'-fu
- Ligands
- NCO
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA oligonucleotide containing (S)-C5'-me-2'-fu | rna | 8 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.34 | 0.74 | 12 | NCO |
Interfaces
1 interface between chains.
- A–B · 394 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5D8T · RNA octamer containing (S)-5' methyl, 2'-F U. · 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 5D8T · PDBe 5D8T
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