MolNFT v1 · #116474 · RNA
RNA oligonucleotide containing (R)-C5'-me-2'F U
5DER · RNA oligonucleotide containing (R)-C5'-me-2'-fu: “RNA oligonucleotide containing (R)-C5'-me-2'F U”. X-ray diffraction, 2 pockets (best druggability 0.41). MolNFT v1 #116474 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5DER
- Type
- RNA
- Length
- 32 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA oligonucleotide containing (R)-C5'-me-2'-fu
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RNA oligonucleotide containing (R)-C5'-me-2'-fu | rna | 8 | — | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.41 | 0.74 | 14 | empty |
| 2 | 50 | 0.21 | 0.72 | 9 | empty |
Interfaces
4 interfaces between chains.
- A–B · 405 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- C–D · 403 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- B–D · 94 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- A–C · 57 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5DER · RNA oligonucleotide containing (R)-C5'-ME-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 5DER · PDBe 5DER
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