Research workbench
Alternatingly modified 2'FLUORO RNA octamer F/RA2U2-P3
Analyse Alternatingly modified 2'FLUORO RNA octamer F/RA2U2-P3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P4B
- Type
- RNA
- Length
- 48 nucleotides
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
- Ligands
- BA
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3' | rna | 8 | — | — |
Ligands and binding sites
- BA · Barium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.55 | 0.73 | 28 | BA |
Interfaces
11 interfaces between chains.
- E–F · 408 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- A–B · 399 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- C–D · 397 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- B–F · 112 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–E · 108 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 24 modified (nucleotide modification).
Compared structures
- 3P4B · Alternatingly modified 2'Fluoro RNA octamer f/rA2U2-P3 · 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 3P4B · PDBe 3P4B
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