MolNFT v1 · #74691 · DNA
2'FLUORO modified RNA octamer FA2U2
3P4A · 2'FLUORO modified RNA 8-mer: “2'FLUORO modified RNA octamer FA2U2”. X-ray diffraction, 2 ligands (SR, MG), 1 pocket (best druggability 0.56). MolNFT v1 #74691 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3P4A
- Type
- DNA
- Length
- 48 nucleotides
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2'FLUORO modified RNA 8-mer
- Ligands
- SR, MG
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 2'FLUORO modified RNA 8-mer | dna | 8 | — | — |
Ligands and binding sites
- SR · Strontium ion · metal · 9 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies
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 | 494 | 0.56 | 0.73 | 29 | SR |
Interfaces
11 interfaces between chains.
- C–D · 404 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- A–B · 393 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- E–F · 392 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- B–D · 114 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–C · 114 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 48 modified (nucleotide modification).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3P4A · PDBe 3P4A
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