MolNFT v1 · #68499 · RNA
X-ray structure of R[CGCG(5-FLUORO)CG]2
3JXQ: “X-ray structure of R[CGCG(5-FLUORO)CG]2”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.42). MolNFT v1 #68499 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3JXQ
- Type
- RNA
- Length
- 24 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- R[CGCG(5-FLUORO)CG]2
- Ligands
- MG
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K, L | R[CGCG(5-FLUORO)CG]2 | rna | 6 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, K, L
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 | 200 | 0.42 | 0.73 | 18 | MG |
Interfaces
6 interfaces between chains.
- A–B · 336 Ų buried · 28 hydrogen bonds · nucleic-nucleic
- K–L · 334 Ų buried · 27 hydrogen bonds · nucleic-nucleic
- B–L · 108 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–K · 69 Ų buried · 1 hydrogen bond · nucleic-nucleic
- A–L · 37 Ų buried · 1 hydrogen bond · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3JXQ · X-Ray structure of r[CGCG(5-fluoro)CG]2 · 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 3JXQ · PDBe 3JXQ
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