Crystallographic and mass spectrometric characterisation of EIF4E with N7-cap derivatives

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 29% strand (DSSP).

Ligands and binding sites

• MGO · [[(2R,3S,4R,5R)-5-(6-amino-3-methyl-4-oxo-5H-imidazo[4, 5-c]pyridin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate · ligand · 2 copies · chains A, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• E–F · 774 Ų buried · 12 hydrogen bonds · protein-protein
• A–B · 695 Ų buried · 8 hydrogen bonds · protein-protein
• A–E · 464 Ų buried · 11 hydrogen bonds · protein-protein
• A–F · 127 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 2V8W · Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives · the same entry in another collection · chain F against F, TM-score 1.00
• P06730 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E (P06730) · a predicted model of the same protein · chain A against A, TM-score 0.99
• Q13541 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E-binding… · a predicted model of the same protein · chain F against A, TM-score 0.71

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P06730
• Every structure of UniProt Q13541
• Elsewhere: RCSB PDB 2V8W · PDBe 2V8W · UniProt P06730 · UniProt Q13541