Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 2 (M7GPPSPAPG D2)

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 31% strand (DSSP).

Ligands and binding sites

• G0Z · [[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-4,5-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · 4 copies · chains A, B, C, D
• GOL · Glycerol · additive · 2 copies · chains A, D, B

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–C · 416 Ų buried · 6 hydrogen bonds · protein-protein
• A–D · 375 Ų buried · 6 hydrogen bonds · protein-protein
• A–B · 346 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 6GKL · Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA… · the same entry in another collection · chain D against D, TM-score 1.00
• P63073 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E (P63073) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P63073
• Elsewhere: RCSB PDB 6GKL · PDBe 6GKL · UniProt P63073