Translation initiation factor 4E in complex with (sp)-M2(7,2'O)GPPSEPG mRNA 5' cap analog (beta-se-arca D2)

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 29% strand (DSSP).

Ligands and binding sites

• 7LO · [[[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-selanyl-phosphoryl] [(2~{R},3~{S},4~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl) oxolan-2-yl]methyl hydrogen phosphate · ligand · 3 copies · chains A, B, C
• CL · Chloride ion · ion · chains B
• GOL · Glycerol · additive · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 386 Ų buried · 3 hydrogen bonds · protein-protein
• B–C · 377 Ų buried · 5 hydrogen bonds · protein-protein
• A–D · 366 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 5M7Z · Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSepG mRNA 5' cap analog… · 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 5M7Z · PDBe 5M7Z · UniProt P63073