Translation initiation factor 4E in complex with (sp)-ipr-M7GPPSPG mRNA 5' cap analog

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 29% strand (DSSP).

Ligands and binding sites

• 7L2 · [[[(3~{A}~{R},4~{R},6~{R},6~{A}~{R})-4-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-2,2-dimethyl-3~{A},4,6,6~{A}-tetrahydrofuro[3,4-D][1, 3]dioxol-6-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{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 · 3 copies · chains A, B

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–C · 433 Ų buried · 7 hydrogen bonds · protein-protein
• B–D · 420 Ų buried · 6 hydrogen bonds · protein-protein
• A–B · 410 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 5M81 · Translation initiation factor 4E in complex with (SP)-iPr-m7GppSpG 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 C 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 5M81 · PDBe 5M81 · UniProt P63073