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

Analyse Crystallographic and mass spectrometric characterisation of EIF4E with N7-cap… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2V8Y
Type: protein
Length: 388 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eukaryotic translation initiation factor 4E; Eukaryotic translation initiation factor…
UniProt: P06730, Q13541
Ligands: MGV
Pockets: 3 · best druggability 0.48

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Eukaryotic translation initiation factor 4E	protein	181	32% helix, 29% strand	P06730
B, F	Eukaryotic translation initiation factor 4E-binding protein 1	protein	14	43% helix, 0% strand	Q13541
E	Eukaryotic translation initiation factor 4E	protein	179	30% helix, 30% strand	P06730

Ligands and binding sites

MGV · P-fluoro-7-benzyl guanine monophosphate · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	136	0.48	0.79	26	empty
2	131	0.48	0.78	17	MGV
3	107	0.43	0.78	21	MGV

Interfaces

4 interfaces between chains.

E–F · 781 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 695 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 475 Å² buried · 5 hydrogen bonds · protein-protein
A–F · 126 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2V8Y · 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 2V8Y · PDBe 2V8Y · UniProt P06730 · UniProt Q13541

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