MolNFT v1 · #114706 · protein

EIF4E complex

5BXV · Eukaryotic translation initiation factor 4E: “EIF4E complex”. X-ray diffraction, 1 ligand (MGP), 5 pockets (best druggability 0.72). MolNFT v1 #114706 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5BXV
Type: protein
Length: 423 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: P63073, Q13541
Ligands: MGP
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Eukaryotic translation initiation factor 4E	protein	174	34% helix, 29% strand	P63073
B	Eukaryotic translation initiation factor 4E-binding protein 1	protein	35	31% helix, 3% strand	Q13541
C	Eukaryotic translation initiation factor 4E	protein	181	32% helix, 29% strand	P63073
D	Eukaryotic translation initiation factor 4E-binding protein 1	protein	33	39% helix, 3% strand	Q13541

Ligands and binding sites

MGP · 7-methyl-guanosine-5'-triphosphate · ligand · 2 copies · chains A, C

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	658	0.72	0.79	66	empty
2	126	0.60	0.85	28	empty
3	113	0.45	0.78	16	MGP
4	95	0.44	0.79	20	MGP
5	64	0.25	0.71	20	empty

Interfaces

5 interfaces between chains.

C–D · 1383 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1353 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 342 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 277 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 152 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5BXV · eIF4E complex · 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
Q13541 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E-binding… · a predicted model of the same protein · chain D against A, TM-score 0.85

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
Every structure of UniProt Q13541
Elsewhere: RCSB PDB 5BXV · PDBe 5BXV · UniProt P63073 · UniProt Q13541

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.