MolNFT v1 · #190667 · protein

EIF4E in complex with a disulphide-free autonomous vh domain

7XTP · Eukaryotic translation initiation factor 4E: “EIF4E in complex with a disulphide-free autonomous vh domain”. X-ray diffraction, 1 ligand (MGO), 6 pockets (best druggability 0.71). MolNFT v1 #190667 on GenesisL1: 3D structure…

PDB: 7XTP
Type: protein
Length: 613 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eukaryotic translation initiation factor 4E; Vh-S4SS
UniProt: P06730
Ligands: MGO
Pockets: 6 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 28% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Eukaryotic translation initiation factor 4E	protein	173	34% helix, 29% strand	P06730
B	Eukaryotic translation initiation factor 4E	protein	174	34% helix, 29% strand	P06730
C	Vh-S4SS	protein	134	18% helix, 46% strand	—
D	Vh-S4SS	protein	132	20% helix, 46% strand	—

Ligands and binding sites

MGO · [[(2R,3S,4R,5R)-5-(6-amino-3-methyl-4-oxo-5H-imidazo[4, 5-c]pyridin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate · ligand · 2 copies · chains A, B

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

Pockets

6 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	898	0.71	0.76	83	empty
2	338	0.56	0.75	35	empty
3	88	0.44	0.79	18	MGO
4	79	0.43	0.80	17	MGO
5	109	0.41	0.77	22	empty

Interfaces

5 interfaces between chains.

A–C · 413 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 387 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 294 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 239 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 37 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7XTP · eIF4E in Complex with a Disulphide-Free Autonomous VH Domain · the same entry in another collection · chain A against A, TM-score 1.00

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
Elsewhere: RCSB PDB 7XTP · PDBe 7XTP · UniProt P06730

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