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Complex of D. melanogaster EIF4E with a designed 4E-binding protein (form II)

Analyse Complex of D. melanogaster EIF4E with a designed 4E-binding protein (form II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4UEB
Type: protein
Length: 622 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eukaryotic translation initiation factor 4E; Designed 4E-bp
UniProt: P48598
Pockets: 7 · best druggability 0.68

Structure

x-ray diffraction · 5 distinct chains · 33% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Eukaryotic translation initiation factor 4E	protein	162	30% helix, 34% strand	P48598
B, D	Designed 4E-bp	protein	41	56% helix, 2% strand	—
C	Eukaryotic translation initiation factor 4E	protein	168	31% helix, 32% strand	P48598
E	Eukaryotic translation initiation factor 4E	protein	171	30% helix, 33% strand	P48598
F	Designed 4E-bp	protein	39	46% helix, 3% strand	—

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	513	0.68	0.78	45	empty
2	462	0.67	0.79	44	empty
3	116	0.53	0.82	20	empty
4	109	0.50	0.81	20	empty
5	91	0.41	0.78	18	empty

Interfaces

6 interfaces between chains.

A–B · 1477 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1417 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1376 Å² buried · 18 hydrogen bonds · protein-protein
C–E · 488 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 224 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4UEB · Complex of D. melanogaster eIF4E with a designed 4E-binding protein (Form II) · the same entry in another collection · chain F against F, TM-score 1.00
P48598 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E1… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P48598
Elsewhere: RCSB PDB 4UEB · PDBe 4UEB · UniProt P48598

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