MolNFT v1 · #126813 · protein

Crystal structure of EIF4E from C. melo bound to a cap analog

5ME6 · Eukaryotic transcription initiation factor 4E: “Crystal structure of EIF4E from C. melo bound to a cap analog”. X-ray diffraction, 1 ligand (M7G), 6 pockets (best druggability 0.69). MolNFT v1 #126813 on GenesisL1: 3D structure…

PDB: 5ME6
Type: protein
Length: 696 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eukaryotic transcription initiation factor 4E
UniProt: Q00LS8
Ligands: M7G
Pockets: 6 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Eukaryotic transcription initiation factor 4E	protein	175	31% helix, 31% strand	Q00LS8
B	Eukaryotic transcription initiation factor 4E	protein	173	31% helix, 32% strand	Q00LS8
C	Eukaryotic transcription initiation factor 4E	protein	179	26% helix, 31% strand	Q00LS8
D	Eukaryotic transcription initiation factor 4E	protein	169	30% helix, 33% strand	Q00LS8

Ligands and binding sites

M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · 2 copies · chains A, D

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

Pockets

6 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	895	0.69	0.75	75	empty
2	516	0.62	0.75	46	empty
3	124	0.53	0.81	13	empty
4	195	0.44	0.73	28	M7G
5	108	0.36	0.74	27	empty

Interfaces

6 interfaces between chains.

B–C · 639 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 428 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 228 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 82 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 35 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5ME6 · Crystal Structure of eiF4E from C. melo bound to a CAP analog · 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 Q00LS8
Elsewhere: RCSB PDB 5ME6 · PDBe 5ME6 · UniProt Q00LS8

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