MolNFT v1 · #113320 · protein

Complex of C. elegans EIF4E-3 with the 4E-binding protein mextli

5ABY · Eukaryotic translation initiation factor 4E-3: “Complex of C. elegans EIF4E-3 with the 4E-binding protein mextli”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.65). MolNFT v1 #113320 on GenesisL1: 3D structure…

PDB: 5ABY
Type: protein
Length: 655 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eukaryotic translation initiation factor 4E-3; 4E-binding protein mextli
UniProt: O61955, Q9XW13
Ligands: MG
Pockets: 7 · best druggability 0.65

Structure

x-ray diffraction · 5 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Eukaryotic translation initiation factor 4E-3	protein	179	31% helix, 30% strand	O61955
B, D	4E-binding protein mextli	protein	39	56% helix, 3% strand	Q9XW13
C	Eukaryotic translation initiation factor 4E-3	protein	181	31% helix, 30% strand	O61955
E	Eukaryotic translation initiation factor 4E-3	protein	178	31% helix, 30% strand	O61955
F	4E-binding protein mextli	protein	39	56% helix, 3% strand	Q9XW13

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains C
GOL · Glycerol · additive · 3 copies · chains A, C, E

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

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	640	0.65	0.75	65	empty
2	154	0.63	0.86	23	empty
3	347	0.62	0.78	35	empty
4	114	0.41	0.76	16	GOL, MG
5	119	0.39	0.75	17	GOL

Interfaces

10 interfaces between chains.

E–F · 1398 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1364 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1362 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 341 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 331 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5ABY · Complex of C. elegans eIF4E-3 with the 4E-binding protein Mextli · the same entry in another collection · chain F against F, TM-score 1.00
O61955 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E-3… · a predicted model of the same protein · chain C against A, TM-score 0.99
Q9XW13 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E-binding… · a predicted model of the same protein · chain B against A, TM-score 0.42

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 O61955
Every structure of UniProt Q9XW13
Elsewhere: RCSB PDB 5ABY · PDBe 5ABY · UniProt O61955 · UniProt Q9XW13

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