Research workbench

Eukaryotic initiation factor EIF2B in complex with isrib

Analyse Eukaryotic initiation factor EIF2B in complex with isrib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6EZO
Type: protein
Length: 3,367 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Translation initiation factor eif-2B subunit alpha; Translation initiation factor eif-2B…
UniProt: Q14232, P49770, Q9NR50, Q9UI10, Q13144
Ligands: C7B
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 8 distinct chains · 27% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Translation initiation factor eif-2B subunit alpha	protein	280	43% helix, 14% strand	Q14232
C	Translation initiation factor eif-2B subunit beta	protein	307	37% helix, 11% strand	P49770
D	Translation initiation factor eif-2B subunit beta	protein	308	37% helix, 10% strand	P49770
E, F	Translation initiation factor eif-2B subunit gamma	protein	347	9% helix, 14% strand	Q9NR50
G	Translation initiation factor eif-2B subunit delta	protein	355	29% helix, 7% strand	Q9UI10
H	Translation initiation factor eif-2B subunit delta	protein	353	29% helix, 8% strand	Q9UI10
I	Human eukaryotic initiation factor EIF2B epsilon subunits	protein	396	18% helix, 12% strand	Q13144
J	Human eukaryotic initiation factor EIF2B epsilon subunits	protein	394	18% helix, 13% strand	Q13144

Ligands and binding sites

C7B · 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy) ethanoylamino]cyclohexyl]ethanamide · ligand · chains C, D, G, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	826	0.88	0.91	169	C7B
2	1013	0.87	0.89	167	empty
3	943	0.87	0.89	143	empty
4	722	0.82	0.86	107	empty
5	597	0.82	0.87	109	empty

Interfaces

18 interfaces between chains.

C–G · 1450 Å² buried · 7 hydrogen bonds · protein-protein
D–H · 1395 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 978 Å² buried · 2 hydrogen bonds · protein-protein
C–I · 670 Å² buried · 4 hydrogen bonds · protein-protein
D–J · 526 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6EZO · Eukaryotic initiation factor EIF2B in complex with ISRIB · the same entry in another collection · chain J against J, TM-score 1.00
Q13144 · AlphaFold monomer V2.0 prediction for translation initiation factor eif-2B subunit… · a predicted model of the same protein · chain I against A, TM-score 0.97

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 Q14232
Every structure of UniProt P49770
Every structure of UniProt Q9NR50
Every structure of UniProt Q9UI10
Every structure of UniProt Q13144
Elsewhere: RCSB PDB 6EZO · PDBe 6EZO · UniProt Q14232 · UniProt P49770 · UniProt Q9NR50 · UniProt Q9UI10 · UniProt Q13144

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