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Electron cryo-microscopy of the eukaryotic translation initiation factor 2B from homo sapiens (updated model of pdb id: 6CAJ)

Analyse Electron cryo-microscopy of the eukaryotic translation initiation factor 2B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7L7G
Type: protein
Length: 3,198 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Translation initiation factor eif-2B subunit epsilon; Translation initiation factor…
UniProt: Q13144, Q9NR50, P49770, Q9UI10, Q14232
Ligands: C7B
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 5 distinct chains · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Translation initiation factor eif-2B subunit epsilon	protein	421	23% helix, 28% strand	Q13144
J, I	Translation initiation factor eif-2B subunit gamma	protein	224	21% helix, 23% strand	Q9NR50
C, D	Translation initiation factor eif-2B subunit beta	protein	318	54% helix, 14% strand	P49770
F, E	Translation initiation factor eif-2B subunit delta	protein	357	45% helix, 14% strand	Q9UI10
H, G	Translation initiation factor eif-2B subunit alpha	protein	279	53% helix, 14% strand	Q14232

Ligands and binding sites

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

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	863	0.84	0.86	82	empty
2	653	0.84	0.88	76	empty
3	584	0.77	0.84	49	empty
4	1177	0.76	0.78	110	empty
5	402	0.76	0.85	48	C7B

Interfaces

22 interfaces between chains.

C–F · 2070 Å² buried · 22 hydrogen bonds · protein-protein
D–E · 2053 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1285 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 1266 Å² buried · 7 hydrogen bonds · protein-protein
H–G · 1249 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

7L7G · Electron cryo-microscopy of the eukaryotic translation initiation factor 2B from Homo… · the same entry in another collection · chain G against G, TM-score 1.00
Q9UI10 · AlphaFold monomer V2.0 prediction for translation initiation factor eif-2B subunit delta… · a predicted model of the same protein · chain E 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 Q13144
Every structure of UniProt Q9NR50
Every structure of UniProt P49770
Every structure of UniProt Q9UI10
Every structure of UniProt Q14232
Elsewhere: RCSB PDB 7L7G · PDBe 7L7G · UniProt Q13144 · UniProt Q9NR50 · UniProt P49770 · UniProt Q9UI10 · UniProt Q14232

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