MolNFT v1 · #158903 · protein

Electron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to translation initiation factor 2 from homo sapiens

6O81 · Translation initiation factor eif-2B subunit epsilon: “Electron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to translation initiation…”. Electron microscopy, 1 ligand (C7B), 20 pockets (best druggability…

PDB: 6O81
Type: protein
Length: 4,977 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Translation initiation factor eif-2B subunit epsilon; Translation initiation factor…
UniProt: Q13144, P49770, Q9UI10, Q14232, Q9NR50, P05198, P41091
Ligands: C7B
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 9 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Translation initiation factor eif-2B subunit epsilon	protein	590	37% helix, 18% strand	Q13144
C	Translation initiation factor eif-2B subunit beta	protein	317	48% helix, 14% strand	P49770
D	Translation initiation factor eif-2B subunit beta	protein	318	50% helix, 14% strand	P49770
E, F	Translation initiation factor eif-2B subunit delta	protein	357	43% helix, 13% strand	Q9UI10
G, H	Translation initiation factor eif-2B subunit alpha	protein	285	49% helix, 14% strand	Q14232
I, J	Translation initiation factor eif-2B subunit gamma	protein	240	28% helix, 22% strand	Q9NR50
L, M	Eukaryotic translation initiation factor 2 subunit 1	protein	275	41% helix, 21% strand	P05198
S, T	Eukaryotic translation initiation factor 2 subunit 3	protein	410	16% helix, 32% strand	P41091
d, e	Translation initiation factor EIF2 beta-subunit	protein	14	86% helix, 0% strand	—

Ligands and binding sites

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

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	1129	0.87	0.88	150	empty
2	765	0.84	0.88	106	empty
3	633	0.84	0.88	70	empty
4	746	0.84	0.87	71	empty
5	876	0.82	0.84	115	empty

Interfaces

34 interfaces between chains.

D–E · 2203 Å² buried · 24 hydrogen bonds · protein-protein
C–F · 2164 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1382 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 1381 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 1285 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6O81 · Electron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to… · the same entry in another collection · chain I against I, 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 Q13144
Every structure of UniProt P49770
Every structure of UniProt Q9UI10
Every structure of UniProt Q14232
Every structure of UniProt Q9NR50
Every structure of UniProt P05198
Every structure of UniProt P41091
Elsewhere: RCSB PDB 6O81 · PDBe 6O81 · UniProt Q13144 · UniProt P49770 · UniProt Q9UI10 · UniProt Q14232 · UniProt Q9NR50 · UniProt P05198 · UniProt P41091

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