Research workbench

Sugar phosphate activation of the stress sensor EIF2B

Analyse Sugar phosphate activation of the stress sensor EIF2B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KMF
Type: protein
Length: 3,005 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Translation initiation factor eif-2B subunit beta; Translation initiation factor eif-2B…
UniProt: P49770, Q9UI10, Q14232, Q13144, Q9NR50
Ligands: F6P
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 10 distinct chains · 36% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Translation initiation factor eif-2B subunit beta	protein	315	49% helix, 12% strand	P49770
D	Translation initiation factor eif-2B subunit beta	protein	314	45% helix, 13% strand	P49770
F	Translation initiation factor eif-2B subunit delta	protein	325	45% helix, 14% strand	Q9UI10
E	Translation initiation factor eif-2B subunit delta	protein	330	41% helix, 13% strand	Q9UI10
H	Translation initiation factor eif-2B subunit alpha	protein	280	48% helix, 15% strand	Q14232
G	Translation initiation factor eif-2B subunit alpha	protein	287	51% helix, 15% strand	Q14232
B	Translation initiation factor eif-2B subunit epsilon	protein	413	19% helix, 25% strand	Q13144
I	Translation initiation factor eif-2B subunit epsilon	protein	416	20% helix, 24% strand	Q13144
J	Translation initiation factor eif-2B subunit gamma	protein	162	20% helix, 30% strand	Q9NR50
K	Translation initiation factor eif-2B subunit gamma	protein	163	19% helix, 23% strand	Q9NR50

Ligands and binding sites

F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains H, G

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	623	0.85	0.90	110	empty
2	604	0.72	0.80	59	empty
3	575	0.72	0.80	56	empty
4	327	0.69	0.83	44	F6P
5	143	0.68	0.89	35	empty

Interfaces

22 interfaces between chains.

D–E · 2087 Å² buried · 27 hydrogen bonds · protein-protein
C–F · 2046 Å² buried · 23 hydrogen bonds · protein-protein
H–G · 1783 Å² buried · 17 hydrogen bonds · protein-protein
C–B · 1251 Å² buried · 8 hydrogen bonds · protein-protein
D–I · 1220 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7KMF · Sugar phosphate activation of the stress sensor eIF2B · the same entry in another collection · chain I against I, 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 F 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 P49770
Every structure of UniProt Q9UI10
Every structure of UniProt Q14232
Every structure of UniProt Q13144
Every structure of UniProt Q9NR50
Elsewhere: RCSB PDB 7KMF · PDBe 7KMF · UniProt P49770 · UniProt Q9UI10 · UniProt Q14232 · UniProt Q13144 · UniProt Q9NR50

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