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Crystal structure of the eukaryotic translation initiation factor 2B from schizosaccharomyces pombe

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

PDB: 5B04
Type: protein
Length: 3,652 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Translation initiation factor eif-2B subunit alpha; Probable translation initiation…
UniProt: Q9USP0, Q9UT76, P56288, Q09924, P56287
Ligands: PO4
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 9 distinct chains · 33% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Translation initiation factor eif-2B subunit alpha	protein	317	44% helix, 14% strand	Q9USP0
B	Translation initiation factor eif-2B subunit alpha	protein	319	48% helix, 13% strand	Q9USP0
C	Probable translation initiation factor eif-2B subunit beta	protein	349	53% helix, 14% strand	Q9UT76
D	Probable translation initiation factor eif-2B subunit beta	protein	346	48% helix, 12% strand	Q9UT76
E	Probable translation initiation factor eif-2B subunit gamma	protein	384	14% helix, 27% strand	P56288
F	Probable translation initiation factor eif-2B subunit gamma	protein	383	18% helix, 27% strand	P56288
G, H	Probable translation initiation factor eif-2B subunit delta	protein	349	45% helix, 15% strand	Q09924
I	Probable translation initiation factor eif-2B subunit epsilon	protein	428	21% helix, 28% strand	P56287
J	Probable translation initiation factor eif-2B subunit epsilon	protein	428	22% helix, 29% strand	P56287

Ligands and binding sites

PO4 · Phosphate ion · ion · 9 copies · chains A, B, C, D, G, H, I

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	948	0.88	0.89	147	empty
2	283	0.77	0.89	49	empty
3	474	0.76	0.84	59	PO4
4	280	0.74	0.88	38	PO4
5	1013	0.74	0.77	95	PO4

Interfaces

24 interfaces between chains.

A–B · 3744 Å² buried · 40 hydrogen bonds · protein-protein
C–G · 2323 Å² buried · 22 hydrogen bonds · protein-protein
D–H · 2317 Å² buried · 25 hydrogen bonds · protein-protein
D–J · 1374 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 1368 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5B04 · Crystal structure of the eukaryotic translation initiation factor 2B from… · the same entry in another collection · chain J against J, TM-score 1.00
P56288 · AlphaFold monomer V2.0 prediction for probable translation initiation factor eif-2B… · 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 Q9USP0
Every structure of UniProt Q9UT76
Every structure of UniProt P56288
Every structure of UniProt Q09924
Every structure of UniProt P56287
Elsewhere: RCSB PDB 5B04 · PDBe 5B04 · UniProt Q9USP0 · UniProt Q9UT76 · UniProt P56288 · UniProt Q09924 · UniProt P56287

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