MolNFT v2 · #217767 · protein

PKR kinase domain- eIF2alpha in complex with compound

8QEL · Eukaryotic translation initiation factor 2 subunit alpha: “PKR kinase domain- eIF2alpha in complex with compound”. X-ray diffraction at 2.451, 1 ligand (UH3), 2 pockets (best druggability 0.77). MolNFT v2 #217767 on GenesisL1: 3D…

PDB: 8QEL
Type: protein
Length: 428 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.451
Source: Homo sapiens; Saccharomyces cerevisiae
Molecule: Eukaryotic translation initiation factor 2 subunit alpha; Interferon-induced…
EC: 2.7.11.1, 2.7.10.2
UniProt: P20459, P19525
Ligands: UH3
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · resolution 2.451 · 2 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Eukaryotic translation initiation factor 2 subunit alpha	protein	161	41% helix, 22% strand	P20459
B	Interferon-induced, double-stranded RNA-activated protein kinase (EC 2.7.11.1, 2.7.10.2)	protein	267	39% helix, 23% strand	P19525

Ligands and binding sites

UH3 · (3~{Z})-3-[(4-methyl-1~{H}-imidazol-5-yl)methylidene]-2-oxidanylidene-1~{H}-indole-5-carboxamide · ligand · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	886	0.77	0.80	76	UH3
2	54	0.33	0.78	12	empty

Interfaces

1 interface between chains.

A–B · 568 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

P20459 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain A against A, TM-score 0.98
P19525 · AlphaFold monomer V2.0 prediction for interferon-induced, double- stranded RNA-activated… · a predicted model of the same protein · chain B 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 P20459
Every structure of UniProt P19525
Elsewhere: RCSB PDB 8QEL · PDBe 8QEL · UniProt P20459 · UniProt P19525

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