8QEL | pdb_00008qel

PKR kinase domain- eIF2alpha in complex with compound

• PDB DOI: https://doi.org/10.2210/pdb8QEL/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-31 Released: 2023-09-13 
• Deposition Author(s): Nawrotek, A., Vuillard, L., Miallau, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

PKR kinase domain- eIF2alpha in complex with compound

Nawrotek, A., Vuillard, L., Miallau, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 52.27 kDa 
• Atom Count: 3,498 
• Modelled Residue Count: 428 
• Deposited Residue Count: 446 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2 subunit alpha	A	173	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SUI2, TIF211, YJR007W, J1429
UniProt
Find proteins for P20459 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20459  Go to UniProtKB:  P20459

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon-induced, double-stranded RNA-activated protein kinase	B	273	Homo sapiens	Mutation(s): 0  Gene Names: EIF2AK2, PKR, PRKR EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P19525 (Homo sapiens) Explore P19525  Go to UniProtKB:  P19525
PHAROS:  P19525 GTEx:  ENSG00000055332

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UH3 (Subject of Investigation/LOI)	C [auth B]	(3~{Z})-3-[(4-methyl-1~{H}-imidazol-5-yl)methylidene]-2-oxidanylidene-1~{H}-indole-5-carboxamide C14 H12 N4 O2 NQRCNELXESTXEP-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.028	α = 90
b = 85.028	β = 90
c = 168.94	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Nawrotek, A., Vuillard, L., Miallau, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary