8QEL

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.278
R-Value Work: 0.241
R-Value Observed: 0.243

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

PKR kinase domain- eIF2alpha in complex with compound

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

To be published.

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

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(by identity cutoff) | 3D Structure

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)) Go to UniProtKB: P20459
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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) Go to UniProtKB: P19525
PHAROS: P19525 GTEx: ENSG00000055332
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UH3 (Subject of Investigation/LOI) Query on UH3 Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	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		Interactions Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on 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
R-Value Work: 0.241
R-Value Observed: 0.243
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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-09-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-09-13
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.