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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.278 (Depositor), 0.279 (DCC)
R-Value Work:
0.241 (Depositor)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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
Modeled Residue Count: 428
Deposited Residue Count: 446
Unique protein chains: 2

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20459
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19525
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] Interactions & Density 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 (Depositor), 0.279 (DCC)
R-Value Work: 0.241 (Depositor)
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

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Ligand Structure Quality Assessment

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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
Version 1.1: 2024-11-13
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.