8CAJ | pdb_00008caj

Crystal structure of SARS-CoV-2 Mpro-E166V mutant in complex with 13b-K

PDB DOI: https://doi.org/10.2210/pdb8CAJ/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-01-24 Released: 2024-08-07
Deposition Author(s): El Kilani, H., Hilgenfeld, R.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.364 (Depositor), 0.370 (DCC)
R-Value Work:
0.261 (Depositor), 0.260 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

13b-K and Nirmatrelvir Resistance Mutations of SARS-CoV-2 Main Protease: Structural, Biochemical, and Biophysical Characterization of Free Enzymes and Inhibitor Complexes

El Kilani, H., Sun, X., Ibrahim, M.F., Curth, U., Hilgenfeld, R.

(2025) Crystals (Basel) 15

DOI: https://doi.org/10.3390/cryst15090758

Macromolecule Content

Total Structure Weight: 33.92 kDa
Atom Count: 2,428
Modeled Residue Count: 302
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 11	A [auth AAA]	302	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UAX (Subject of Investigation/LOI) Query on UAX Download Ideal Coordinates CCD File SDF format, chain B [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA]	~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{S})-3-oxidanyl-4-oxidanylidene-1-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate C₃₁ H₄₁ N₅ O₇ FRACPXUHUTXLCX-VZVHPENPSA-N		Interactions Focus chain B [auth AAA] Interactions & Density Focus chain B [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.364 (Depositor), 0.370 (DCC)
R-Value Work: 0.261 (Depositor), 0.260 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.784	α = 90
b = 53.524	β = 99.906
c = 45.468	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
European Commission	European Union	--

Revision History (Full details and data files)

Version 1.0: 2024-08-07
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary
Version 1.2: 2025-09-03
Changes: Database references

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.