8UH8

Crystal structure of SARS-CoV-2 main protease E166V (Apo structure)

PDB DOI: https://doi.org/10.2210/pdb8UH8/pdb

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

Deposited: 2023-10-07 Released: 2024-01-24
Deposition Author(s): Bulut, H., Hayashi, H., Kuwata, N., Tsuji, K., Das, D., Tamamura, H., Mitsuya, H.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.265
R-Value Work: 0.210
R-Value Observed: 0.213

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

TKB272, an Orally Available SARS-CoV-2-Mpro Inhibitor Containing 5-Fluorobenzothiazole, Potently Blocks SARS-CoV-2 Replication without Ritonavir

Higashi-Kuwata, N., Bulut, H., Hayashi, H., Tsuji, K., Ogata-Aoki, H., Kiso, M., Takamune, N., Kishimoto, N., Hattori, S., Ishii, T., Kobayakawa, T., Nakano, K., Das, D., Saruwatari, J., Hasegawa, K., Murayama, K., Sukenaga, Y., Takamatsu, Y., Yoshimura, K., Aoki, M., Okamura, T., Yamayoshi, S., Kawaoka, Y., Misumi, S., Tamamura, H., Mitsuya, H.

To be published.

Macromolecule Content

Total Structure Weight: 33.32 kDa
Atom Count: 2,380
Modelled 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
ORF1a polyprotein	A	302	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 Gene Names: ORF1ab
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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.265
R-Value Work: 0.210
R-Value Observed: 0.213
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.069	α = 90
b = 53.764	β = 100.91
c = 44.642	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
MOLREP	phasing
DIALS	data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-01-24
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.