9ART

Crystal structure of SARS-CoV-2 main protease A191T mutant in complex with an inhibitor 5h

• PDB DOI: https://doi.org/10.2210/pdb9ART/pdb

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


• Deposited: 2024-02-23 Released: 2024-04-24 
• Deposition Author(s): Bulut, H., Hattori, S., Hayashi, H., Hasegawa, K., Li, M., Wlodawer, A., Tamamura, H., Mitsuya, H.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.231 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

Structural and virologic mechanism of emergence of main protease inhibitor-resistance in SARS-CoV-2 as selected with main protease inhibitors

Hattori, S., Bulut, H., Hayashi, H., Kishimoto, N., Takamune, N., Hasegawa, K., Murayama, K., Mi, L., Wlodawer, A., Tamamura, H., Misumi, S., Mitsuya, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 68.61 kDa 
• Atom Count: 5,102 
• Modelled Residue Count: 610 
• Deposited Residue Count: 610 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B [auth D]	305	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V7G (Subject of Investigation/LOI)	C [auth A], D	N-[(2S)-1-({(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide C30 H35 N5 O5 S DHQWCSDZTRDSRP-XIBGDNMGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.231 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.111	α = 114.79
b = 53.54	β = 97.99
c = 63.86	γ = 89.99

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Bulut, H., Hattori, S., Hayashi, H., Hasegawa, K., Li, M., Wlodawer, A., Tamamura, H., Mitsuya, H.

---

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

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release