9M29 | pdb_00009m29

Crystal Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor AD05

• PDB DOI: https://doi.org/10.2210/pdb9M29/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-27 Released: 2026-03-04 
• Deposition Author(s): Yin, W., Kong, W.P., Wong, K.Y.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.216 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.173 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor AD05

Yin, W., Kong, W.P., Wong, K.Y.

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: 34.72 kDa 
• Atom Count: 2,548 
• Modeled Residue Count: 304 
• Deposited Residue Count: 313 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	310	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
inhibitor AD05	B	3	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.216 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.173 (DCC) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.52	α = 90
b = 80.14	β = 97.467
c = 88.966	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-04 
Deposition Author(s): Yin, W., Kong, W.P., Wong, K.Y.

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Funding Organization	Location	Grant Number
Other government	Hong Kong	--

Revision History  

• Version 1.0: 2026-03-04
  Type: Initial release