7DAV | pdb_00007dav

The native crystal structure of COVID-19 main protease

• PDB DOI: https://doi.org/10.2210/pdb7DAV/pdb

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


• Deposited: 2020-10-18 Released: 2021-11-03 
• Deposition Author(s): He, Z.S., He, B., Cao, P., Jiang, H.D., Gong, Y., Gao, X.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.247 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

A comparison of Remdesivir versus gold cluster in COVID-19 animal model: A better therapeutic outcome of gold cluster.

He, Z., Ye, F., Zhang, C., Fan, J., Du, Z., Zhao, W., Yuan, Q., Niu, W., Gao, F., He, B., Cao, P., Zhao, L., Gao, X., Gao, X., Sun, B., Dong, Y., Zhao, J., Qi, J., Liang, X.J., Jiang, H., Gong, Y., Tan, W., Gao, X.

(2022) Nano Today 44: 101468

• DOI: https://doi.org/10.1016/j.nantod.2022.101468

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.83 kDa 
• Atom Count: 2,589 
• Modeled Residue Count: 301 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COVID-19 MAIN PROTEASE	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.247 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.941	α = 90
b = 53.795	β = 101.534
c = 44.716	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): He, Z.S., He, B., Cao, P., Jiang, H.D., Gong, Y., Gao, X.Y.

Revision History  

• Version 1.0: 2021-11-03
  Type: Initial release
  
• Version 1.1: 2022-04-27
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description