7DAT

The crystal structure of COVID-19 main protease treated by AF

• PDB DOI: https://doi.org/10.2210/pdb7DAT/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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.228 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Starting Model: experimental

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8B0S

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: 34.22 kDa 
• Atom Count: 2,441 
• Modelled 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU (Subject of Investigation/LOI)	B [auth A], C [auth A]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.228 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.279	α = 90
b = 53.985	β = 101.849
c = 44.678	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
SCALA	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