7WQK | pdb_00007wqk

wild-type SARS-CoV-2 main protease in complex with MG-132

• PDB DOI: https://doi.org/10.2210/pdb7WQK/pdb

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


• Deposited: 2022-01-25 Released: 2023-08-02 
• Deposition Author(s): Wang, Y.C., Yang, C.S., Hou, M.H., Tsai, C.L., Chen, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.289 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

wild-type SARS-CoV-2 main protease in complex with MG-132

Wang, Y.C., Yang, C.S., Hou, M.H., Tsai, C.L., Chen, 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.38 kDa 
• Atom Count: 2,499 
• Modeled Residue Count: 300 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	307	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), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ALD (Subject of Investigation/LOI)	C [auth A]	N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide C26 H43 N3 O5 WUJQMWDTZKIKQZ-VABKMULXSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001210 (ALD)	C [auth A]	PHQ-Leu-Leu-Leu-aldehyde MG-132, bound form	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.289 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.978	α = 90
b = 55.14	β = 102.34
c = 47.111	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Wang, Y.C., Yang, C.S., Hou, M.H., Tsai, C.L., Chen, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	109-2311-B241-001

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary