6Z2E | pdb_00006z2e

Crystal structure of SARS-CoV-2 Mpro in complex with the activity-based probe, biotin-PEG(4)-Abu-Tle-Leu-Gln-vinylsulfone

• PDB DOI: https://doi.org/10.2210/pdb6Z2E/pdb

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


• Deposited: 2020-05-15 Released: 2020-06-17 
• Deposition Author(s): Zhang, L., Hilgenfeld, R.
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 Mpro in complex with the activity-based probe, biotin-PEG(4)-Abu-Tle-Leu-Gln-vinylsulfone

Zhang, L., Hilgenfeld, R.

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: 34.91 kDa 
• Atom Count: 2,670 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A [auth AAA]	306	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q5T (Subject of Investigation/LOI)	B [auth AAA]	(4~{S})-4-[[(2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-[3-[2-[2-[2-[2-[5-[(3~{a}~{S},4~{R},6~{a}~{R})-2-oxidanylidene-3,3~{a},4,6~{a}-tetrahydro-1~{H}-thieno[3,4-d]imidazol-4-yl]pentanoylamino]ethoxy]ethoxy]ethoxy]ethoxy]propanoylamino]butanoyl]amino]-3,3-dimethyl-butanoyl]amino]-4-methyl-pentanoyl]amino]-6-methylsulfonyl-hexanamide C44 H80 N8 O13 S2 GNJWOJZWTQAVJG-ZFKAINLFSA-N
CL	C [auth AAA], D [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.083	α = 90
b = 104.083	β = 90
c = 91.246	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Zhang, L., Hilgenfeld, R.

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Funding Organization	Location	Grant Number
European Union (EU)	Germany	# 101003627

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2021-04-28
  Changes: Source and taxonomy, Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary