Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology, gel filtration

Macromolecule Content

• Total Structure Weight: 34.14 kDa 
• Atom Count: 2,950 
• Modelled Residue Count: 304 
• Deposited Residue Count: 306 
• Unique protein chains: 1

 6Y84

SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19)

• PDB DOI:  https://doi.org/10.2210/pdb6Y84/pdb

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


• Deposited: 2020-03-03 Released: 2020-03-11 
• Deposition Author(s): Owen, C.D., Lukacik, P., Strain-Damerell, C.M., Douangamath, A., Powell, A.J., Fearon, D., Brandao-Neto, J., Crawshaw, A.D., Aragao, D., Williams, M., Flaig, R., Hall, D.R., McAuley, K.E., Mazzorana, M., Stuart, D.I., von Delft, F., Walsh, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.200 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

COVID-19 main protease with unliganded active site

Owen, C.D., Lukacik, P., Strain-Damerell, C.M., Douangamath, A., Powell, A.J., Fearon, D., Brandao-Neto, J., Crawshaw, A.D., Aragao, D., Williams, M., Flaig, R., Hall, D., McAauley, K., Stuart, D.I., von Delft, F., Walsh, M.A.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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
DMS	B [auth A], C [auth A], D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.200 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.812	α = 90
b = 52.949	β = 103.16
c = 44.631	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
DIALS	data reduction
xia2	data reduction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-11 
Deposition Author(s): Owen, C.D., Lukacik, P., Strain-Damerell, C.M., Douangamath, A., Powell, A.J., Fearon, D., Brandao-Neto, J., Crawshaw, A.D., Aragao, D., Williams, M., Flaig, R., Hall, D.R., McAuley, K.E., Mazzorana, M., Stuart, D.I., von Delft, F., Walsh, M.A.

Revision History  

• Version 1.0: 2020-03-11
  Type: Initial release
  
• Version 1.1: 2020-03-25
  Type: Coordinate replacement
  Reason: Atomic clashes
  Changes: Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2021-12-22
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.4: 2023-03-29
  Changes: Structure summary