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

Macromolecule Content

• Total Structure Weight: 34.35 kDa 
• Atom Count: 2,962 
• Modelled Residue Count: 305 
• Deposited Residue Count: 305 
• Unique protein chains: 1

 6YB7

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

• PDB DOI:  https://doi.org/10.2210/pdb6YB7/pdb

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


• Deposited: 2020-03-16 Released: 2020-03-25 
• 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.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.180 
• R-Value Work: 0.142 
• R-Value Observed: 0.144 

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	A	305	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.180 
• R-Value Work: 0.142 
• R-Value Observed: 0.144 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.429	α = 90
b = 52.798	β = 103.03
c = 44.611	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
DIALS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-25 
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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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2020-03-25
  Type: Initial release
  
• Version 2.0: 2020-04-01
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2020-04-08
  Changes: Source and taxonomy
• Version 2.2: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 2.3: 2020-10-21
  Changes: Advisory, Structure summary
• Version 3.0: 2021-12-22
  Type: Coordinate replacement
  Reason: Chirality error
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 3.1: 2023-03-29
  Changes: Structure summary