5R8T

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 main protease screened against DSI poised (Enamine), Fraglites and Peplites (Newcastle university), Mini Frags (Astex), York 3D (York university), electrophile cysteine covalent (Weizman institute) fragment libraries

• PDB DOI:  https://doi.org/10.2210/pdb5R8T/pdb
• Deposition Group: G_1002144 (ground state) ExploreG_1002144

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


• Deposited: 2020-03-03 Released: 2020-04-01 
• Deposition Author(s): Fearon, D., Owen, C.D., Douangamath, A., Lukacik, P., Powell, A.J., Strain-Damerell, C.M., Resnick, E., Krojer, T., Gehrtz, P., Wild, C., Aimon, A., Brandao-Neto, J., Carbery, A., Dunnett, L., Skyner, R., Snee, M., London, N., Walsh, M.A., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.208 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Literature

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 main protease fragment screening

Fearon, D., Owen, C.D., Douangamath, A., Lukacik, P., Powell, A.J., Strain-Damerell, C.M., Resnick, E., Krojer, T., Gehrtz, P., Wild, C., Aimon, A., Brandao-Neto, J., Carbery, A., Dunnett, L., Skyner, R., Snee, M., London, N., Walsh, M.A., von Delft, F.

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)

Macromolecule Content

• Total Structure Weight: 34.06 kDa 
• Atom Count: 2,720 
• Modelled Residue Count: 304 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	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]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.208 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.207	α = 90
b = 52.596	β = 102.99
c = 44.631	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Fearon, D., Owen, C.D., Douangamath, A., Lukacik, P., Powell, A.J., Strain-Damerell, C.M., Resnick, E., Krojer, T., Gehrtz, P., Wild, C., Aimon, A., Brandao-Neto, J., Carbery, A., Dunnett, L., Skyner, R., Snee, M., London, N., Walsh, M.A., von Delft, F.

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2021-01-27
  Changes: Data collection, Structure summary