5RF1

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with NCL-00023830


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

PanDDA analysis group deposition of SARS-CoV-2 mainprotease fragment screen

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T5G
Query on T5G

Download CCD File 
A
4-bromobenzene-1-sulfonamide
C6 H6 Br N O2 S
STYQHICBPYRHQK-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.485α = 90
b = 52.653β = 102.74
c = 44.429γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references, Structure summary
  • Version 1.2: 2020-05-06
    Changes: Database references, Source and taxonomy, Structure summary