7KQW

Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, methylated)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.93 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.

Schuller, M.Correy, G.J.Gahbauer, S.Fearon, D.Wu, T.Diaz, R.E.Young, I.D.Carvalho Martins, L.Smith, D.H.Schulze-Gahmen, U.Owens, T.W.Deshpande, I.Merz, G.E.Thwin, A.C.Biel, J.T.Peters, J.K.Moritz, M.Herrera, N.Kratochvil, H.T.Aimon, A.Bennett, J.M.Brandao Neto, J.Cohen, A.E.Dias, A.Douangamath, A.Dunnett, L.Fedorov, O.Ferla, M.P.Fuchs, M.R.Gorrie-Stone, T.J.Holton, J.M.Johnson, M.G.Krojer, T.Meigs, G.Powell, A.J.Rack, J.G.M.Rangel, V.L.Russi, S.Skyner, R.E.Smith, C.A.Soares, A.S.Wierman, J.L.Zhu, K.O'Brien, P.Jura, N.Ashworth, A.Irwin, J.J.Thompson, M.C.Gestwicki, J.E.von Delft, F.Shoichet, B.K.Fraser, J.S.Ahel, I.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abf8711
  • Primary Citation of Related Structures:  
    5RS7, 5RS8, 5RS9, 5RSB, 5RSC, 5RSD, 5RSE, 5RSF, 5RSG, 5RSH, 5RSI, 5RSJ, 5RSK, 5RSL, 5RSM, 5RSN, 5RSO, 5RSP, 5RSQ, 5RSR, 5RSS, 5RST, 5RSU, 5RSV, 5RSW, 5RSX, 5RSY, 5RSZ, 5RT0, 5RT1, 5RT2, 5RT3, 5RT4, 5RT5, 5RT6, 5RT7, 5RT8, 5RT9, 5RTA, 5RTB, 5RTC, 5RTD, 5RTE, 5RTF, 5RTG, 5RTH, 5RTI, 5RTJ, 5RTK, 5RTL

  • PubMed Abstract: 

    The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate-ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.


  • Organizational Affiliation

    Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 3173Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.93 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.146α = 90
b = 30.647β = 96.69
c = 39.608γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States2031205

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Structure summary
  • Version 1.2: 2021-06-30
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection