Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with HEPES

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

Starting Model: experimental
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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain.

Ni, X.Schroder, M.Olieric, V.Sharpe, M.E.Hernandez-Olmos, V.Proschak, E.Merk, D.Knapp, S.Chaikuad, A.

(2021) ACS Med Chem Lett 12: 603-609

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00684
  • Primary Citation of Related Structures:  
    6YWK, 6YWL, 6YWM, 7BF3, 7BF4, 7BF5, 7BF6

  • PubMed Abstract: 

    The nsP3 macrodomain is a conserved protein interaction module that plays essential regulatory roles in the host immune response by recognizing and removing posttranslational ADP-ribosylation sites during SARS-CoV-2 infection. Thus targeting this protein domain may offer a therapeutic strategy to combat current and future virus pandemics. To assist inhibitor development efforts, we report here a comprehensive set of macrodomain crystal structures complexed with diverse naturally occurring nucleotides, small molecules, and nucleotide analogues including GS-441524 and its phosphorylated analogue, active metabolites of remdesivir. The presented data strengthen our understanding of the SARS-CoV-2 macrodomain structural plasticity and provide chemical starting points for future inhibitor development.

  • Organizational Affiliation

    Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, 60438 Frankfurt am Main, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NSP3 macrodomain
A, B, C, D, E
173Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: (PDB Primary Data), 3.4.22 (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE (Subject of Investigation/LOI)
Query on EPE

Download Ideal Coordinates CCD File 
CA [auth E],
DA [auth E],
J [auth C]
C8 H18 N2 O4 S
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D]
EA [auth E]
F [auth A]
FA [auth E]
G [auth A]
AA [auth D],
EA [auth E],
F [auth A],
FA [auth E],
G [auth A],
H [auth A],
K [auth C],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth D],
R [auth D],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
C2 H6 O2
Query on MG

Download Ideal Coordinates CCD File 
BA [auth E],
I [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.227α = 90
b = 111.765β = 90
c = 196.369γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description