ISDA: 7BF5

Deposition Date 2020-12-31

Release Date 2021-01-13

Last Version Date 2025-10-15

Entry Detail

PDB ID:

7BF5

Keywords:

VIRAL PROTEIN

Title:

Crystal structure of SARS-CoV-2 macrodomain in complex with ADP-ribose-phosphate (ADP-ribose-2'-phosphate, ADPRP)

Biological Source:

Source Organism(s):

Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)

Expression System(s):

Escherichia coli bl21(de3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.05 Å

R-Value Free:

0.21

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 21 21 21

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:NSP3 macrodomain
Gene (Uniprot):rep
Chain IDs:A, B, C, D, E
Chain Length:173
Number of Molecules:5
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTD1 Pfam ID:PF01661 EC:2.7.7.48

Ligand Molecules

A2R

EDO

Primary Citation

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.Show

Acs Med.Chem.Lett. 12 603 609 (2021)

PMID: 33850605 DOI: 10.1021/acsmedchemlett.0c00684

Abstact

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.

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Primary Citation of related structures

Abstact

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