SMTL ID : 9azx.1 (2 other biounits)

Crystal structure of SARS-CoV-2 (Covid-19) Nsp3 macrodomain in complex with NDPr

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

1 x 01: {(2R,3S,4R,5R)-5-[(8S)-4-aminopyrrolo[2,1-f][1,2,4]triazin-7-yl]-5-cyano-3,4-dihydroxyoxolan-2-yl}methyl [(2R,3S,4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methyl dihydrogen diphosphate

01.1: 30 residues within 4Å: Chain A: A.21, D.22, I.23, V.24, A.38, A.39, N.40, K.44, H.45, G.46, G.47, G.48, V.49, A.50, G.51, A.52, P.125, L.126, L.127, S.128, A.129, G.130, I.131, F.132, G.133, A.154, V.155, F.156, D.157, L.160 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.49 Hydrogen bonds: A:D.22, A:D.22, A:I.23, A:N.40, A:G.46, A:G.46, A:G.48, A:V.49, A:A.50, A:S.128, A:A.129, A:G.130, A:I.131, A:F.132, A:F.156, A:D.157 Water bridges: A:H.45, A:L.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peng, K. et al., GS-441524-Diphosphate-Ribose Derivatives as Nanomolar Binders and Fluorescence Polarization Tracers for SARS-CoV-2 and Other Viral Macrodomains. Acs Chem.Biol. (2024)

Release Date

2024-05-01

Peptides

Non-structural protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 3

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