SMTL ID : 7qg7.1 (1 other biounit)

SARS-CoV-2 macrodomain Nsp3b bound to the remdesivir nucleoside GS-441524

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

1 x U08: (2~{R},3~{R},4~{S},5~{R})-2-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolane-2-carbonitrile(Non-covalent)

U08.1: 15 residues within 4Å: Chain A: A.22, D.23, I.24, G.49, V.50, A.53, L.127, A.130, G.131, A.155, V.156, F.157, D.158, L.161 Ligands: EDO.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.50 Hydrogen bonds: A:D.23, A:I.24, A:A.130, A:G.131, A:F.157, A:D.158 Water bridges: A:S.129, A:A.130

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 8 residues within 4Å: Chain A: S.6, F.7, S.8, Y.10, K.20, E.27, K.30, V.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.8, A:E.27 Water bridges: A:K.30 EDO.3: 4 residues within 4Å: Chain A: G.131, D.158, L.161 Ligands: U08.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.131, A:D.158, A:D.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsika, A.C. et al., Binding Adaptation of GS-441524 Diversifies Macro Domains and Downregulates SARS-CoV-2 de-MARylation Capacity. J.Mol.Biol. (2022)

Release Date

2021-12-15

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3

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