SMTL ID : 7lg7.1

Crystal structure of CoV-2 Nsp3 Macrodomain complex with PARG345

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x XYJ: 3-[(1,3-dimethyl-2,6-dioxo-2,3,6,9-tetrahydro-1H-purin-8-yl)sulfanyl]-N-{[2-(morpholin-4-yl)ethyl]sulfonyl}propanamide(Non-covalent)

XYJ.1: 17 residues within 4Å: Chain A: D.22, I.23, A.38, N.40, K.44, G.47, G.48, V.49, A.50, L.126, S.128, A.129, G.130, I.131, F.132, A.154, F.156 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.38, A:V.49 Hydrogen bonds: A:I.23, A:N.40, A:L.126, A:S.128, A:A.129, A:G.130, A:F.132 Water bridges: A:N.40, A:G.46, A:V.49, A:I.131, A:I.131, A:A.154

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: G.47, G.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.48 SO4.3: 3 residues within 4Å: Chain A: S.7, G.8, Y.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.8, A:Y.9 SO4.4: 1 residues within 4Å: Chain A: Y.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.68 SO4.5: 2 residues within 4Å: Chain A: S.84, H.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.84 Water bridges: A:H.86 Salt bridges: A:H.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brosey, C.A. et al., Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors. Prog.Biophys.Mol.Biol. (2021)

Release Date

2021-02-17

Peptides

Non-structural protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 3

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