SMTL ID : 7kxb.1

Crystal structure of SARS-CoV-2 Nsp3 Macrodomain complex with PARG329

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x XB1: N-{3-[(1,3-dimethyl-2,6-dioxo-2,3,6,9-tetrahydro-1H-purin-8-yl)sulfanyl]propyl}-N'-[2-(morpholin-4-yl)ethyl]thiourea(Non-covalent)

XB1.1: 20 residues within 4Å: Chain A: A.21, D.22, I.23, A.38, A.39, N.40, K.44, G.46, G.47, G.48, V.49, A.50, L.126, S.128, A.129, G.130, I.131, F.132, A.154, F.156 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.49 Hydrogen bonds: A:I.23, A:G.46, A:G.47, A:G.130 Water bridges: A:N.40, A:V.49, A:V.49, A:A.129, A:I.131, A:I.131, A:F.156, A:F.156

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 3 residues within 4Å: Chain A: K.55, N.58, N.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.58

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

SO4.3: 2 residues within 4Å: Chain A: S.7, G.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.8 Water bridges: A:Y.9, A:Y.9 SO4.4: 3 residues within 4Å: Chain A: S.7, K.19, K.29 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.19, A:K.29 SO4.5: 2 residues within 4Å: Chain A: G.47, G.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.48

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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