SMTL ID : 7kg3.1

Crystal structure of CoV-2 Nsp3 Macrodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 5 residues within 4Å: Chain A: D.22, I.23, G.48, A.52, F.156 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.52 Hydrogen bonds: A:I.23 MLI.2: 2 residues within 4Å: Chain A: Y.68, C.81 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.68

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 10 residues within 4Å: Chain A: A.38, A.39, N.40, K.44, A.50, S.128, A.129, G.130, I.131, F.132 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.40, A:S.128, A:G.130, A:F.132 Water bridges: A:G.46, A:V.49, A:A.129, A:A.129, A:I.131

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: L.140, R.141, L.164, V.165, S.167 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.165

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

SO4.5: 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 SO4.6: 3 residues within 4Å: Chain A: S.7, K.19, K.29 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.7 Salt bridges: A:K.19, A:K.29 SO4.7: 2 residues within 4Å: Chain A: G.47, G.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.48 Water bridges: A:G.47

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

2020-10-28

Peptides

Non-structural protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 3

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