SMTL ID : 6ywm.3 (2 other biounits)

Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with MES

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

monomer

Ligands

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

MES.1: 9 residues within 4Å: Chain A: A.39, N.41, K.45, A.51, S.129, A.130, G.131, I.132, F.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.41, A:S.129, A:G.131, A:F.133 Water bridges: A:V.50

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.158 Ligands: EDO.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.158, H2O.1

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

EDO.3: 4 residues within 4Å: Chain A: D.158, N.160, L.161 Ligands: MG.2 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: N.118, Q.119, E.121, T.150 No protein-ligand interaction detected (PLIP) EDO.5: 1 residues within 4Å: Chain A: R.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.149, A:R.149 EDO.6: 6 residues within 4Å: Chain A: A.22, D.23, I.24, A.155, V.156, F.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.24, A:F.157 Water bridges: A:D.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, X. et al., Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain. Acs Med.Chem.Lett. (2021)

Release Date

2020-05-06

Peptides

NSP3 macrodomain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

NSP3 macrodomain

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