SMTL ID : 7d7l.2 (1 other biounit)

The crystal structure of SARS-CoV-2 papain-like protease in complex with YM155

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.186, C.189, C.221, C.223 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.186, A:C.189, A:C.221, A:C.223

1 x CFF: CAFFEINE(Non-covalent)

CFF.2: 4 residues within 4Å: Chain A: T.262, C.267, G.268, H.269 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.269

3 x GXU: 1-(2-methoxyethyl)-2-methyl-3-(pyrazin-2-ylmethyl)benzo[f]benzimidazol-3-ium-4,9-dione(Non-covalent)

GXU.3: 9 residues within 4Å: Chain A: D.161, P.244, P.245, Y.261, G.263, N.264, Y.265, Y.270, T.298 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.245, A:Y.261, A:Y.261, A:Y.265, A:Y.265 Hydrogen bonds: A:Y.265 Water bridges: A:D.161 GXU.4: 4 residues within 4Å: Chain A: F.66, E.67, H.70 Ligands: SO4.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.66, A:F.66, A:E.67 pi-Stacking: A:F.66, A:H.70, A:H.70 GXU.5: 4 residues within 4Å: Chain A: C.189, Q.192, T.222, C.223 No protein-ligand interaction detected (PLIP)

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

SO4.6: 6 residues within 4Å: Chain A: H.70, N.125, P.126, Q.171, H.172 Ligands: GXU.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.125, A:H.172 Salt bridges: A:H.70, A:H.172 SO4.7: 4 residues within 4Å: Chain A: E.277, T.278, S.290, S.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.277, A:T.278 Salt bridges: A:H.252 SO4.8: 3 residues within 4Å: Chain A: S.290, S.291, E.292 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.291, A:S.291, A:E.292 Water bridges: A:K.289 SO4.9: 2 residues within 4Å: Chain A: R.163, M.205 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., High-throughput screening identifies established drugs as SARS-CoV-2 PLpro inhibitors. Protein Cell (2021)

Release Date

2021-04-21

Peptides

Non-structural protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Non-structural protein 3

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