SMTL ID : 7d7k.2 (1 other biounit)

The crystal structure of SARS-CoV-2 papain-like protease in apo form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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: 5 residues within 4Å: Chain A: W.103, T.262, C.267, G.268, H.269 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.269

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

EDO.3: 6 residues within 4Å: Chain A: L.117, I.120, E.121, L.122, F.124, Y.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.120, A:L.122 Water bridges: A:L.122, A:F.124 EDO.4: 3 residues within 4Å: Chain A: Q.130, D.131, Y.134 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.134 EDO.5: 4 residues within 4Å: Chain A: D.161, P.245, Y.261, Y.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.161 EDO.6: 3 residues within 4Å: Chain A: S.290, S.291, E.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.291, A:E.292 EDO.7: 3 residues within 4Å: Chain A: Q.118, Q.119, I.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.120 EDO.10: 8 residues within 4Å: Chain A: N.106, S.108, Y.109, L.159, G.160, Y.261, G.268, Y.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.106, A:G.160, A:Y.261

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

SO4.8: 5 residues within 4Å: Chain A: H.70, N.125, P.126, Q.171, H.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.125 Salt bridges: A:H.70, A:H.172 SO4.9: 3 residues within 4Å: Chain A: Q.171, G.198, V.199 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.199 Water bridges: A:Q.171, A:D.176, A:K.197, A:E.200

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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