SMTL ID : 9vao.1

Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.192, C.195, C.227, C.229 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.192, A:C.195, A:C.227, A:C.229

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: H.50, S.52 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.52, A:S.52 Water bridges: A:S.52 Salt bridges: A:H.50 PO4.3: 5 residues within 4Å: Chain A: H.76, N.131, P.132, Q.177, H.178 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.131, A:Q.177 Salt bridges: A:H.76, A:H.178

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: S.88, N.91, H.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.91 Water bridges: A:H.92 GOL.5: 4 residues within 4Å: Chain A: S.296, E.298, Y.299, K.300 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.296, A:K.300, A:K.300 Water bridges: A:S.296, A:E.298, A:E.298 GOL.6: 6 residues within 4Å: Chain A: T.12, Q.22, F.34, V.60, N.63, L.67 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.12, A:T.12, A:Q.22, A:N.63 GOL.7: 4 residues within 4Å: Chain A: V.191, K.221, T.234, Y.236 No protein-ligand interaction detected (PLIP) GOL.8: 5 residues within 4Å: Chain A: D.167, P.251, Y.267, Y.276, T.304 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.167, A:Y.267, A:Y.276 Water bridges: A:V.168, A:Y.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arya, R. et al., Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2. To Be Published

Release Date

2025-06-18

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3