SMTL ID : 7nfv.1

Structure of SARS-CoV-2 Papain-like protease PLpro

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.189, C.192, C.224, C.226 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.189, A:C.192, A:C.224, A:C.226

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: L.162, G.163, D.164, Y.264, Y.273, T.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.273 Water bridges: A:V.165

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: K.126, F.127, Q.133 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: F.258, T.259, Y.305, K.306 Ligand excluded by PLIP

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

PO4.4: 5 residues within 4Å: Chain A: H.73, N.128, P.129, Q.174, H.175 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.128 Water bridges: A:N.128, A:Q.174, A:A.176 Salt bridges: A:H.73, A:H.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srinivasan, V. et al., Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease. Commun Biol (2022)

Release Date

2021-02-24

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Papain-like protease nsp3

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