SMTL ID : 7ofs.1

Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 4-(2-hydroxyethyl)phenol

Coordinates

PDB Format Compare

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.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

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

CL.2: 4 residues within 4Å: Chain A: K.126, F.127, Q.133, Y.136 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: F.258, T.259, Y.305, K.306 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: K.157, G.163, D.164, E.167 Ligand excluded by PLIP

1 x YRL: 4-(2-hydroxyethyl)phenol(Non-covalent)

YRL.4: 10 residues within 4Å: Chain A: T.10, V.11, Y.56, V.57, P.59, A.68, Y.72, T.74, F.79, L.80 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.11, A:P.59, A:Y.72, A:L.80, A:L.80 Hydrogen bonds: A:V.11, A:V.57

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

PO4.6: 5 residues within 4Å: Chain A: H.73, N.128, P.129, Q.174, H.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.128 Salt bridges: A:H.73, A:H.175

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: S.85, N.88, H.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.88

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

2021-05-12

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3

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