SMTL ID : 7oft.1

Structure of SARS-CoV-2 Papain-like protease PLpro in complex with p-hydroxybenzaldehyde

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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

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

CL.2: 3 residues within 4Å: Chain A: K.126, F.127, Q.133 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.4: 3 residues within 4Å: Chain A: E.143, A.144, A.145 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: G.201, V.202 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: K.157, G.163, D.164, E.167 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: H.73, N.128, P.129, H.175 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: I.44, K.45 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: Q.97, G.100 Ligand excluded by PLIP

1 x HBA: P-HYDROXYBENZALDEHYDE(Non-covalent)

HBA.10: 9 residues within 4Å: Chain A: T.10, V.11, Y.56, V.57, P.59, 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.57 Water bridges: A:L.80

2 x K: POTASSIUM ION(Non-covalent)

K.11: 2 residues within 4Å: Chain A: D.179 Ligands: K.12 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.179, H2O.3, H2O.9, H2O.11 K.12: 4 residues within 4Å: Chain A: N.128, Q.174, A.176 Ligands: K.11 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:A.176, H2O.4, H2O.4, H2O.5, H2O.8, H2O.11

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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