SMTL ID : 8uvm.4 (3 other biounits)

SARS-CoV-2 papain-like protease (PLpro) complex with covalent inhibitor Jun11313

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

monomer

Ligands

1 x Y3R: ethyl 4-oxo-4-(2-{3-[2-({(1S)-1-[(3P)-3-(thiophen-3-yl)phenyl]ethyl}carbamoyl)phenyl]propanoyl}hydrazinyl)butanoate(Covalent)

Y3R.1: 18 residues within 4Å: Chain A: W.109, N.112, N.113, C.114, Y.115, L.165, G.166, D.167, E.170, P.250, P.251, Y.267, Y.271, Q.272, G.274, H.275, Y.276, T.304 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.109, A:D.167, A:P.250, A:P.251, A:Y.267, A:Y.267, A:Y.267, A:Y.271, A:Y.271 Hydrogen bonds: A:C.114, A:G.166, A:G.166, A:D.167, A:Q.272, A:G.274, A:G.274 Salt bridges: A:H.275 pi-Stacking: A:Y.271

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

SO4.2: 5 residues within 4Å: Chain A: H.76, N.131, P.132, Q.177, H.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.131 Salt bridges: A:H.76, A:H.178

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

CL.3: 2 residues within 4Å: Chain A: S.296, S.297 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: K.129, F.130, Q.136, Y.139 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.192, C.195, C.227, C.229 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.192, A:C.195, A:C.227, A:C.229, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, B. et al., Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model. Science (2024)

Release Date

2024-04-03

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Papain-like protease nsp3

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