SMTL ID : 8x1x.1

SARS-CoV-2 Papain like protease (PLpro) in complex with inhibitor Lithocholic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

3 x 4OA: (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid(Non-covalent)

4OA.1: 9 residues within 4Å: Chain A: F.70, H.74, N.129, Q.175, H.176, A.177, N.178, L.179, D.180 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.70, A:H.74 Hydrogen bonds: A:N.129, A:L.179 4OA.2: 2 residues within 4Å: Chain A: N.268, Q.270 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.270 Hydrogen bonds: A:N.268 4OA.3: 10 residues within 4Å: Chain A: Y.214, E.215, K.218, T.258, Y.306, K.307, E.308, N.309, S.310 Ligands: NA.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.214, A:Y.214, A:Y.306 Hydrogen bonds: A:T.258

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: H.18, D.62, T.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.62, A:T.64 GOL.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 4 residues within 4Å: Chain A: K.307, E.308, N.309 Ligands: 4OA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choudhary, S. et al., SARS-CoV-2 Papain like protease (PLpro) in complex with inhibitor Lithocholic acid. To Be Published

Release Date

2025-05-14

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3