SMTL ID : 7ybg.1

Crystal structure of the SARS-CoV-2 papain-like protease (C111S mutant)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.1: 9 residues within 4Å: Chain A: L.165, G.166, D.167, P.251, Y.267, Y.271, Q.272, Y.276, T.304 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.167, A:D.167, A:Q.272, A:Y.276

1 x MLA: MALONIC ACID(Non-covalent)

MLA.2: 7 residues within 4Å: Chain A: W.109, N.112, N.113, S.114, G.274, H.275 Ligands: NA.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.112 Hydrogen bonds: A:W.109, A:S.114, A:G.274, A:Y.276 Salt bridges: A:H.275, A:H.275

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.192, C.195, C.227, C.229 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.192, A:C.195, A:C.227, A:C.229

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

NA.4: 4 residues within 4Å: Chain A: N.112, S.114, Y.115 Ligands: MLA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.114, A:S.114, A:Y.115 NA.5: 4 residues within 4Å: Chain A: S.88, A.89, T.161, V.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.88, A:V.162 Water bridges: A:A.89

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

CL.6: 3 residues within 4Å: Chain A: K.129, F.130, Q.136 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, R. et al., Crystal structure of the SARS-CoV-2 papain-like protease (C111S mutant). To Be Published

Release Date

2023-07-19

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3