SMTL ID : 8fwn.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: W.107, N.110, N.111, S.112, G.272, H.273 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.110, A:S.112, A:S.112, A:S.112, A:S.112 Water bridges: A:Y.113, A:H.273 Salt bridges: A:H.273 PO4.4: 5 residues within 4Å: Chain A: H.74, N.129, P.130, Q.175, H.176 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.129 Water bridges: A:N.129 Salt bridges: A:H.74, A:H.176 PO4.5: 2 residues within 4Å: Chain A: H.48, S.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.50 Water bridges: A:S.50 Salt bridges: A:H.48

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: D.165, Y.265, N.268, Y.269, Y.274, T.302 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.269, A:Y.274 Water bridges: A:D.165, A:V.166 GOL.3: 3 residues within 4Å: Chain A: S.86, N.89, H.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.86, A:N.89 GOL.7: 4 residues within 4Å: Chain A: H.90, K.93, W.94, D.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.90, A:D.109 GOL.8: 6 residues within 4Å: Chain A: H.18, Q.20, D.62, T.64, L.65 Ligands: ACT.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.18, A:Q.20, A:Q.20 Water bridges: A:T.64

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 5 residues within 4Å: Chain A: Q.31, F.32, V.58, N.61 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.32 Hydrogen bonds: A:N.61

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 4 residues within 4Å: Chain A: C.190, C.193, C.225, C.227 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.190, A:C.193, A:C.225, A:C.227

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

CL.10: 5 residues within 4Å: Chain A: T.11, V.12, D.13, N.16, E.68 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bezerra, E.H.S. et al., Crystal structure of SARS-CoV-2 papain-like protease C111S mutant. To Be Published

Release Date

2023-05-17

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3