SMTL ID : 6wrh.1

The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 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

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

PO4.2: 6 residues within 4Å: Chain A: W.109, N.112, N.113, S.114, G.274, H.275 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.109, A:N.112, A:N.112, A:S.114, A:S.114 Water bridges: A:N.112, A:Y.115 Salt bridges: A:H.275 PO4.3: 2 residues within 4Å: Chain A: H.50, S.52 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.52, A:S.52, A:S.52 Water bridges: A:S.52 Salt bridges: A:H.50 PO4.4: 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.5: 3 residues within 4Å: Chain A: K.129, F.130, Q.136 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: T.13, V.14, D.15, N.18, H.20, E.70 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: S.88, N.91, H.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.88, A:N.91, A:H.92 GOL.8: 6 residues within 4Å: Chain A: D.167, Y.267, N.270, Y.271, Y.276, T.304 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.167, A:Y.271 Water bridges: A:V.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Nat Commun (2021)

Release Date

2020-05-06

Peptides

Non-structural protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 3

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