SMTL ID : 7rbr.1

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with a Lys48-linked di-ubiquitin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-1-1-mer

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

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

CL.2: 2 residues within 4Å: Chain A: F.130, Q.136 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain A: T.13, V.14, D.15, N.18, H.20, E.70 Ligand excluded by PLIP

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 12 residues within 4Å: Chain A: S.106, S.114, A.117, T.118, L.121, H.275, Y.276, K.277, H.278, I.288, D.289, G.290 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.106, A:H.275, A:G.290 EDO.5: 5 residues within 4Å: Chain B: T.7, L.8, I.36, L.69, L.71 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.8, B:L.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wydorski, P.M. et al., Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin. Nat Commun (2023)

Release Date

2021-09-29

Peptides

Papain-like protease: A
Ubiquitin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Papain-like protease

Ubiquitin

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