SMTL ID : 7jit.1

The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder495 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x Y95: 5-[(carbamoylcarbamoyl)amino]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide(Non-covalent)

Y95.1: 12 residues within 4Å: Chain A: L.165, G.166, D.167, E.170, P.250, P.251, Y.267, Y.271, Q.272, Y.276, T.304 Ligands: ACT.11 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:D.167, A:P.250, A:P.251, A:Y.267, A:Y.267, A:Y.271, A:Y.271, A:T.304 Hydrogen bonds: A:D.167, A:E.170, A:E.170, A:Y.271, A:Y.271, A:Q.272, A:Q.272, A:Y.276 pi-Stacking: A:Y.271, A:Y.271

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 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 ZN.3: 3 residues within 4Å: Chain A: H.20, T.66, E.70 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.20, A:E.70, A:E.70, H2O.8, H2O.8 ZN.4: 2 residues within 4Å: Chain A: H.92, D.111 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.92, A:D.111, H2O.6 ZN.5: 3 residues within 4Å: Chain A: H.76 Ligands: CL.7, CL.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76

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

CL.6: 6 residues within 4Å: Chain A: T.13, V.14, D.15, N.18, H.20, E.70 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.5, CL.8 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.5, CL.7 Ligand excluded by PLIP

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.9: 3 residues within 4Å: Chain A: A.42, D.43, N.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.43, A:N.91

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

ACT.10: 7 residues within 4Å: Chain A: W.109, N.112, N.113, S.114, L.165, G.274, H.275 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.112, A:L.165 Hydrogen bonds: A:N.112, A:S.114, A:S.114 Salt bridges: A:H.275 ACT.11: 6 residues within 4Å: Chain A: D.167, R.169, E.170, M.211, Y.271 Ligands: Y95.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.170 Water bridges: A:R.169 Salt bridges: A:R.169

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

2020-08-05

Peptides

Papain-like protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease

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