SMTL ID : 7lfv.1 (1 other biounit)

Crystal structure of the SARS CoV-1 Papain-like protease in complex with peptide inhibitor VIR251

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

monomer

Ligands

1 x ACY- 73O- DPP- GLY- GVE: Papain-like protease peptide inhibitor VIR251(Non-covalent)

ACY-73O-DPP-GLY-GVE.1: 17 residues within 4Å: Chain A: W.107, N.110, C.112, Y.113, L.163, G.164, D.165, E.168, P.248, P.249, Y.265, Y.269, Q.270, C.271, G.272, H.273, Y.274 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.249, A:Y.265 Hydrogen bonds: A:G.164, A:G.164, A:D.165, A:Y.265, A:Y.265, A:Y.269, A:G.272, A:G.272 Water bridges: A:Y.269 Salt bridges: A:H.273 pi-Stacking: A:Y.269

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.190, C.193, C.225, C.227 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.225, A:C.227

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

EDO.3: 4 residues within 4Å: Chain A: H.48, N.50, H.51, K.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.48, A:K.54 Water bridges: A:N.50 EDO.4: 3 residues within 4Å: Chain A: L.17, H.18, T.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.18, A:T.19, A:T.19 EDO.5: 5 residues within 4Å: Chain A: F.57, M.85, L.88, N.147 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.147 Water bridges: A:G.39 EDO.6: 4 residues within 4Å: Chain A: N.14, R.139, N.147 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.14, A:N.147 EDO.7: 4 residues within 4Å: Chain A: T.27, G.29, Q.30, T.43 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.27, A:T.27, A:Q.30 EDO.8: 4 residues within 4Å: Chain A: H.90, K.93, W.94, D.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.90 EDO.9: 3 residues within 4Å: Chain A: S.86, N.89, H.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.89 EDO.10: 5 residues within 4Å: Chain A: A.69, F.70, T.75, D.77, E.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.69, A:E.78 Water bridges: A:F.70 EDO.11: 4 residues within 4Å: Chain A: T.75, L.76, Y.155, H.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.76 EDO.12: 4 residues within 4Å: Chain A: R.167, T.171, V.203, M.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.167, A:T.171 EDO.13: 7 residues within 4Å: Chain A: Q.123, L.124, E.125, S.241, F.242, L.260, K.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.125, A:K.307 EDO.14: 5 residues within 4Å: Chain A: T.10, H.18, Q.20, D.62, L.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.10

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.15: 2 residues within 4Å: Chain A: N.50, K.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.50 Salt bridges: A:K.54 SO4.16: 4 residues within 4Å: Chain A: K.106, W.107, A.289, H.290 3 PLIP interactions: 3 interactions with chain A Water bridges: A:W.107 Salt bridges: A:K.106, A:H.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patchett, S. et al., A molecular sensor determines the ubiquitin substrate specificity of SARS-CoV-2 papain-like protease. Cell Rep (2021)

Release Date

2021-11-10

Peptides

papain-like protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

papain-like protease

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