SMTL ID : 7ofu.1

Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 3, 4-Dihydroxybenzoic acid, methyl ester

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

2 x HE9: methyl 3,4-bis(oxidanyl)benzoate(Non-covalent)

HE9.1: 5 residues within 4Å: Chain A: F.69, E.70, H.73 Chain B: E.203 Ligands: PO4.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.69 Hydrogen bonds: A:E.70 Salt bridges: A:H.73 pi-Stacking: A:H.73 HE9.10: 5 residues within 4Å: Chain A: E.203 Chain B: F.69, E.70, H.73 Ligands: PO4.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.69 Hydrogen bonds: B:E.70 Salt bridges: B:H.73 pi-Stacking: B:H.73

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: S.85, N.88, H.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.88, A:H.89 GOL.3: 7 residues within 4Å: Chain A: T.9, Q.19, Q.30, F.31, V.57, N.60, L.64 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.9, A:Q.19, A:N.60 Water bridges: A:N.60 GOL.11: 3 residues within 4Å: Chain B: S.85, N.88, H.89 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.88, B:H.89 GOL.12: 7 residues within 4Å: Chain B: T.9, Q.19, Q.30, F.31, V.57, N.60, L.64 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.9, B:T.9, B:N.60 Water bridges: B:Q.19, B:N.60

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.189, C.192, C.224, C.226 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.189, A:C.192, A:C.224, A:C.226 ZN.13: 4 residues within 4Å: Chain B: C.189, C.192, C.224, C.226 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.189, B:C.192, B:C.224, B:C.226

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

PO4.5: 7 residues within 4Å: Chain A: H.73, N.128, P.129, Q.174, H.175 Chain B: E.203 Ligands: HE9.1 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.128, B:E.203, B:E.203, B:E.203 Salt bridges: A:H.73, A:H.175 PO4.6: 6 residues within 4Å: Chain A: G.163, D.164, Y.264, N.267, Y.273 Chain B: R.65 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.164, A:Y.264 Water bridges: B:R.65 Salt bridges: B:R.65 PO4.7: 2 residues within 4Å: Chain A: H.47, S.49 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.49, A:S.49, A:S.49 Salt bridges: A:H.47 PO4.8: 1 residues within 4Å: Chain A: H.255 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.255, A:S.294 Salt bridges: A:H.255 PO4.14: 7 residues within 4Å: Chain A: E.203 Chain B: H.73, N.128, P.129, Q.174, H.175 Ligands: HE9.10 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.128, A:E.203, A:E.203 Water bridges: B:H.73, B:H.73 Salt bridges: B:H.73, B:H.175 PO4.15: 6 residues within 4Å: Chain A: R.65 Chain B: G.163, D.164, Y.264, N.267, Y.273 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.164, B:D.164, B:Y.264, B:Y.273 Water bridges: A:R.65 Salt bridges: A:R.65 PO4.16: 2 residues within 4Å: Chain B: H.47, S.49 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.49, B:S.49, B:S.49 Salt bridges: B:H.47 PO4.17: 1 residues within 4Å: Chain B: H.255 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.294 Salt bridges: B:H.255

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

CL.9: 3 residues within 4Å: Chain A: K.126, F.127, Q.133 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: K.126, F.127, Q.133 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srinivasan, V. et al., Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease. Commun Biol (2022)

Release Date

2021-05-12

Peptides

Papain-like protease nsp3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Papain-like protease nsp3

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