SMTL ID : 7qci.1

Structure of SARS-CoV-2 Papain-like Protease bound to N-(3,4-dihydroxybenzylidene)-thiosemicarbazone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

1 x A6Q: N-(3,4-dihydroxybenzylidene)-thiosemicarbazone(Non-covalent)

A6Q.1: 13 residues within 4Å: Chain A: L.58, P.59, R.65, V.66, A.68, F.69, Y.72, T.74, T.75, D.76, P.77, F.79, L.80 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.59, A:A.68, A:T.75 Hydrogen bonds: A:R.65, A:D.76, A:F.79, A:L.80

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: S.85, N.88, H.89 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.85, A:N.88, A:H.89 Water bridges: A:G.38 GOL.3: 6 residues within 4Å: Chain A: T.9, H.17, Q.19, D.61, T.63, L.64 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.17, A:Q.19, A:D.61, A:T.63 Water bridges: A:T.9

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: C.189, T.191, C.192, C.224, C.226, K.228 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.189, A:C.192, A:C.224, A:C.226

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

PO4.5: 5 residues within 4Å: Chain A: H.73, N.128, P.129, Q.174, H.175 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.128 Water bridges: A:N.128, A:Q.174, A:H.175 Salt bridges: A:H.73, A:H.175 PO4.6: 8 residues within 4Å: Chain A: L.162, G.163, D.164, P.248, Y.264, Y.268, Y.273, T.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.273 PO4.7: 6 residues within 4Å: Chain A: H.89, K.92, W.93, A.107, D.108, V.159 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.93, A:D.108, A:D.108 Water bridges: A:K.92 Salt bridges: A:H.89 PO4.8: 1 residues within 4Å: Chain A: E.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.1 PO4.9: 1 residues within 4Å: Chain A: H.255 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.255 Salt bridges: A:H.255

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

CL.10: 4 residues within 4Å: Chain A: K.126, F.127, Q.133, Y.136 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ewert, W. et al., Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease. Front Chem (2022)

Release Date

2022-03-16

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3

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