SMTL ID : 7qcj.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: H.17, Q.19, D.61, T.63, L.64 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.17, A:Q.19, A:Q.19, A:D.61 GOL.2: 4 residues within 4Å: Chain A: M.84, S.85, N.88, H.89 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.85, A:S.85, A:N.88, A:H.89 Water bridges: A:S.85 GOL.3: 3 residues within 4Å: Chain A: H.47, N.48, S.49 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.48, A:N.48, A:S.49, A:S.49 GOL.4: 3 residues within 4Å: Chain A: Q.133, D.134, Y.137 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.130, A:Q.133, A:Q.133 GOL.6: 10 residues within 4Å: Chain A: T.9, H.17, Q.19, Q.30, F.31, V.57, N.60, D.61, L.64 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.9, A:Q.19, A:F.31, A:N.60

1 x A4O: N-(2,4-dihydroxybenzylidene)-thiosemicarbazone(Non-covalent)

A4O.5: 13 residues within 4Å: Chain A: L.58, P.59, R.65, A.68, F.69, Y.72, T.74, T.75, D.76, P.77, F.79, L.80 Ligands: PO4.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.59, A:A.68 Hydrogen bonds: A:R.65, A:R.65, A:F.79, A:L.80

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 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

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

PO4.8: 5 residues within 4Å: Chain A: H.73, N.128, P.129, Q.174, H.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.128 Salt bridges: A:H.73, A:H.175 PO4.9: 3 residues within 4Å: Chain A: R.65, P.77 Ligands: A4O.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.65 PO4.10: 4 residues within 4Å: Chain A: A.39, N.88, K.91, K.92 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.88, A:N.88, A:N.88 Salt bridges: A:K.91, A:K.92

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

CL.11: 4 residues within 4Å: Chain A: H.89, K.92, W.93, D.108 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: K.126, F.127, Q.133, Y.136 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: H.255 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: K.94, P.96, K.105, A.288 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: F.258, T.259, Y.305, K.306 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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