SMTL ID : 8g62.1 (2 other biounits)

Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 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

3 x YOO: 3-methoxy-5-(1-methylpiperidin-4-yl)-N-[4-(pyrrolidine-1-sulfonyl)phenyl]benzamide(Non-covalent)

YOO.2: 10 residues within 4Å: Chain A: G.166, D.167, R.169, M.211, P.250, P.251, Y.267, N.270, Y.271, Y.276 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.251, A:Y.267 Hydrogen bonds: A:R.169, A:Y.276 Salt bridges: A:D.167 pi-Stacking: A:Y.271 pi-Cation interactions: A:Y.267 YOO.3: 11 residues within 4Å: Chain A: G.31, Q.32, Q.33, F.34, G.35, P.36, Y.38, L.61, N.63, G.84 Ligands: ACT.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.36, A:L.61 Hydrogen bonds: A:N.63 YOO.10: 4 residues within 4Å: Chain A: V.69, F.72, E.73, H.76 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.69, A:E.73 pi-Stacking: A:F.72

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: L.123, I.126, Y.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.139

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

CL.5: 3 residues within 4Å: Chain A: K.129, F.130, Q.136 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: F.261, T.262, Y.308, K.309 Ligand excluded by PLIP

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

ACT.7: 4 residues within 4Å: Chain A: Q.22, D.64, L.67 Ligands: ACT.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.67 Hydrogen bonds: A:Q.22, A:D.64 Salt bridges: A:H.20 ACT.8: 6 residues within 4Å: Chain A: S.215, Y.216, E.217, Y.254, T.260, Y.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.216, A:E.217 ACT.9: 6 residues within 4Å: Chain A: T.12, Q.22, F.34, V.60 Ligands: YOO.3, ACT.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.60 Water bridges: A:N.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004. To Be Published

Release Date

2023-02-22

Peptides

Non-structural protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 3

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