SMTL ID : 5y3e.1

Crystal structure of SARS coronavirus papain-like protease in complex with glycerol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.190, C.193, C.225, C.227 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.190, A:C.193, A:C.225, A:C.227

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

NA.2: 4 residues within 4Å: Chain A: K.218, L.235, Y.311, T.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.311, A:T.313, A:T.313 NA.3: 5 residues within 4Å: Chain A: S.116, A.120, A.262, N.263, H.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.262, A:H.276 NA.4: 6 residues within 4Å: Chain A: S.104, S.115, L.119, I.286, D.287, G.288 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.104, A:G.288 NA.5: 3 residues within 4Å: Chain A: Y.72, A.132, A.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.72, A:A.136 NA.6: 7 residues within 4Å: Chain A: R.184, V.206, M.207, Y.208, V.243, M.244, M.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.184, A:R.184, A:V.206, A:M.244

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: Y.252, K.253, L.254, Q.255, T.258, Y.306 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.252, A:Q.255, A:Y.306 Water bridges: A:Y.214, A:D.215, A:D.215 GOL.8: 6 residues within 4Å: Chain A: D.165, P.249, Y.265, N.268, Y.274, T.302 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.268 Water bridges: A:D.165, A:V.166 GOL.9: 5 residues within 4Å: Chain A: W.107, N.110, C.112, G.272, H.273 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.110, A:C.112, A:G.272, A:H.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, M.H. et al., Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes. Antiviral Res. (2017)

Release Date

2018-01-10

Peptides

Replicase polyprotein 1a: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Replicase polyprotein 1a

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