SMTL ID : 8gfr.1

Room temperature X-ray structure of truncated SARS-CoV-2 main protease C145A mutant, residues 1-304, in complex with NBH2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x ZGO: (1R,2S,5S)-N-{(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl}-6,6-dimethyl-3-[3-methyl-N-({1-[(2-methylpropane-2-sulfonyl)methyl]cyclohexyl}carbamoyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide(Non-covalent)

ZGO.1: 20 residues within 4Å: Chain A: H.41, M.49, F.140, L.141, N.142, G.143, S.144, A.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, R.188, Q.189, T.190, A.191, Q.192 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:H.41, A:M.165, A:E.166, A:L.167 Hydrogen bonds: A:F.140, A:G.143, A:S.144, A:A.145, A:H.164, A:E.166, A:E.166, A:E.166, A:Q.189 pi-Stacking: A:H.41 ZGO.2: 20 residues within 4Å: Chain B: H.41, M.49, F.140, L.141, N.142, G.143, S.144, A.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, R.188, Q.189, T.190, A.191, Q.192 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:H.41, B:M.165, B:E.166, B:L.167 Hydrogen bonds: B:F.140, B:G.143, B:S.144, B:A.145, B:H.164, B:E.166, B:E.166, B:E.166, B:E.166, B:Q.189 pi-Stacking: B:H.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovalevsky, A. et al., Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors. J.Biol.Chem. (2023)

Release Date

2023-07-12

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5

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