SMTL ID : 9ez4.1

Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp5/6 substrate peptide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: V.35, G.79, H.80, S.81, K.88, K.90 No protein-ligand interaction detected (PLIP) EDO.2: 6 residues within 4Å: Chain A: Y.118, N.119, L.141, N.142 Chain B: S.301, G.302 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.119 EDO.3: 6 residues within 4Å: Chain A: R.131, K.137, D.197, T.198, T.199, D.289 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.137 EDO.4: 6 residues within 4Å: Chain A: G.2, F.3, R.4, L.282, G.283 Chain B: K.137 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain A: K.137 Chain B: G.2, F.3, R.4, L.282, G.283 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.3

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 10 residues within 4Å: Chain A: E.14, G.15, C.16, M.17, V.18, W.31, A.70, G.71, N.95, K.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.97 Water bridges: A:G.71 PEG.7: 5 residues within 4Å: Chain B: Y.118, N.119, S.123, L.141, N.142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.119

1 x GLN: GLUTAMINE(Non-covalent)

GLN.8: 12 residues within 4Å: Chain A: S.1 Chain B: F.140, L.141, N.142, G.143, S.144, A.145, H.163, H.164, M.165, E.166, H.172 5 PLIP interactions: 5 interactions with chain B, Hydrogen bonds: B:F.140, B:G.143, B:A.145, B:H.163, B:H.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fornasier, E. et al., Allostery in homodimeric SARS-CoV-2 main protease. Commun Biol (2024)

Release Date

2025-02-12

Peptides

Replicase polyprotein 1a: A
Non-structural protein 7: B
GLY-VAL-THR-PHE-GLN-SER-ALA-VAL: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Replicase polyprotein 1a

Non-structural protein 7

GLY-VAL-THR-PHE-GLN-SER-ALA-VAL

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