SMTL ID : 9n6n.1

Room Temperature X-Ray Structure of SARS-CoV-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Pomotrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x ZQB: Pomotrelvir bound form(Covalent)

ZQB.1: 16 residues within 4Å: Chain A: H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, T.168, H.171, D.186, R.187 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.140, A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166 ZQB.3: 16 residues within 4Å: Chain B: H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, T.168, H.171, D.186, R.187 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:F.140, B:G.143, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:E.166

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

NA.2: 6 residues within 4Å: Chain A: N.220, R.221, F.222, D.262, A.265, S.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.220, A:D.262 NA.4: 6 residues within 4Å: Chain B: N.220, R.221, F.222, D.262, A.265, S.266 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.220, B:S.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhandari, D. et al., Characterization of an unusual SARS-CoV-2 main protease natural variant exhibiting resistance to nirmatrelvir and ensitrelvir. Commun Biol (2025)

Release Date

2025-07-30

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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