SMTL ID : 8drz.1 (3 other biounits)

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp13-nsp14 (C13) cut site sequence

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: R.4, K.5 Chain B: R.4, K.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.4, B:R.4, B:K.5, A:R.4, A:K.5 PEG.3: 5 residues within 4Å: Chain A: K.61, S.62, N.63, H.64, H.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.63, A:H.64 PEG.7: 2 residues within 4Å: Chain A: A.255, Q.256 No protein-ligand interaction detected (PLIP)

5 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 3 residues within 4Å: Chain A: R.60, K.61, N.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.61, A:K.61, A:N.65 Water bridges: A:S.62 TRS.5: 4 residues within 4Å: Chain A: R.40, M.82, N.84, C.85 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.40, A:R.40 Water bridges: A:Y.54, A:N.84 TRS.6: 3 residues within 4Å: Chain A: G.278, R.279, T.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.279, A:R.279, A:T.280, A:T.280 TRS.9: 4 residues within 4Å: Chain B: R.60, K.61, H.64, N.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.60, B:K.61, B:N.65 TRS.10: 3 residues within 4Å: Chain B: S.62, N.63, H.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.63, B:N.63, B:H.64

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 7 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, R.298 Chain B: S.123, L.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.127 Water bridges: A:M.6 1PE.11: 5 residues within 4Å: Chain B: R.40, E.55, N.84, V.186, R.188 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.40, B:R.40, B:R.188, B:R.188 Water bridges: B:N.84, B:D.187

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

NA.8: 1 residues within 4Å: Chain B: S.46 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.46, B:S.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J. et al., X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun (2022)

Release Date

2022-09-28

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5

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