SMTL ID : 8dru.3 (3 other biounits)

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp7-nsp8 (C7) cut site sequence

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: R.40, P.52, N.53, Y.54, E.55 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:P.52, A:Y.54, A:E.55, A:E.55, A:E.55 Water bridges: A:R.40 Salt bridges: A:R.40 PO4.5: 3 residues within 4Å: Chain A: K.5 Chain B: R.4, K.5 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.5, B:R.4 Hydrogen bonds: B:K.5

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

PEG.2: 2 residues within 4Å: Chain A: N.84, C.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.84 PEG.3: 2 residues within 4Å: Chain A: Y.101, F.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.101 PEG.4: 5 residues within 4Å: Chain A: Q.19, T.21, T.26, L.67, Q.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.19, A:Q.69 PEG.6: 4 residues within 4Å: Chain A: Y.118, N.142 Chain B: R.298, R.302 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.298, B:R.302, B:R.302 PEG.7: 3 residues within 4Å: Chain B: Y.101, K.102, F.103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.103

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

2022-09-21

Peptides

Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
F

Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site

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