SMTL ID : 8drw.4 (6 other biounits)

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp9-nsp10 (C9) cut site sequence

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

homo-dimer

Ligands

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

1PE.1: 7 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, D.295, R.298 Chain B: S.123 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.123, B:S.123, A:D.295 Water bridges: A:R.298 1PE.6: 7 residues within 4Å: Chain A: Y.118, S.123 Chain B: M.6, A.7, F.8, D.295, R.298 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.118, A:Y.118, A:S.123, B:R.298 1PE.7: 7 residues within 4Å: Chain B: N.63, I.78, G.79, H.80, S.81, K.88, K.90 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.63, B:H.80, B:K.90 1PE.9: 3 residues within 4Å: Chain B: R.40, N.84, V.186 No protein-ligand interaction detected (PLIP)

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

PEG.2: 10 residues within 4Å: Chain A: R.4, K.5, A.7, Y.126, Q.127 Chain B: K.5, V.125, Y.126, Q.127 Ligands: PO4.13 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.127, A:R.4, A:Q.127 PEG.8: 3 residues within 4Å: Chain B: D.92, T.93, A.94 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.94 PEG.10: 3 residues within 4Å: Chain B: P.108, H.246, F.294 No protein-ligand interaction detected (PLIP)

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

PO4.3: 3 residues within 4Å: Chain A: S.62, N.63, H.64 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.62, A:N.63, A:H.64 Salt bridges: A:H.64 PO4.4: 2 residues within 4Å: Chain A: L.27, N.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.142, A:N.142 PO4.11: 3 residues within 4Å: Chain B: S.62, N.63, H.64 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.63, B:N.63, B:H.64 Salt bridges: B:H.64 PO4.12: 5 residues within 4Å: Chain B: T.25, L.27, H.41, M.49, N.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.142, B:G.143 PO4.13: 4 residues within 4Å: Chain A: K.5 Chain B: R.4, K.5 Ligands: PEG.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.5, A:Q.127 Salt bridges: B:R.4, A:K.5

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

NA.5: 7 residues within 4Å: Chain B: N.221, R.222, F.223, T.224, D.263, A.266, S.267 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.263

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 nsp9-nsp10 (C9) cut site: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site

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