SMTL ID : 8drw.7 (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

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

NA.1: 5 residues within 4Å: Chain A: N.221, F.223, D.263, A.266, S.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.221, A:D.263, A:D.263, A:S.267 NA.5: 5 residues within 4Å: Chain B: N.221, F.223, D.263, M.264, S.267 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.267

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

1PE.2: 7 residues within 4Å: Chain A: M.6, F.8, F.294, D.295, R.298 Chain B: Y.118, S.123 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:M.6, A:R.298, A:R.298, A:R.298, B:S.123 1PE.8: 6 residues within 4Å: Chain A: Y.118, S.123 Chain B: M.6, F.8, D.295, R.298 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.298, B:R.298

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

PEG.3: 9 residues within 4Å: Chain A: M.17, V.18, Q.19, Q.69, A.70, G.71, N.119, G.120, S.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.71 PEG.6: 3 residues within 4Å: Chain B: A.255, Q.256, G.258 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.256 PEG.7: 11 residues within 4Å: Chain A: K.5, A.7, V.125, Y.126, Q.127 Chain B: R.4, K.5, A.7, V.125, Y.126, Q.127 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.4, B:K.5, B:Q.127, A:Q.127 PEG.9: 6 residues within 4Å: Chain A: R.4 Chain B: R.131, K.137, E.288, D.289, E.290 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.4, B:K.137

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

PO4.4: 3 residues within 4Å: Chain A: S.62, N.63, H.64 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.63, A:N.63, A:H.64 Salt bridges: A:H.64

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
M

B
N

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

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