SMTL ID : 8ds2.1

Structure of SARS-CoV-2 Mpro in complex with the nsp13-nsp14 (C13) cut site sequence (form 2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: R.105, F.134, F.181, Y.182, G.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.105, A:F.181, A:G.183 GOL.2: 9 residues within 4Å: Chain A: M.165, E.166, L.167, P.168, R.188, Q.189, T.190, Q.192 Ligands: GOL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.166, A:T.190, A:T.190, A:Q.192 Water bridges: A:Q.192 GOL.3: 3 residues within 4Å: Chain A: E.166, L.167 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.166, A:L.167 GOL.4: 10 residues within 4Å: Chain A: M.6, A.7, F.8, S.113, Q.127, D.295, R.298 Chain B: S.123, G.124 Ligands: GOL.5 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.123, A:S.113 Water bridges: A:Q.127, A:D.295, A:R.298 GOL.5: 5 residues within 4Å: Chain A: M.6, R.298, Q.299 Chain B: S.123 Ligands: GOL.4 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:S.139 Hydrogen bonds: A:R.298, A:R.298 GOL.7: 6 residues within 4Å: Chain B: W.218, F.219, L.220, N.221, E.270, N.277 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.220 Water bridges: B:N.221, B:E.270, B:G.275 GOL.8: 9 residues within 4Å: Chain B: M.165, E.166, L.167, P.168, R.188, Q.189, T.190, Q.192 Ligands: GOL.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.166, B:R.188, B:T.190, B:Q.192 Water bridges: B:T.190, B:Q.192 GOL.9: 3 residues within 4Å: Chain B: E.166, L.167 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.166, B:L.167, B:Q.189 GOL.10: 5 residues within 4Å: Chain B: D.33, T.98, P.99, K.100, Y.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.98, B:P.99 Water bridges: B:D.33 GOL.11: 8 residues within 4Å: Chain A: S.123, G.124 Chain B: M.6, A.7, F.8, S.113, Q.127, R.298 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.127, B:Q.127, A:S.123 Water bridges: B:R.298 GOL.12: 4 residues within 4Å: Chain B: P.184, A.191, Q.192, A.193 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.193

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

NA.6: 6 residues within 4Å: Chain B: N.221, R.222, F.223, D.263, A.266, S.267 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.221, B:N.221, B:S.267 Water bridges: B:S.267

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
B

B
A

3C-like proteinase nsp5