SMTL ID : 9epl.1

Mpro from SARS-CoV-2 with 298Q mutation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, D.295, Q.298, Q.299 Chain B: S.123, G.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.295, A:D.295 Water bridges: A:Q.127 GOL.6: 9 residues within 4Å: Chain A: S.123, G.124 Chain B: M.6, A.7, F.8, Q.127, D.295, Q.298, Q.299 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.295 Water bridges: B:Q.127

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: R.40, P.52, N.53, Y.54, E.55, D.56, M.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.54, A:E.55, A:E.55 EDO.7: 7 residues within 4Å: Chain B: R.40, P.52, N.53, Y.54, E.55, D.56, M.82 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.54, B:E.55

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

NA.3: 7 residues within 4Å: Chain A: S.284, A.285, L.286 Chain B: S.284, A.285, L.286 Ligands: NA.8 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.284, B:L.286, A:S.284, A:S.284, A:L.286 NA.8: 7 residues within 4Å: Chain A: S.284, A.285, L.286 Chain B: S.284, A.285, L.286 Ligands: NA.3 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.284, B:S.284, B:L.286, A:S.284, A:L.286

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: V.297, Q.298, Q.299, C.300 Chain B: L.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.300, A:C.300 SO4.5: 6 residues within 4Å: Chain A: T.25, L.27, H.41, V.42, C.44, M.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.25, A:H.41 Salt bridges: A:H.41 SO4.9: 5 residues within 4Å: Chain A: L.141 Chain B: V.297, Q.298, Q.299, C.300 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.300, B:C.300 SO4.10: 6 residues within 4Å: Chain B: T.25, L.27, H.41, V.42, C.44, M.49 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.25, B:H.41 Salt bridges: B:H.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lis, K. et al., SARS-CoV-2 M pro oligomerization as a potential target for therapy. Int.J.Biol.Macromol. (2024)

Release Date

2024-04-17

Peptides

Non-structural protein 11: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Non-structural protein 11