SMTL ID : 9ez6.1

Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp14/15 substrate peptide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-2-1-mer

Ligands

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 6 residues within 4Å: Chain A: R.40, P.52, N.53, Y.54, E.55, M.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.54 DMS.3: 2 residues within 4Å: Chain A: R.105, N.180 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.105

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

EDO.2: 7 residues within 4Å: Chain A: R.105, I.106, Q.107, P.108, F.134, Y.182, G.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.105, A:R.105, A:Q.107 EDO.4: 6 residues within 4Å: Chain A: S.301, G.302 Chain B: Y.118, L.141, N.142 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.302 EDO.5: 8 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, R.298 Chain B: S.123, G.124 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.298, A:R.298 EDO.6: 6 residues within 4Å: Chain A: S.1, N.214, G.215 Chain B: P.168, T.169, G.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.1 EDO.8: 5 residues within 4Å: Chain A: Q.110, I.249, T.292, P.293, F.294 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.292 EDO.9: 8 residues within 4Å: Chain A: Y.118, L.141, N.142, G.143 Chain B: S.301, G.302 Chain C: L.8 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.142 EDO.11: 6 residues within 4Å: Chain A: R.4, K.5 Chain B: K.5, Y.126, Q.127 Ligands: EDO.18 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.4, A:K.5, A:K.5, B:Q.127 EDO.12: 7 residues within 4Å: Chain A: V.35, G.79, H.80, S.81, K.88, L.89, K.90 No protein-ligand interaction detected (PLIP) EDO.13: 2 residues within 4Å: Chain A: A.191 Chain C: T.1 No protein-ligand interaction detected (PLIP) EDO.15: 9 residues within 4Å: Chain A: M.6, R.298, Q.299, S.301 Chain B: Y.118, S.123, L.141 Ligands: EDO.4, EDO.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.123 EDO.17: 7 residues within 4Å: Chain A: F.140, L.141, N.142, E.166 Chain B: S.1 Chain C: Q.6 Ligands: EDO.9 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Water bridges: C:Q.6 Hydrogen bonds: B:S.1, A:N.142 EDO.18: 6 residues within 4Å: Chain A: F.3, R.4, L.282, G.283 Chain B: K.137 Ligands: EDO.11 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.282, B:K.137

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

PEG.7: 11 residues within 4Å: Chain A: E.14, G.15, C.16, M.17, V.18, W.31, A.70, N.95, P.96, K.97 Chain B: Q.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.97 PEG.10: 6 residues within 4Å: Chain A: R.131, K.137, D.289, E.290 Chain B: F.3, R.4 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.137 Water bridges: A:R.131, A:K.137, A:D.289, B:F.3

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

NA.14: 5 residues within 4Å: Chain A: N.221, R.222, F.223, D.263, A.266 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.221, A:F.223, A:D.263 NA.19: 5 residues within 4Å: Chain B: N.221, F.223, D.263, A.266, S.267 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.221, B:F.223, B:D.263, B:S.267

1 x GLN: GLUTAMINE(Non-covalent)

GLN.16: 12 residues within 4Å: Chain A: S.1 Chain B: F.140, L.141, N.142, G.143, S.144, A.145, H.163, H.164, M.165, E.166, H.172 8 PLIP interactions: 8 interactions with chain B, Hydrogen bonds: B:F.140, B:G.143, B:S.144, B:S.144, B:A.145, B:H.163, B:H.164, B:E.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fornasier, E. et al., Allostery in homodimeric SARS-CoV-2 main protease. Commun Biol (2024)

Release Date

2025-02-12

Peptides

Replicase polyprotein 1a: AB
THR-PHE-THR-ARG-LEU-GLN-SER-LEU-GLU-ASN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Replicase polyprotein 1a

THR-PHE-THR-ARG-LEU-GLN-SER-LEU-GLU-ASN

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