SMTL ID : 8dd6.1

SARS-CoV-2 Main Protease (Mpro) H163A Mutant in Complex with GC376

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 3 residues within 4Å: Chain A: Q.74, L.75, R.76 No protein-ligand interaction detected (PLIP) DMS.3: 3 residues within 4Å: Chain B: Q.74, L.75, R.76 No protein-ligand interaction detected (PLIP)

2 x K36: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

K36.2: 19 residues within 4Å: Chain A: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.164, M.165, E.166, P.168, H.172, D.187, R.188, Q.189, T.190 Chain B: S.1 14 PLIP interactions: 2 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:S.1, B:S.1, A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:Q.189, A:Q.189 Hydrophobic interactions: A:H.41, A:M.165, A:P.168 Water bridges: A:M.165 K36.4: 19 residues within 4Å: Chain A: S.1 Chain B: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.164, M.165, E.166, P.168, H.172, D.187, R.188, Q.189, T.190 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.41, B:M.165, B:P.168 Hydrogen bonds: B:G.143, B:S.144, B:C.145, B:H.164, B:E.166, B:Q.189, B:Q.189, A:S.1 Water bridges: B:M.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, N. et al., The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease. Nat Commun (2023)

Release Date

2023-09-27

Peptides

ORF1a polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ORF1a polyprotein

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