SMTL ID : 8ddl.1

SARS-CoV-2 Main Protease (Mpro) H163A Mutant Apo Structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 11 residues within 4Å: Chain A: T.25, H.41, C.44, T.45, M.49, H.164, M.165, V.186, D.187, R.188, Q.189 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.25, A:T.25, A:Q.189, A:Q.192 PGE.3: 7 residues within 4Å: Chain A: S.123, L.141 Chain B: M.6, F.8, Q.127, D.295, R.298 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.127, B:D.295, B:R.298, B:R.298, A:N.119

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

NA.2: 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:F.223, A:F.223, A:S.267

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

PEG.4: 5 residues within 4Å: Chain B: G.79, H.80, S.81, K.88, K.90 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.90 PEG.5: 9 residues within 4Å: Chain B: E.14, G.15, C.16, M.17, W.31, A.70, N.95, P.96, K.97 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.97

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

EDO.6: 8 residues within 4Å: Chain B: P.132, N.133, F.134, P.184, F.185, A.193, A.194, G.195 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.195

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

2023-06-28

Peptides

ORF1a polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ORF1a polyprotein

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