SMTL ID : 7tc4.1

Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 15/16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x PHE- TYR- PRO- LYS- LEU- GLN- SER- SER- GLN: Nonstructural protein 15/16(Non-covalent)

PHE-TYR-PRO-LYS-LEU-GLN-SER-SER-GLN.1: 22 residues within 4Å: Chain A: T.24, T.25, T.26, H.41, M.49, F.140, L.141, N.142, G.143, S.144, A.145, H.163, H.164, M.165, E.166, P.168, H.172, D.187, Q.189, T.190, A.191, Q.192 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:H.41, A:M.165, A:P.168, A:Q.189, A:A.191, A:Q.192 Hydrogen bonds: A:T.24, A:T.25, A:T.26, A:T.26, A:H.41, A:F.140, A:G.143, A:S.144, A:A.145, A:H.164, A:E.166, A:E.166, A:Q.189, A:Q.189 Water bridges: A:N.119, A:N.119, A:N.142, A:G.143, A:Q.189 PHE-TYR-PRO-LYS-LEU-GLN-SER-SER-GLN.2: 25 residues within 4Å: Chain B: T.24, T.25, T.26, H.41, S.46, M.49, F.140, L.141, N.142, G.143, S.144, A.145, H.163, H.164, M.165, E.166, P.168, H.172, D.187, R.188, Q.189, T.190, A.191, Q.192 Ligands: GOL.4 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:H.41, B:M.49, B:M.165, B:Q.189, B:A.191, B:Q.192 Hydrogen bonds: B:T.25, B:T.26, B:T.26, B:F.140, B:G.143, B:A.145, B:H.164, B:E.166, B:E.166, B:Q.189, B:Q.189 Water bridges: B:S.46, B:S.46, B:N.142, B:N.142, B:Q.189

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: N.53, D.56, R.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.53, A:R.60 Water bridges: A:D.56 GOL.4: 5 residues within 4Å: Chain A: S.301 Chain B: Y.118, L.141, N.142 Ligands: PHE-TYR-PRO-LYS-LEU-GLN-SER-SER-GLN.2 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.119, B:N.119 GOL.5: 2 residues within 4Å: Chain B: N.180, F.181 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shaqra, A.M. et al., Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance. Nat Commun (2022)

Release Date

2022-06-22

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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