SMTL ID : 7t8r.1

Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 7/8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

2 x ASN- ARG- ALA- THR- LEU- GLN- ALA- ILE: Nonstructural protein 7/8(Non-covalent)

ASN-ARG-ALA-THR-LEU-GLN-ALA-ILE.1: 24 residues within 4Å: Chain A: T.24, T.25, T.26, L.27, 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, R.188, Q.189, T.190, A.191, Q.192 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:T.25, A:T.26, A:L.27, A:H.41, A:M.49, A:N.142, A:M.165, A:P.168, A:D.187, A:Q.189 Hydrogen bonds: 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:P.168, A:Q.189, A:T.190 Water bridges: A:N.142, A:A.191 ASN-ARG-ALA-THR-LEU-GLN-ALA-ILE.9: 24 residues within 4Å: Chain B: T.24, T.25, T.26, L.27, 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, R.188, Q.189, T.190, A.191, Q.192 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:T.25, B:T.26, B:L.27, B:H.41, B:M.49, B:N.142, B:M.165, B:P.168, B:D.187, B:Q.189 Hydrogen bonds: B:T.26, B:T.26, B:H.41, B:F.140, B:G.143, B:S.144, B:A.145, B:H.164, B:E.166, B:E.166, B:E.166, B:P.168, B:Q.189, B:T.190 Water bridges: B:N.142, B:E.166, B:A.191

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

EDO.2: 5 residues within 4Å: Chain A: P.52, N.53, Y.54, E.55, R.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.54, A:E.55, A:R.188 Water bridges: A:R.40 EDO.3: 8 residues within 4Å: Chain A: M.17, V.18, Q.19, Q.69, A.70, G.71, N.119, G.120 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.17, A:Q.19, A:G.71 Water bridges: A:N.119 EDO.5: 4 residues within 4Å: Chain A: G.11, K.12, G.15, K.97 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.97 EDO.6: 4 residues within 4Å: Chain A: Q.256, C.300, S.301 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.256 EDO.7: 4 residues within 4Å: Chain A: F.3, R.4, K.5 Chain B: K.5 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.4, A:K.5 Water bridges: A:K.5, B:Q.127 EDO.8: 4 residues within 4Å: Chain A: I.213, C.300 Chain B: L.141 Ligands: EDO.6 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.1, A:Q.256, A:Q.256, A:Q.256, A:Q.256 EDO.10: 5 residues within 4Å: Chain B: P.52, N.53, Y.54, E.55, R.188 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.54, B:E.55, B:R.188 Water bridges: B:R.40 EDO.11: 8 residues within 4Å: Chain B: M.17, V.18, Q.19, Q.69, A.70, G.71, N.119, G.120 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.17, B:Q.19, B:G.71 Water bridges: B:N.119 EDO.13: 4 residues within 4Å: Chain B: G.11, K.12, G.15, K.97 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.97 EDO.14: 4 residues within 4Å: Chain B: Q.256, C.300, S.301 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.256 EDO.15: 4 residues within 4Å: Chain A: K.5 Chain B: F.3, R.4, K.5 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:Q.127, B:K.5 Hydrogen bonds: B:R.4, B:K.5 EDO.16: 4 residues within 4Å: Chain A: L.141 Chain B: I.213, C.300 Ligands: EDO.14 5 PLIP interactions: 5 interactions with chain B Water bridges: B:S.1, B:Q.256, B:Q.256, B:Q.256, B:Q.256

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: F.8, I.152, Y.154, R.298, V.303, T.304 Chain B: P.122, S.123 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.154, A:R.298, A:R.298, B:P.122 GOL.12: 8 residues within 4Å: Chain A: P.122, S.123 Chain B: F.8, I.152, Y.154, R.298, V.303, T.304 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.154, B:R.298, B:R.298, A:P.122

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
A

3C-like proteinase

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