SMTL ID : 7t70.1

Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 4/5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-2-2-mer

Ligands

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: G.15, M.17, W.31, A.70, G.71, N.95, K.97 Ligand excluded by PLIP GOL.2: 6 residues within 4Å: Chain A: R.105, F.134, F.181, Y.182, G.183, P.184 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: A.266, E.270, Q.273 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: P.132, N.133, T.196, E.240 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: S.254, A.255, G.258, A.260 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: P.108, G.109, I.200, V.202, E.240, H.246 Ligand excluded by PLIP GOL.12: 2 residues within 4Å: Chain A: L.272 Ligands: DMS.4 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: E.47, D.48, N.51, P.52, N.53, L.57 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain A: D.33, T.98, P.99, K.100, Y.101 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain A: K.137 Chain B: F.3, R.4, L.282 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain B: V.73, Q.74, L.75, R.76, D.92, T.93 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: Q.83, N.84, E.178, N.180 Ligands: GOL.25 Ligand excluded by PLIP GOL.24: 8 residues within 4Å: Chain B: M.17, Q.19, Q.69, G.71, N.119, G.120, S.121 Ligands: DMS.18 Ligand excluded by PLIP GOL.25: 2 residues within 4Å: Chain B: N.84 Ligands: GOL.21 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain B: Q.256, C.300, S.301 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain B: N.221, F.223, T.224, A.266, K.269, E.270 Ligand excluded by PLIP GOL.31: 3 residues within 4Å: Chain A: A.191 Chain C: T.1, S.2 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain B: T.25, S.46, M.49, N.142 Chain D: L.5, S.7, G.8 Ligands: DMS.30 Ligand excluded by PLIP

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

DMS.3: 6 residues within 4Å: Chain A: F.3, W.207, L.282, S.284, E.288, F.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.284 Salt bridges: A:E.288 DMS.4: 7 residues within 4Å: Chain A: L.271, L.272, G.275, A.285, L.286, L.287 Ligands: GOL.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.276 DMS.5: 1 residues within 4Å: Chain A: A.191 No protein-ligand interaction detected (PLIP) DMS.6: 3 residues within 4Å: Chain A: K.12, T.98, P.99 No protein-ligand interaction detected (PLIP) DMS.9: 2 residues within 4Å: Chain A: R.40, N.84 No protein-ligand interaction detected (PLIP) DMS.13: 2 residues within 4Å: Chain A: N.277, R.279 No protein-ligand interaction detected (PLIP) DMS.15: 5 residues within 4Å: Chain A: S.1, G.2, L.282 Chain B: T.169, G.170 No protein-ligand interaction detected (PLIP) DMS.18: 7 residues within 4Å: Chain B: G.15, M.17, V.18, A.70, G.71, K.97 Ligands: GOL.24 No protein-ligand interaction detected (PLIP) DMS.19: 5 residues within 4Å: Chain A: G.11, K.12 Chain B: G.11, E.14, G.15 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.14 DMS.22: 5 residues within 4Å: Chain A: T.304, F.305 Chain B: Y.118, N.119, S.121 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.119 DMS.23: 5 residues within 4Å: Chain B: F.3, W.207, L.282, E.288, F.291 No protein-ligand interaction detected (PLIP) DMS.26: 2 residues within 4Å: Chain B: M.276, G.278 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.276, B:G.278 DMS.27: 2 residues within 4Å: Chain B: V.104, R.105 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.105 DMS.30: 2 residues within 4Å: Chain B: N.142 Ligands: GOL.32 No protein-ligand interaction detected (PLIP)

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
Nonstructural protein 4/5: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3C-like proteinase

Nonstructural protein 4/5

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