SMTL ID : 6yb7.1

SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

14 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.2: 2 residues within 4Å: Chain A: H.64, N.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.65 DMS.3: 6 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, R.298 Chain B: S.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.298 Salt bridges: A:D.295 pi-Cation interactions: A:F.8 DMS.4: 9 residues within 4Å: Chain A: F.140, L.141, N.142, S.144, C.145, H.163, E.166, H.172 Chain B: S.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.166 DMS.5: 7 residues within 4Å: Chain A: E.14, G.15, M.17, V.18, W.31, G.71, K.97 No protein-ligand interaction detected (PLIP) DMS.6: 2 residues within 4Å: Chain A: K.100, Y.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.101 pi-Cation interactions: A:Y.101 DMS.8: 3 residues within 4Å: Chain A: R.40, N.84, C.85 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.40, A:D.187 DMS.9: 3 residues within 4Å: Chain B: Q.74, L.75, R.76 No protein-ligand interaction detected (PLIP) DMS.10: 2 residues within 4Å: Chain B: H.64, N.65 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.65 DMS.11: 6 residues within 4Å: Chain A: S.123 Chain B: M.6, A.7, F.8, Q.127, R.298 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.298 Salt bridges: B:D.295 pi-Cation interactions: B:F.8 DMS.12: 9 residues within 4Å: Chain A: S.1 Chain B: F.140, L.141, N.142, S.144, C.145, H.163, E.166, H.172 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.166 DMS.13: 7 residues within 4Å: Chain B: E.14, G.15, M.17, V.18, W.31, G.71, K.97 No protein-ligand interaction detected (PLIP) DMS.14: 2 residues within 4Å: Chain B: K.100, Y.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.101 pi-Cation interactions: B:Y.101 DMS.16: 3 residues within 4Å: Chain B: R.40, N.84, C.85 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.40, B:R.40

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

PEG.7: 4 residues within 4Å: Chain A: L.272, Q.273, N.274, G.275 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.272 PEG.15: 4 residues within 4Å: Chain B: L.272, Q.273, N.274, G.275 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.272 Water bridges: B:Y.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Owen, C.D. et al., COVID-19 main protease with unliganded active site. To Be Published

Release Date

2020-03-25

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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