SMTL ID : 7e6k.1

Viral protease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

6 x HYR: N-(2-phenoxyethyl)methanethioamide(Covalent)

HYR.1: 8 residues within 4Å: Chain A: H.41, C.44, N.142, G.143, S.144, C.145 Ligands: HYR.2, DMS.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.41 HYR.2: 12 residues within 4Å: Chain A: H.41, C.44, T.45, M.49, L.50, P.52, Y.54, M.165, D.187, R.188, Q.189 Ligands: HYR.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.41, A:M.165 Hydrogen bonds: A:Y.54 Water bridges: A:M.49 HYR.3: 5 residues within 4Å: Chain A: K.100, Y.101, K.102, C.156, V.157 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.100, A:K.100 HYR.8: 8 residues within 4Å: Chain B: H.41, C.44, N.142, G.143, S.144, C.145 Ligands: HYR.9, DMS.11 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.41, B:H.41, B:H.41 HYR.9: 12 residues within 4Å: Chain B: H.41, C.44, T.45, M.49, L.50, P.52, Y.54, M.165, D.187, R.188, Q.189 Ligands: HYR.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:H.41, B:M.165 Hydrogen bonds: B:Y.54 Water bridges: B:M.49 HYR.10: 5 residues within 4Å: Chain B: K.100, Y.101, K.102, C.156, V.157 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.100, B:K.100

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

DMS.4: 9 residues within 4Å: Chain A: F.140, L.141, N.142, S.144, H.163, M.165, E.166, H.172 Ligands: HYR.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.166 DMS.5: 3 residues within 4Å: Chain A: R.40, N.84, C.85 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.40 DMS.11: 9 residues within 4Å: Chain B: F.140, L.141, N.142, S.144, H.163, M.165, E.166, H.172 Ligands: HYR.8 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.166 DMS.12: 3 residues within 4Å: Chain B: R.40, N.84, C.85 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.40

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 8 residues within 4Å: Chain A: E.14, G.15, C.16, M.17, W.31, A.70, G.71, K.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.15 Water bridges: A:G.71 Salt bridges: A:K.97 SO4.7: 4 residues within 4Å: Chain A: R.4, K.5 Chain B: K.5 Ligands: SO4.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.5 Water bridges: A:R.4, A:R.4 Salt bridges: A:R.4 SO4.13: 8 residues within 4Å: Chain B: E.14, G.15, C.16, M.17, W.31, A.70, G.71, K.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.15 Water bridges: B:G.71 Salt bridges: B:K.97 SO4.14: 4 residues within 4Å: Chain A: K.5 Chain B: R.4, K.5 Ligands: SO4.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.5 Water bridges: B:R.4, B:R.4 Salt bridges: B:R.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Viral protease. To be published

Release Date

2022-02-23

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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