SMTL ID : 8ilc.1

Crystal structure of Se-Met CoV-Y domain of Nsp3 in SARS-CoV-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.206, S.242, E.243, Q.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.243, A:Q.244 Salt bridges: A:R.206 SO4.2: 1 residues within 4Å: Chain A: K.31 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.31 SO4.3: 2 residues within 4Å: Chain A: D.188, S.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.189, A:S.189 SO4.4: 3 residues within 4Å: Chain A: K.17, N.18, K.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.18 Water bridges: A:G.19 Salt bridges: A:K.17, A:K.109 SO4.5: 3 residues within 4Å: Chain A: S.20, H.22, R.35 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.20, A:S.20 Water bridges: A:Y.33 Salt bridges: A:H.22, A:R.35

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: S.181, R.250 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: T.152 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, K. et al., The CoV-Y domain of SARS-CoV-2 Nsp3 interacts with BRAP to stimulate NF-kappa B signaling and induce host inflammatory responses. Int.J.Biol.Macromol. (2024)

Release Date

2023-05-24

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3