SMTL ID : 5lkg.1

Protruding domain of GII.17 norovirus Kawasaki308 in complex with 2-fucosyllactose (2'FL)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose

GLC-GAL-FUC.1: 8 residues within 4Å: Chain A: S.125, T.126, R.127, D.156, Q.158 Chain B: G.220, G.221, Y.222 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.126, A:R.127, A:R.127, A:D.156, A:Q.158, B:G.221 Water bridges: A:N.117, A:S.125, A:D.156, B:S.219 Hydrophobic interactions: B:Y.222 GLC-GAL-FUC.2: 8 residues within 4Å: Chain A: G.220, G.221, Y.222 Chain B: S.125, T.126, R.127, D.156, Q.158 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.126, B:R.127, B:R.127, B:D.156, B:Q.158, A:G.221 Water bridges: B:S.125, B:D.156, B:Q.158, A:S.219, A:Y.222 Hydrophobic interactions: A:Y.222

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.6, L.7, I.9, R.294, F.295 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain B: S.6, L.7, I.9, R.294, F.295 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koromyslova, A. et al., Human norovirus inhibition by a human milk oligosaccharide. Virology (2017)

Release Date

2017-05-24

Peptides

Capsid protein VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein VP1

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