SMTL ID : 5j3o.1

Protruding domain of GII.4 human norovirus NSW0514 in complex with 3-fucosyllactose (3FL)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: L.51, L.52, G.53, T.55, I.96, L.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.55 Water bridges: A:L.51, A:G.53 EDO.2: 6 residues within 4Å: Chain A: N.258, T.261, R.263, V.264, L.265, P.289 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.258, A:T.261, A:T.261, A:R.263, A:R.263 EDO.3: 6 residues within 4Å: Chain A: L.265, F.266, H.284, L.286, V.287, M.309 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.284, A:V.287 EDO.5: 6 residues within 4Å: Chain B: L.51, L.52, G.53, T.55, I.96, L.100 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.55 Water bridges: B:L.51, B:G.53 EDO.6: 6 residues within 4Å: Chain B: N.258, T.261, R.263, V.264, L.265, P.289 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.258, B:T.261, B:R.263, B:R.263 EDO.7: 5 residues within 4Å: Chain B: L.265, H.284, L.286, V.287, M.309 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.284, B:V.287

2 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.4: 7 residues within 4Å: Chain A: S.122, T.123, R.124, D.153 Chain B: S.221, G.222, Y.223 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.223 Hydrogen bonds: B:S.221, B:G.222, A:R.124, A:R.124, A:D.153 Water bridges: B:C.220 FUC.8: 7 residues within 4Å: Chain A: S.221, G.222, Y.223 Chain B: S.122, T.123, R.124, D.153 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.223 Hydrogen bonds: A:G.222, B:R.124, B:R.124, B:D.153 Water bridges: A:C.220, B:E.155

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Singh, B.K. et al., Structural basis for GII.4 norovirus inhibition by human milk oligosaccharides. To be published

Release Date

2017-04-12

Peptides

VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VP1

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