SMTL ID : 5j35.1

Protruding domain of GII.4 human norovirus NSW0514 in complex with 2-fucosyllactose (2'FL)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

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

GLC-GAL-FUC.1: 9 residues within 4Å: Chain A: S.122, T.123, R.124, D.153 Chain B: D.170, H.175, S.221, G.222, Y.223 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.124, A:R.124, A:D.153, B:G.222, B:S.221, B:S.221 Water bridges: A:G.125, B:C.220, B:D.170, B:Y.223 Hydrophobic interactions: B:Y.223 GLC-GAL-FUC.2: 9 residues within 4Å: Chain A: D.170, H.175, S.221, G.222, Y.223 Chain B: S.122, T.123, R.124, D.153 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.124, B:R.124, B:D.153, A:G.222, A:S.221, A:S.221 Water bridges: B:G.125, B:E.155, A:C.220, A:S.221 Hydrophobic interactions: A:Y.223

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

EDO.3: 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.4: 5 residues within 4Å: Chain A: L.265, 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: 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

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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