SMTL ID : 5iyw.1

Protruding domain of GII.4 human norovirus CHDC2094 in complex with 3-fucosyllactose (3FL)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-dimer

Ligands

2 x GLC- FUC- GAL: alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]alpha-D-glucopyranose(Non-functional Binders)

GLC-FUC-GAL.1: 8 residues within 4Å: Chain A: S.120, T.121, R.122, H.124, D.151 Chain B: S.218, G.219, Y.220 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.220 Hydrogen bonds: B:G.219, A:T.121, A:R.122, A:R.122, A:D.151, A:D.151, B:S.218 Water bridges: A:D.151, A:D.151, A:Q.153, A:Q.153, A:Q.153, B:Y.220, B:Y.220, B:S.218 GLC-FUC-GAL.2: 8 residues within 4Å: Chain A: S.218, G.219, Y.220 Chain B: S.120, T.121, R.122, H.124, D.151 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.121, B:R.122, B:R.122, B:D.151, A:G.219, A:S.218 Water bridges: B:Q.153, B:Q.153, B:R.122, B:D.151, A:Y.220, A:Y.220, A:S.218 Hydrophobic interactions: A:Y.220

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

EDO.3: 3 residues within 4Å: Chain A: H.277, Y.281, M.306 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.281 EDO.4: 8 residues within 4Å: Chain A: T.10, V.11, E.12, F.253, I.285, P.286, P.287, G.289 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.11, A:E.12, A:G.289

1 x FLC: CITRATE ANION(Non-functional Binders)

FLC.5: 3 residues within 4Å: Chain B: S.132, V.133, H.134 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.133 Water bridges: B:H.134, B:Q.143, B:Q.143 Salt bridges: B:H.134, B:H.134

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

2017-04-05

Peptides

VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VP1

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