SMTL ID : 5hzb.1

Crystal structure of GII.10 P domain in complex with 2-fucosyllactose (2'FL)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

GLC-GAL-FUC.1: 9 residues within 4Å: Chain A: A.131, N.132, R.133, D.162 Chain B: S.178, D.180, G.227, G.228, Y.229 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.229, A:A.131 Hydrogen bonds: B:G.228, A:N.132, A:R.133, A:R.133, A:D.162, B:S.178, B:S.178, B:D.180, B:D.180, B:G.228 Water bridges: A:D.162, B:V.179, B:Y.229, B:Y.229

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

EDO.2: 3 residues within 4Å: Chain A: E.136, W.158, K.226 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:E.136 Hydrogen bonds: A:K.226 EDO.3: 6 residues within 4Å: Chain A: R.76, G.77, V.138, S.156, T.157, W.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.156 EDO.4: 4 residues within 4Å: Chain A: G.228, Y.229 Chain B: A.131, N.132 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.228, A:G.228, B:N.132 EDO.5: 5 residues within 4Å: Chain B: R.76, G.77, V.138, S.156, W.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.156 Water bridges: B:S.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weichert, S. et al., Structural Basis for Norovirus Inhibition by Human Milk Oligosaccharides. J.Virol. (2016)

Release Date

2016-03-02

Peptides

Capsid protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein

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