SMTL ID : 5hza.1

Crystal structure of GII.10 P domain in complex with 3-fucosyllactose (3 FL)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

1 x BGC- FUC- GAL: alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]beta-D-glucopyranose

BGC-FUC-GAL.1: 7 residues within 4Å: Chain A: A.131, N.132, R.133, D.162 Chain B: G.227, G.228, Y.229 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.162, B:K.226, A:D.162, A:S.164, A:S.164, A:D.162 Hydrophobic interactions: A:A.131, B:Y.229 Hydrogen bonds: A:N.132, A:R.133, A:R.133, A:D.162, B:G.228, B:Y.229

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

EDO.2: 5 residues within 4Å: Chain A: P.20, P.57, T.58 Chain B: P.20, P.57 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:P.20, A:T.58 EDO.3: 5 residues within 4Å: Chain A: Q.54, N.86, L.87, N.88, L.102 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.87, A:N.88, A:N.88 Water bridges: A:N.88, A:L.102 EDO.4: 6 residues within 4Å: Chain A: R.76, G.77, V.138, S.156, T.157, W.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.156 Water bridges: A:R.76 EDO.5: 5 residues within 4Å: Chain A: L.49, Q.50, G.51, T.53, L.102 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.53 Water bridges: A:L.49, A:G.51, A:D.97, A:N.202 EDO.6: 4 residues within 4Å: Chain A: G.228, Y.229 Chain B: A.131, N.132 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.132, A:G.228, A:G.228 EDO.7: 5 residues within 4Å: Chain A: P.7, E.241, H.245 Chain B: Q.244, Q.248 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.245 Water bridges: B:Q.244 EDO.8: 6 residues within 4Å: Chain A: Q.244, Q.248 Chain B: P.7, L.9, E.241, H.245 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.244, A:Q.244, A:Q.248 Hydrogen bonds: B:H.245 EDO.9: 5 residues within 4Å: Chain B: R.76, G.77, S.156, T.157, W.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.156, B:S.156 EDO.10: 8 residues within 4Å: Chain A: P.22 Chain B: L.56, T.58, G.59, A.62, R.64, L.87, K.170 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.58, B:R.64 EDO.11: 5 residues within 4Å: Chain B: Q.54, N.86, L.87, N.88, L.102 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.87, B:N.88, B:N.88 Water bridges: B:N.88, B:L.102 EDO.12: 6 residues within 4Å: Chain B: P.94, T.95, E.96, D.97, K.149, N.202 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.97, B:K.149, B:K.149, B:N.202

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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