SMTL ID : 4z4r.1

Crystal structure of GII.10 P domain in complex with 300mM fucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 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 B: V.138, S.156, T.157, W.158 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.156 EDO.5: 5 residues within 4Å: Chain B: V.25, Y.27, R.220, F.222, P.291 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.220 EDO.6: 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.7: 7 residues within 4Å: Chain A: P.22 Chain B: L.56, T.58, G.59, A.62, L.87, K.170 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.58

4 x FUL: beta-L-fucopyranose(Non-covalent)

FUL.2: 3 residues within 4Å: Chain A: E.136, W.158, K.226 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.158 Hydrogen bonds: A:K.226, A:K.226 Water bridges: A:W.158, B:H.135, B:E.136, B:E.159 FUL.3: 7 residues within 4Å: Chain A: A.131, N.132, R.133, D.162 Chain B: G.227, G.228, Y.229 9 PLIP interactions: 2 interactions with chain B, 7 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 Water bridges: A:H.135, A:D.162 FUL.8: 3 residues within 4Å: Chain B: E.136, W.158, K.226 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.158 Hydrogen bonds: B:K.226, B:K.226 Water bridges: A:E.136, A:E.159 FUL.9: 7 residues within 4Å: Chain A: G.227, G.228, Y.229 Chain B: A.131, N.132, R.133, D.162 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.131, A:Y.229 Hydrogen bonds: B:N.132, B:R.133, B:R.133, B:D.162, A:G.228 Water bridges: B:H.135, B:D.162, B:S.164, B:S.164

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Koromyslova, A.D. et al., The sweet quartet: Binding of fucose to the norovirus capsid. Virology (2015)

Release Date

2015-05-27

Peptides

Capsid protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein

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