SMTL ID : 4z4u.1

Crystal structure of GII.10 P domain in complex with 37.5mM fucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: Y.27, R.220, F.222, P.291 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.220 EDO.2: 5 residues within 4Å: Chain A: P.22, I.23, D.24 Chain B: L.56, N.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.23 EDO.3: 5 residues within 4Å: Chain A: R.76, G.77, S.156, T.157, W.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.156 EDO.4: 6 residues within 4Å: Chain A: L.56, T.58, G.59, A.62, K.170 Chain B: P.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.58, A:T.58 EDO.6: 5 residues within 4Å: Chain A: P.20, P.57, T.58 Chain B: P.57, T.58 No protein-ligand interaction detected (PLIP) EDO.7: 5 residues within 4Å: Chain B: Q.54, N.86, L.87, N.88, L.102 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.87, B:N.88, B:N.88 Water bridges: B:N.88 EDO.8: 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.9: 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

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

FUL.5: 1 residues within 4Å: Chain A: F.309 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.309 FUL.10: 7 residues within 4Å: Chain A: G.227, G.228, Y.229 Chain B: A.131, N.132, R.133, D.162 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.131 Hydrogen bonds: B:N.132, B:R.133, B:R.133, B:D.162, A:G.228 Water bridges: B:D.162

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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