SMTL ID : 4z4z.1

Crystal structure of GII.10 P domain in complex with 30mM B antigen (trisaccharide)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x GLA- FUC- GLA: alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose(Non-functional Binders)

GLA-FUC-GLA.1: 9 residues within 4Å: Chain A: A.131, N.132, R.133, H.135, D.162 Chain B: G.227, G.228, Y.229 Ligands: EDO.8 7 PLIP interactions: 2 interactions with chain B, 5 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 GLA-FUC-GLA.2: 9 residues within 4Å: Chain A: G.227, G.228, Y.229 Chain B: A.131, N.132, R.133, H.135, D.162 Ligands: EDO.3 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.229, B:A.131 Hydrogen bonds: A:G.228, B:N.132, B:R.133, B:R.133, B:D.162 Water bridges: B:E.159, B:Q.161

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

EDO.3: 5 residues within 4Å: Chain A: E.136, W.158, K.226 Chain B: H.135 Ligands: GLA-FUC-GLA.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.226, B:H.135 EDO.4: 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.5: 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:N.88, A:N.88 Water bridges: A:L.87, A:L.87, A:N.88 EDO.6: 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.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:T.90 EDO.8: 5 residues within 4Å: Chain A: H.135 Chain B: E.136, W.158, K.226 Ligands: GLA-FUC-GLA.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:E.136 Hydrogen bonds: B:E.136, B:K.226 EDO.9: 6 residues within 4Å: Chain B: R.76, G.77, V.138, S.156, T.157, W.158 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.156

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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