SMTL ID : 4z4s.1

Crystal structure of GII.10 P domain in complex with 150mM fucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: P.20, P.57, T.58 Chain B: P.20, P.57 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:P.20, B:P.173, A:T.58 EDO.2: 6 residues within 4Å: Chain A: L.49, Q.50, G.51, T.53, V.98, L.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.53 Water bridges: A:G.51 EDO.3: 6 residues within 4Å: Chain A: L.56, T.58, G.59, A.62, K.170 Chain B: P.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.58 Water bridges: A:T.58, A:K.170 EDO.4: 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.8: 4 residues within 4Å: Chain B: V.138, S.156, T.157, W.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.156 Water bridges: B:R.76 EDO.9: 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:T.90, B:L.102 EDO.10: 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.5: 7 residues within 4Å: Chain A: A.131, N.132, R.133, D.162 Chain B: G.227, G.228, Y.229 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B 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 Water bridges: A:H.135, A:D.162, A:S.164, A:S.164 FUL.6: 3 residues within 4Å: Chain A: E.136, W.158, K.226 8 PLIP interactions: 4 interactions with chain A, 4 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, B:E.159 FUL.11: 3 residues within 4Å: Chain B: E.136, W.158, K.226 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: A:H.135, A:E.136, A:E.159 Hydrophobic interactions: B:W.158 Hydrogen bonds: B:K.226, B:K.226 FUL.12: 8 residues within 4Å: Chain A: G.227, G.228, Y.229 Chain B: A.131, N.132, R.133, D.162 Ligands: NO3.7 9 PLIP interactions: 2 interactions with chain A, 7 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:H.135, B:D.162

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 3 residues within 4Å: Chain A: G.228, Y.229 Ligands: FUL.12 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.228, A:G.228

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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