SMTL ID : 5lkk.1

Protruding domain of GII.17 norovirus Kawasaki308 in complex with 3-fucosyllactose (3FL)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-dimer

Ligands

2 x GLC- FUC- GAL: alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]alpha-D-glucopyranose(Non-functional Binders)

GLC-FUC-GAL.1: 8 residues within 4Å: Chain A: S.125, T.126, R.127, D.156, Q.158 Chain B: G.220, G.221, Y.222 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.126, A:R.127, A:R.127, A:D.156, B:G.221, A:D.156 Water bridges: A:S.125, A:D.156, A:Q.158, A:Q.158, B:S.219, B:S.219, A:Q.158, B:Y.222 Hydrophobic interactions: B:Y.222 GLC-FUC-GAL.2: 8 residues within 4Å: Chain A: G.220, G.221, Y.222 Chain B: S.125, T.126, R.127, D.156, Q.158 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.222 Hydrogen bonds: A:G.221, B:T.126, B:R.127, B:R.127, B:D.156, B:Q.158, B:D.156 Water bridges: A:S.219, A:S.219, B:N.117, B:S.125, B:D.156, A:Y.222

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

EDO.3: 4 residues within 4Å: Chain A: Y.240, Q.241, S.243 Chain B: I.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.243, A:S.243 EDO.4: 6 residues within 4Å: Chain A: P.8, L.10, E.234, H.238 Chain B: Q.237, Q.241 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.238 Water bridges: B:Q.237, B:Q.237, B:Q.241 EDO.5: 6 residues within 4Å: Chain A: L.50, Q.51, G.52, T.54, V.96, L.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.54 Water bridges: A:G.52 EDO.6: 5 residues within 4Å: Chain A: Q.55, N.84, L.85, N.86, L.100 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.85, A:N.86, A:N.86, A:L.100 Water bridges: A:N.86, A:L.100 EDO.8: 6 residues within 4Å: Chain A: Q.237, Q.241 Chain B: P.8, L.10, E.234, H.238 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:H.238 Water bridges: A:Q.237, A:Q.237, A:Q.241 EDO.9: 5 residues within 4Å: Chain B: Q.55, N.84, L.85, N.86, L.100 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.85, B:N.86, B:N.86, B:L.100 Water bridges: B:N.86, B:L.100 EDO.10: 6 residues within 4Å: Chain B: L.50, Q.51, G.52, T.54, V.96, L.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.54 Water bridges: B:G.52

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.7: 5 residues within 4Å: Chain A: S.6, L.7, I.9, R.294, F.295 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain B: S.6, L.7, I.9, R.294, F.295 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Singh, B.K. et al., Structural basis of HMOs interaction with the emerging GII.17 norovirus Kawasaki308. To be published

Release Date

2017-05-24

Peptides

Major capsid protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Major capsid protein

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