SMTL ID : 5lkk.1

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

Coordinates

PDB Format Compare

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

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 B, 1 interactions with chain A Hydrogen bonds: B:T.126, B:R.127, B:R.127, B:D.156, B:Q.158, A:G.221, B:D.156 Water bridges: B:N.117, B:S.125, B:D.156, A:S.219, A:S.219, A:Y.222 Hydrophobic interactions: A:Y.222

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

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)

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   PDBe-KB   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

Related Entries With Identical Sequence