SMTL ID : 5lkc.1

Protruding domain of GII.17 norovirus Kawasaki308 in complex with HBGA type A (triglycan)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

2 x GLA- FUC- A2G: alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose

GLA-FUC-A2G.1: 9 residues within 4Å: Chain A: S.125, T.126, R.127, D.153, D.156, Q.158 Chain B: G.220, G.221, Y.222 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:Y.222 Hydrogen bonds: B:G.221, A:T.126, A:R.127, A:R.127, A:D.156 Water bridges: B:S.219, A:S.125, A:D.156, A:Q.158, A:Q.158, A:Q.158 GLA-FUC-A2G.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 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.126, B:R.127, B:R.127, B:D.156, B:Q.158, A:G.221 Water bridges: B:N.117, B:S.125, A:S.219 Hydrophobic interactions: A:Y.222

4 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: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.237, B:Q.237, B:Q.241 Hydrogen bonds: A:H.238 EDO.6: 5 residues within 4Å: Chain B: Q.55, N.84, L.85, N.86, L.100 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.85, B:N.86, B:N.86 Water bridges: B:N.86, B:L.100 EDO.7: 7 residues within 4Å: Chain A: Q.237, Q.241 Chain B: P.8, L.10, E.234, Q.237, H.238 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.234 Water bridges: A:Q.237, A:Q.237, A:Q.241

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: S.6, L.7, I.9, R.294, F.295 No protein-ligand interaction detected (PLIP) MG.8: 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

Koromyslova, A. et al., Human norovirus inhibition by a human milk oligosaccharide. Virology (2017)

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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