SMTL ID : 4wze.1

Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type Ley (tetraglycan)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-dimer

Ligands

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

NDG-GAL-FUC-FUC.1: 9 residues within 4Å: Chain A: S.121, T.122, R.123, D.152 Chain B: Q.168, G.170, S.220, G.221, Y.222 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.122, A:R.123, A:R.123, A:D.152, B:S.220, B:G.221, B:Y.222, B:S.220, B:S.220 Hydrophobic interactions: B:Y.222 Water bridges: B:S.220 NDG-GAL-FUC-FUC.2: 9 residues within 4Å: Chain A: Q.168, G.170, S.220, G.221, Y.222 Chain B: S.121, T.122, R.123, D.152 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.222 Hydrogen bonds: A:G.221, B:T.122, B:R.123, B:R.123, B:D.152, A:Y.222, A:S.220, A:S.220, A:S.220

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 6 residues within 4Å: Chain A: L.264, H.283, L.285, V.286, I.287, M.308 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.264, A:L.285 Hydrogen bonds: A:V.286 Salt bridges: A:H.283 ACT.4: 6 residues within 4Å: Chain B: L.264, H.283, L.285, V.286, I.287, M.308 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.264, B:L.285 Hydrogen bonds: B:V.286, B:V.286 Salt bridges: B:H.283

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Singh, B.K. et al., Human noroviruses' fondness for histo-blood group antigens. J.Virol. (2015)

Release Date

2014-12-17

Peptides

VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VP1

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