SMTL ID : 4wzk.1

Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type H2 (triglycan)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-dimer

Ligands

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

NDG-GAL-FUC.1: 9 residues within 4Å: Chain A: S.122, T.123, R.124, D.153 Chain B: G.171, S.172, S.221, G.222, Y.223 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.123, A:R.124, A:R.124, A:D.153, B:S.221, B:G.222, B:S.221, B:S.221, B:G.171 Water bridges: A:D.153, A:D.153, A:E.155, B:C.220, A:D.153, B:G.171 Hydrophobic interactions: B:Y.223 NDG-GAL-FUC.2: 9 residues within 4Å: Chain A: G.171, S.172, S.221, G.222, Y.223 Chain B: S.122, T.123, R.124, D.153 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.223 Hydrogen bonds: A:G.222, B:T.123, B:R.124, B:R.124, B:D.153, A:S.221, A:G.171, A:Y.223 Water bridges: B:H.126, B:D.153, B:D.153, A:C.220, A:S.221, A:S.221, B:D.153, A:G.171, A:S.221

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

ACT.3: 5 residues within 4Å: Chain A: F.266, H.284, L.286, V.287, M.309 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.286 Hydrogen bonds: A:V.287, A:V.287 Salt bridges: A:H.284 ACT.4: 6 residues within 4Å: Chain B: L.265, F.266, H.284, L.286, V.287, M.309 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.265, B:L.286 Hydrogen bonds: B:V.287 Salt bridges: B:H.284

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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