SMTL ID : 4x06.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-dimer

Ligands

2 x GLA- FUC- GLA: alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose(Non-functional Binders)

GLA-FUC-GLA.1: 10 residues within 4Å: Chain A: S.122, T.123, R.124, G.125, H.126, D.153 Chain B: K.127, S.221, G.222, Y.223 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.123, A:R.124, A:R.124, A:D.153, B:G.222, B:K.127 Water bridges: A:D.153, A:D.153, A:E.155, A:G.125, A:H.126, A:H.126, A:H.126, A:H.126, A:N.152, A:D.153, A:D.153 Hydrophobic interactions: B:Y.223 GLA-FUC-GLA.2: 10 residues within 4Å: Chain A: K.127, S.221, G.222, Y.223 Chain B: S.122, T.123, R.124, G.125, H.126, D.153 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.123, B:R.124, B:R.124, B:D.153, A:G.222, A:K.127 Water bridges: B:D.153, B:D.153, B:G.125, B:D.153, B:D.153 Hydrophobic interactions: A:Y.223

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

ACT.3: 6 residues within 4Å: Chain A: F.266, H.284, L.286, V.287, I.288, 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 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.265 Hydrogen bonds: B:V.287 Salt bridges: B:H.284

Links

RCSB   PDBe   PDBe-KB   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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