SMTL ID : 4x07.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 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(Non-functional Binders)

GLA-FUC-A2G.1: 8 residues within 4Å: Chain A: S.120, T.121, R.122, H.124, D.151 Chain B: S.219, G.220, Y.221 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Water bridges: A:N.150, B:K.125, A:D.151, A:D.151, B:S.219, B:S.219 Hydrophobic interactions: B:Y.221 Hydrogen bonds: B:G.220, A:T.121, A:R.122, A:R.122, A:D.151 GLA-FUC-A2G.2: 8 residues within 4Å: Chain A: S.219, G.220, Y.221 Chain B: S.120, T.121, R.122, H.124, D.151 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Water bridges: B:N.150, A:K.125, B:D.151, B:E.153, A:S.219, A:S.219 Hydrogen bonds: B:T.121, B:R.122, B:R.122, B:D.151, A:G.220 Hydrophobic interactions: A:Y.221

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

ACT.3: 5 residues within 4Å: Chain A: H.282, L.284, V.285, I.286, M.307 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.284 Hydrogen bonds: A:V.285, A:M.307 Salt bridges: A:H.282 ACT.4: 5 residues within 4Å: Chain B: H.282, L.284, V.285, I.286, M.307 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.284 Hydrogen bonds: B:V.285, B:V.285 Salt bridges: B:H.282

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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