SMTL ID : 4wzt.1

Crystal structure of P domain from norovirus strain NSW0514 in complex with HBGA type A (triglycan)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 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: 9 residues within 4Å: Chain A: S.120, T.121, R.122, H.124, D.151 Chain B: K.125, S.219, G.220, Y.221 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Water bridges: A:H.124, A:D.151, B:K.125, A:S.120, A:D.151, B:G.169, B:G.169 Hydrogen bonds: A:T.121, A:R.122, A:R.122, A:D.151, B:G.220 Hydrophobic interactions: B:Y.221 GLA-FUC-A2G.2: 9 residues within 4Å: Chain A: K.125, S.219, G.220, Y.221 Chain B: S.120, T.121, R.122, H.124, D.151 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Water bridges: A:K.125, A:K.125, B:H.124, B:D.151, B:D.151, A:S.219 Hydrogen bonds: B:T.121, B:R.122, B:R.122, B:D.151, A:S.219, A:G.220 Hydrophobic interactions: A:Y.221

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: F.27, F.34, Q.179, W.180, F.210, R.212, D.227 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.180, A:R.212, A:D.227 Water bridges: A:Q.179, A:Q.281 EDO.4: 7 residues within 4Å: Chain A: L.263, F.264, H.282, L.284, V.285, I.286, M.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.282, A:V.285, A:V.285 Water bridges: A:M.307 EDO.5: 4 residues within 4Å: Chain A: E.24, K.25, L.284, I.286 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.12, A:E.12, A:E.12, A:L.26 EDO.6: 8 residues within 4Å: Chain B: F.27, S.31, F.34, Q.179, W.180, F.210, R.212, D.227 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.180, B:R.212, B:D.227 Water bridges: B:P.30, B:Q.179, B:Q.281

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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