SMTL ID : 4x0c.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

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

NDG-FUC-GAL.1: 10 residues within 4Å: Chain A: S.120, T.121, R.122, D.151 Chain B: K.125, G.169, C.218, S.219, G.220, Y.221 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.221 Hydrogen bonds: B:S.219, B:G.220, A:T.121, A:R.122, A:R.122, A:D.151, B:Y.221, B:S.219, B:S.219 Water bridges: A:S.120, B:Y.221, B:S.219 NDG-FUC-GAL.2: 9 residues within 4Å: Chain A: K.125, G.169, S.219, G.220, Y.221 Chain B: S.120, T.121, R.122, D.151 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.221 Hydrogen bonds: A:S.219, A:G.220, B:T.121, B:R.122, B:R.122, B:D.151, A:Y.221, A:S.219, A:S.219 Water bridges: B:D.151, B:E.153, A:G.169, A:G.169, A:Y.221, A:Y.221, B:D.151, B:D.151, A:S.219

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

EDO.3: 8 residues within 4Å: Chain A: F.27, F.34, Q.179, W.180, F.210, R.212, D.227, Q.281 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.180, A:R.212, A:D.227, A:D.227 Water bridges: A:P.30, A:Q.179, A:Q.281, A:Q.281 EDO.4: 6 residues within 4Å: Chain A: L.263, F.264, H.282, L.284, V.285, M.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.282, A:V.285, A:V.285, A:M.307 EDO.6: 8 residues within 4Å: Chain B: T.10, V.11, E.12, F.254, I.286, P.287, P.288, G.290 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.10, B:V.11, B:E.12, B:E.12, B:G.290 EDO.7: 7 residues within 4Å: Chain B: F.27, F.34, Q.179, W.180, F.210, R.212, D.227 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:W.180, B:R.212, B:D.227, B:D.227 Water bridges: B:P.30, B:Q.179, B:R.212, B:Q.281

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 4 residues within 4Å: Chain A: E.13 Chain B: L.49, L.55, Y.239 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.13, B:Y.239 FMT.8: 3 residues within 4Å: Chain B: H.278, T.279, P.306 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.279, B:T.279 Water bridges: B:H.278, B:H.278, B:T.279 FMT.9: 6 residues within 4Å: Chain B: L.263, F.264, H.282, L.284, V.285, M.307 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.282, B:V.285 FMT.10: 3 residues within 4Å: Chain B: S.5, R.293, F.294 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.294 Water bridges: B:R.293, B:R.293, B:F.294 FMT.11: 4 residues within 4Å: Chain A: V.8 Chain B: Y.239, Q.240, A.242 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.239 FMT.12: 6 residues within 4Å: Chain B: S.82, Q.83, Y.88, I.94, P.97, L.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.82, B:L.98 Water bridges: B:Q.83

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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