SMTL ID : 5iyn.1

Protruding domain of GII.4 human norovirus CHDC2094

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: L.49, L.50, G.51, T.53, I.94, L.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.53 Water bridges: A:L.49, A:G.51 EDO.2: 8 residues within 4Å: Chain A: T.10, V.11, E.12, F.253, I.285, P.286, P.287, G.289 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.11, A:E.12, A:E.12, A:G.289 Water bridges: A:T.10, A:E.12 EDO.3: 4 residues within 4Å: Chain A: H.277, Y.281, M.306 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.306 Water bridges: A:Y.281 EDO.4: 7 residues within 4Å: Chain A: Y.27, F.34, Q.178, W.179, F.209, R.211, D.226 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.179, A:R.211, A:D.226 Water bridges: A:Y.27, A:Y.27, A:Y.27, A:Y.27, A:Q.178 EDO.5: 7 residues within 4Å: Chain A: L.262, F.263, Y.281, L.283, V.284, M.306 Ligands: EDO.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.284, A:V.284, A:M.306 Water bridges: A:Y.281 EDO.6: 6 residues within 4Å: Chain B: L.49, L.50, G.51, T.53, I.94, L.98 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.53 Water bridges: B:L.49, B:G.51, B:G.51, B:E.93 EDO.7: 8 residues within 4Å: Chain B: Y.27, G.29, P.30, Q.178, W.179, F.209, R.211, D.226 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.29, B:W.179, B:R.211, B:D.226, B:D.226 Water bridges: B:Q.178 EDO.8: 8 residues within 4Å: Chain B: T.10, V.11, E.12, F.253, I.285, P.286, P.287, G.289 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.11, B:E.12, B:G.289 EDO.9: 5 residues within 4Å: Chain A: S.218, G.219 Chain B: S.120, T.121, R.122 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.218, A:G.219, B:T.121, B:R.122 Water bridges: B:R.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, B.K. et al., Four decades of structural evolution of GII.4 norovirus. To be published

Release Date

2017-04-05

Peptides

VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VP1

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