SMTL ID : 3ry8.1

Structural basis for norovirus inhibition and fucose mimicry by citrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: Q.58, N.90, L.91, N.92, L.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.91, A:N.92, A:N.92 Water bridges: A:T.94 EDO.2: 6 residues within 4Å: Chain A: L.53, Q.54, G.55, T.57, V.102, L.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.57 Water bridges: A:L.53, A:G.55, A:D.101 EDO.3: 7 residues within 4Å: Chain A: L.60, T.62, G.63, A.66, L.91, K.174 Chain B: P.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.62, A:T.62 EDO.4: 6 residues within 4Å: Chain A: G.16, P.26, I.27, D.28 Chain B: L.60, N.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.27 EDO.5: 5 residues within 4Å: Chain A: G.81, V.142, S.160, T.161, W.162 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.81, A:G.81, A:S.160 Water bridges: A:Q.114, A:S.160 EDO.6: 4 residues within 4Å: Chain A: R.122 Chain B: F.226, I.227, P.228 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.122 EDO.7: 8 residues within 4Å: Chain A: L.15, V.29, L.30, Y.266, V.296, A.298, P.299, T.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.30, A:L.30, A:Y.266, A:P.299 EDO.9: 7 residues within 4Å: Chain A: P.26 Chain B: L.60, T.62, G.63, A.66, L.91, K.174 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.62 EDO.10: 6 residues within 4Å: Chain B: L.53, Q.54, G.55, T.57, V.102, L.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.57 Water bridges: B:G.55 EDO.11: 5 residues within 4Å: Chain B: Q.58, N.90, L.91, N.92, L.106 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.91, B:N.92, B:N.92 Water bridges: B:N.92, B:L.106 EDO.12: 6 residues within 4Å: Chain A: L.60, N.92 Chain B: G.16, P.26, I.27, D.28 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.27 Water bridges: A:N.92

1 x FLC: CITRATE ANION(Non-covalent)

FLC.8: 7 residues within 4Å: Chain A: A.135, N.136, R.137, D.166, S.168 Chain B: G.231, G.232 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.123, A:N.136, A:N.136, A:R.137, A:R.137, A:S.168, B:G.232 Salt bridges: A:R.137, A:R.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hansman, G.S. et al., Structural basis for norovirus inhibition and fucose mimicry by citrate. J.Virol. (2012)

Release Date

2011-11-09

Peptides

Capsid protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein

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