SMTL ID : 7yqg.1

Functional and Structural Characterization of Norovirus GII.6 in Recognizing Histo-blood Group Antigens

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose(Non-covalent)

GAL-FUC.1: 7 residues within 4Å: Chain A: A.138, T.139, R.140, D.168 Chain B: G.229, G.230, Y.231 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.138, B:Y.231 Hydrogen bonds: A:R.140, A:R.140, A:D.168, B:G.230 Water bridges: A:N.130, A:D.168 GAL-FUC.2: 7 residues within 4Å: Chain A: G.229, G.230, Y.231 Chain B: A.138, T.139, R.140, D.168 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.231, B:A.138 Hydrogen bonds: A:G.230, B:R.140, B:R.140, B:D.168 Water bridges: B:N.130, B:D.168, B:D.168

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: S.257, W.307, V.308 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.307 GOL.4: 6 residues within 4Å: Chain A: L.51, Q.52, G.53, T.55, V.109, L.113 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.55 Water bridges: A:L.51, A:G.53, A:G.53, A:E.108, A:E.108 GOL.5: 8 residues within 4Å: Chain A: F.213, P.214, E.216, K.277, Q.310, F.311, Y.312, T.313 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.214, A:E.216, A:E.216, A:K.277 Water bridges: A:F.311, A:L.314 GOL.6: 6 residues within 4Å: Chain B: L.51, Q.52, G.53, T.55, V.109, L.113 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.52, B:T.55 Water bridges: B:G.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cong, X. et al., Functional and structural characterization of Norovirus GII.6 in recognizing histo-blood group antigens. Virol Sin (2023)

Release Date

2023-06-07

Peptides

VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VP1

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