SMTL ID : 6h9v.1

Crystal structure of deaminated P domain from norovirus strain Saga GII-4 in complex with Fuc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

2 x MFU: methyl alpha-L-fucopyranoside(Non-covalent)

MFU.1: 7 residues within 4Å: Chain A: S.122, T.123, R.124, D.153 Chain B: S.221, G.222, Y.223 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.123, A:R.124, A:R.124, A:D.153, B:G.222 Water bridges: A:H.126 Hydrophobic interactions: B:Y.223 MFU.3: 7 residues within 4Å: Chain A: S.221, G.222, Y.223 Chain B: S.122, T.123, R.124, D.153 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.223 Hydrogen bonds: A:G.222, B:T.123, B:R.124, B:R.124, B:D.153 Water bridges: B:D.153

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: F.266, E.267, A.307, P.308, M.309 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.307 MG.4: 5 residues within 4Å: Chain B: F.266, E.267, A.307, P.308, M.309 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.307, H2O.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mallagaray, A. et al., A post-translational modification of human Norovirus capsid protein attenuates glycan binding. Nat Commun (2019)

Release Date

2019-04-03

Peptides

VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VP1