SMTL ID : 5zvc.1

P domain of GII.13 norovirus capsid complexed with Lewis A trisaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

NAG-GAL-FUC.1: 7 residues within 4Å: Chain A: W.77, S.136, T.138, S.139, N.174, N.176, T.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.176, A:S.136, A:T.138, A:T.138, A:N.174, A:N.176, A:N.176, A:T.177, A:T.177, A:N.176 Water bridges: A:D.75, A:D.78, A:S.139 Hydrophobic interactions: A:W.77 NAG-GAL-FUC.2: 7 residues within 4Å: Chain B: W.77, S.136, T.138, S.139, N.174, N.176, T.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.136, B:T.138, B:N.174, B:N.176, B:N.176, B:T.177, B:N.176 Water bridges: B:D.75, B:D.75, B:W.77, B:T.138, B:T.138, B:S.139, B:S.139 Hydrophobic interactions: B:W.77

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: A.31, P.32, N.33, N.36, Q.181, W.182, F.212, R.214, D.231 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.33, A:N.36, A:R.214, A:D.231, A:D.231 GOL.4: 9 residues within 4Å: Chain B: A.31, P.32, N.33, N.36, Q.181, W.182, F.212, R.214, D.231 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.33, B:R.214, B:D.231 Water bridges: B:Y.29, B:Q.181

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Qian, Y. et al., Structural Adaptations of Norovirus GII.17/13/21 Lineage through Two Distinct Evolutionary Paths. J. Virol. (2019)

Release Date

2018-10-03

Peptides

Major capsid protein VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Major capsid protein VP1

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