SMTL ID : 3ast.1

Crystal structure of P domain Q389N mutant from Norovirus Funabashi258 stain in the complex with Lewis-b

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

NAG-GAL-FUC-FUC.1: 14 residues within 4Å: Chain A: D.115, H.117, S.137, W.171, S.173, N.174, P.175, S.176, P.224 Chain B: S.128, S.129, G.130, D.131 Ligands: NPO.4 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:G.130, A:D.115, A:H.117, A:S.173, A:S.173 Water bridges: B:S.128, B:S.128, B:S.129, A:N.174, A:N.174, A:N.174, A:D.155, A:S.176 Hydrophobic interactions: A:W.171, A:P.224 NAG-GAL-FUC-FUC.2: 14 residues within 4Å: Chain A: S.128, S.129, G.130, D.131 Chain B: D.115, H.117, S.137, W.171, S.173, N.174, P.175, S.176, P.224 Ligands: NPO.5 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.130, B:N.174, B:D.115, B:H.117, B:S.173, B:S.173 Water bridges: A:S.128, B:N.174, B:D.155, B:S.176 Hydrophobic interactions: B:W.171, B:P.224

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: F.145, D.190, G.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.190 NA.6: 3 residues within 4Å: Chain B: F.145, D.190, G.192 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.190

2 x NPO: P-NITROPHENOL(Non-functional Binders)

NPO.4: 1 residues within 4Å: Ligands: NAG-GAL-FUC-FUC.1 No protein-ligand interaction detected (PLIP) NPO.5: 1 residues within 4Å: Ligands: NAG-GAL-FUC-FUC.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Kubota, T. et al., Structural basis for the recognition of Lewis antigens by genogroup I norovirus. J.Virol. (2012)

Release Date

2012-01-25

Peptides

Capsid protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein