SMTL ID : 3asr.1

Crystal structure of P domain from Norovirus Funabashi258 stain in the complex with Lewis-a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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: 10 residues within 4Å: Chain A: D.115, H.117, W.171, S.173, Q.174, S.176, P.224 Chain B: S.128, S.129, G.130 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.171 Hydrogen bonds: A:Q.174, B:G.130, A:S.173, A:S.173 Water bridges: A:D.115, A:S.137, A:G.180 NAG-GAL-FUC.2: 12 residues within 4Å: Chain A: S.128, S.129, G.130 Chain B: D.115, H.117, W.171, S.173, Q.174, P.175, S.176, P.224 Ligands: NPO.5 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.130, B:Q.174, B:Q.174, B:S.173, B:S.173 Hydrophobic interactions: B:W.171 Water bridges: B:D.115, B:S.137, B:S.137, B:D.155

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

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

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

Links

RCSB   PDBe   PDBe-KB   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

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