SMTL ID : 3asp.1

Crystal structure of P domain from Norovirus Funabashi258 stain in the complex with A-antigen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x NAG- GAL- FUC- A2G: alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-GAL-FUC-A2G.1: 7 residues within 4Å: Chain A: D.115, H.117, Q.139, W.171, S.173, Q.174, S.176 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.117, A:S.173, A:S.173, A:S.176, A:S.176 Water bridges: B:G.130 NAG-GAL-FUC-A2G.2: 7 residues within 4Å: Chain B: D.115, H.117, Q.139, W.171, S.173, Q.174, S.176 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.117, B:S.173, B:S.173, B:S.176, B:S.176 Water bridges: B:P.175, B:G.180, A:G.130, B:Q.139

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:F.145 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:D.190

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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