SMTL ID : 3r6k.1

Crystal Structure of the Capsid P Domain from Norwalk Virus Strain Hiroshima/1999 in complex with HBGA type B (triglycan)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x GAL- FUC- GLA: alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose

GAL-FUC-GLA.1: 9 residues within 4Å: Chain A: A.124, C.125, R.126, H.128, D.155, H.157 Chain B: K.216, G.217, G.218 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:C.125, A:R.126, A:R.126, A:D.155, B:G.218, B:K.216, B:K.216, B:K.216 GAL-FUC-GLA.4: 9 residues within 4Å: Chain A: K.216, G.217, G.218 Chain B: A.124, C.125, R.126, H.128, D.155, H.157 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:C.125, B:R.126, B:R.126, B:D.155, A:G.218, A:K.216, A:K.216, A:K.216

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: S.65, F.66, R.67, T.86, N.87, I.88, P.102, L.103, T.105 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.65, A:R.67, A:N.87 Water bridges: A:T.86, A:I.88 EDO.3: 5 residues within 4Å: Chain A: P.10, E.231, H.235 Chain B: Q.234, Q.238 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.234, B:Q.234, B:Q.238 Hydrogen bonds: A:H.235 EDO.5: 9 residues within 4Å: Chain B: S.65, F.66, R.67, T.86, N.87, I.88, P.102, L.103, T.105 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.65, B:R.67, B:N.87 Water bridges: B:T.86, B:I.88 EDO.6: 5 residues within 4Å: Chain A: Q.234, Q.238 Chain B: P.10, E.231, H.235 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:H.235 Water bridges: A:Q.234, A:Q.234, A:Q.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hansman, G.S. et al., Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability. J.Virol. (2011)

Release Date

2011-05-11

Peptides

VP1 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

VP1 protein

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