SMTL ID : 3ony.1 (4 other biounits)

Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with Fucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: Q.57, N.89, L.90, N.91, L.105 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.90, A:N.91, A:N.91 Water bridges: A:N.91, A:L.105 EDO.2: 9 residues within 4Å: Chain A: P.10, L.12, E.244, Q.247, H.248 Chain B: Q.247, H.248, Q.251 Ligands: EDO.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.247, B:Q.247 Hydrogen bonds: A:H.248 EDO.3: 8 residues within 4Å: Chain A: L.59, T.61, G.62, A.65, R.67, L.90, K.173 Chain B: P.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.61 EDO.5: 5 residues within 4Å: Chain A: R.121, K.173 Chain B: F.225, I.226, P.227 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.121, A:K.173, B:F.225 EDO.6: 9 residues within 4Å: Chain A: Q.247, H.248, Q.251 Chain B: P.10, L.12, E.244, Q.247, H.248 Ligands: EDO.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.247, A:H.248 Hydrogen bonds: B:H.248 EDO.7: 9 residues within 4Å: Chain A: P.25 Chain B: L.59, T.61, G.62, A.65, F.66, R.67, L.90, K.173 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.61, B:R.67, B:R.67 EDO.8: 6 residues within 4Å: Chain B: Q.57, N.89, L.90, N.91, T.93, L.105 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.90, B:N.91, B:N.91 Water bridges: B:N.91, B:L.105

2 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.4: 7 residues within 4Å: Chain A: A.134, N.135, R.136, D.165 Chain B: G.230, G.231, Y.232 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.232, A:A.134 Hydrogen bonds: B:G.231, A:N.135, A:R.136, A:R.136, A:D.165 Water bridges: B:K.229, A:D.165 FUC.9: 7 residues within 4Å: Chain A: G.230, G.231, Y.232 Chain B: A.134, N.135, R.136, D.165 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.232, B:A.134 Hydrogen bonds: A:G.231, B:N.135, B:R.136, B:R.136, B:D.165

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

Capsid protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein

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