SMTL ID : 3pa1.2 (2 other biounits)

Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA type A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

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

GAL-FUC-A2G.1: 7 residues within 4Å: Chain A: A.135, N.136, R.137, H.139, E.163, D.166 Ligands: EDO.7 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.163, A:E.163, A:E.163, A:E.163 Hydrophobic interactions: A:A.135 Hydrogen bonds: A:N.136, A:R.137, A:R.137, A:D.166

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

EDO.2: 6 residues within 4Å: Chain A: R.80, G.81, V.142, S.160, T.161, W.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.160 EDO.3: 6 residues within 4Å: Chain A: L.53, Q.54, G.55, T.57, V.102, L.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.57 Water bridges: A:G.55, A:D.101 EDO.4: 5 residues within 4Å: Chain A: Q.58, N.90, L.91, N.92, L.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.91, A:N.92, A:N.92 Water bridges: A:N.92 EDO.5: 7 residues within 4Å: Chain A: L.60, T.62, G.63, A.66, R.68, L.91, K.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.62, A:T.62, A:R.68 EDO.6: 2 residues within 4Å: Chain A: G.232, Y.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.232, A:G.232 EDO.7: 5 residues within 4Å: Chain A: N.123, A.135, R.137, D.166 Ligands: GAL-FUC-A2G.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.123, A:R.137, A:D.166 Water bridges: A:D.166, A:S.168 EDO.8: 3 residues within 4Å: Chain A: R.68, R.122, K.174 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.68 Water bridges: A:R.68, A:R.68, A:S.120 EDO.9: 2 residues within 4Å: Chain A: P.24, P.61 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.24, A:P.61, A:P.177

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.10: 3 residues within 4Å: Chain A: E.140, W.162, K.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.230, A:K.230

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Capsid protein

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