SMTL ID : 3q38.1

Crystal structure of P domain from norwalk virus strain vietnam 026 in complex with HBGA type B (triglycan)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

homo-dimer

Ligands

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

GAL-FUC-GLA.1: 10 residues within 4Å: Chain A: A.135, N.136, R.137, H.139, E.163, D.166 Chain B: G.231, G.232, Y.233 Ligands: IMD.25 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.233, A:A.135 Hydrogen bonds: B:G.232, A:N.136, A:R.137, A:R.137, A:D.166, B:G.232 Water bridges: B:W.162, A:E.163

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

EDO.2: 8 residues within 4Å: Chain A: L.60, T.62, G.63, A.66, R.68, L.91, K.174 Chain B: P.26 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: H.139, E.140, W.162 Chain B: E.140, K.230 Ligands: IMD.13, IMD.25 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: P.24, P.61, T.62 Chain B: P.24, P.61, T.62 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: R.80, G.81, V.142, S.160, T.161, W.162 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: Q.58, N.90, L.91, N.92, L.106 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: E.17 Chain B: L.53, L.59, L.106, Y.251 Ligands: EDO.15 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: G.16, P.26, I.27, D.28 Chain B: L.60, N.92 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: P.26, D.28 Chain B: R.68 Ligands: EDO.16 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: F.189, Q.191, R.224, P.236, A.237 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: P.11, L.13, E.245, H.249 Chain B: Q.248, Q.252 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: P.26 Chain B: L.60, T.62, G.63, A.66, R.68, L.91, K.174 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: Q.58, N.90, L.91, N.92, L.106 Ligands: EDO.7 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: F.226, I.227, P.228 Chain B: R.68, R.122, K.174 Ligands: EDO.9 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: K.6, Q.252, E.253 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: T.72, N.85, M.86, T.87, N.156, I.157 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: R.68, G.69, K.70, P.172, T.173 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: R.68 Chain B: P.26, D.28 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: G.81, V.142, S.160, T.161, W.162 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: P.98, T.99, E.100, D.101, K.153, N.206 Ligand excluded by PLIP

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.12: 6 residues within 4Å: Chain A: L.53, Q.54, G.55, T.57, V.102, L.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.57 IMD.13: 5 residues within 4Å: Chain A: E.140, W.162, K.230 Chain B: H.139 Ligands: EDO.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.140, A:K.230, B:H.139 IMD.23: 6 residues within 4Å: Chain B: L.53, Q.54, G.55, T.57, V.102, L.106 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.57 IMD.24: 4 residues within 4Å: Chain A: I.12 Chain B: Y.251, Q.252, S.254 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.251 Water bridges: B:Y.251, B:S.254 IMD.25: 6 residues within 4Å: Chain A: H.139 Chain B: E.140, W.162, K.230 Ligands: GAL-FUC-GLA.1, EDO.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.230 Water bridges: B:E.140 pi-Stacking: B:W.162 pi-Cation interactions: B:K.230 IMD.26: 4 residues within 4Å: Chain B: D.50, G.51, E.52, S.254 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.254 Water bridges: B:S.254

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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