SMTL ID : 3pa1.1 (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

homo-dimer

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: 12 residues within 4Å: Chain A: A.135, N.136, R.137, H.139, E.163, D.166 Chain B: W.162, G.231, G.232, Y.233 Ligands: EDO.7, IMD.18 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Water bridges: A:E.163, A:E.163, A:E.163, A:E.163, B:K.230 Hydrophobic interactions: A:A.135, B:Y.233 Hydrogen bonds: A:N.136, A:R.137, A:R.137, A:D.166, B:G.232, B:G.232

15 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: 8 residues within 4Å: Chain A: L.60, T.62, G.63, A.66, R.68, L.91, K.174 Chain B: P.26 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.62, A:T.62, A:R.68 EDO.6: 4 residues within 4Å: Chain A: G.232, Y.233 Chain B: A.135, N.136 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.136, 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 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.123, A:R.137, A:D.166 Water bridges: A:D.166, A:S.168, B:Y.233, B:Y.233 EDO.8: 6 residues within 4Å: Chain A: R.68, R.122, K.174 Chain B: F.226, I.227, P.228 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: 5 residues within 4Å: Chain A: P.24, P.61 Chain B: P.24, P.61, T.62 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:P.24, A:P.61, A:P.177, B:T.62 EDO.11: 8 residues within 4Å: Chain A: P.26 Chain B: L.60, T.62, G.63, A.66, R.68, L.91, K.174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.62, B:R.68 EDO.12: 5 residues within 4Å: Chain B: Q.58, N.90, L.91, N.92, L.106 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.92, B:N.92 Water bridges: B:L.91, B:L.91, B:N.92 EDO.13: 6 residues within 4Å: Chain A: F.226, I.227, P.228 Chain B: R.68, R.122, K.174 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.68, B:R.122 Water bridges: B:K.174, A:F.226 EDO.14: 2 residues within 4Å: Chain B: R.224, N.235 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.224, B:R.224 Water bridges: B:Y.31, B:Y.31, B:Y.31, B:Y.31, B:N.235 EDO.15: 6 residues within 4Å: Chain B: L.53, Q.54, G.55, T.57, V.102, L.106 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.57 Water bridges: B:G.55, B:D.101 EDO.16: 3 residues within 4Å: Chain A: E.17 Chain B: Q.58, L.59 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.59, A:E.17, A:E.17 EDO.17: 5 residues within 4Å: Chain A: Q.252 Chain B: P.11, E.245, Q.248, H.249 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.252, A:Q.252, B:Q.248 Water bridges: A:H.249, B:Q.252

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.10: 4 residues within 4Å: Chain A: E.140, W.162, K.230 Chain B: H.139 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.230, A:K.230, B:H.139 IMD.18: 4 residues within 4Å: Chain A: H.139 Chain B: E.140, K.230 Ligands: GAL-FUC-A2G.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.230 Water bridges: B:E.140

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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