SMTL ID : 3q39.1

Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA type H2 (diglycan)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

1 x GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose(Non-covalent)

GAL-FUC.1: 7 residues within 4Å: Chain A: A.135, N.136, R.137, D.166 Chain B: G.231, G.232, Y.233 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.136, A:R.137, A:R.137, A:D.166, B:G.232, B:G.232 Hydrophobic interactions: B:Y.233 Water bridges: A:D.166

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

EDO.2: 5 residues within 4Å: Chain A: P.26, D.28, F.226 Chain B: R.68 Ligands: EDO.23 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: L.60, T.62, G.63, A.66, L.91, K.174 Chain B: P.26 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: E.17 Chain B: L.53, L.59, L.106, Y.251 Ligand excluded by PLIP EDO.5: 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.6: 5 residues within 4Å: Chain A: F.189, Q.191, R.224, P.236, A.237 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: H.83, V.142, I.143, A.144, S.147, Q.158, F.159, S.160 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: R.122, K.174 Chain B: F.226, I.227, P.228 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: Q.58, N.90, L.91, N.92, L.106 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: L.53, Q.58, L.59 Chain B: E.17 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: P.24, P.61 Chain B: P.24, P.61, T.62 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: Y.146, T.193, L.194, P.195, S.196 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: R.80, G.81, V.142, S.160, T.161, W.162 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: H.139, E.140, W.162 Chain B: E.140, K.230 Ligands: IMD.15, IMD.26 Ligand excluded by PLIP EDO.17: 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.18: 5 residues within 4Å: Chain B: Q.58, N.90, L.91, N.92, L.106 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: R.80, S.160, T.161, W.162 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: F.189, Q.191, R.224, P.236, A.237 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: L.60, R.68, N.92 Chain B: P.26, I.27, D.28 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 EDO.23: 6 residues within 4Å: Chain A: F.226, I.227, P.228 Chain B: R.122, K.174 Ligands: EDO.2 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: P.11, L.13, L.18, W.246, Y.303, F.304 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: V.183, D.184, A.185, S.187, H.188, F.189 Ligand excluded by PLIP

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.15: 5 residues within 4Å: Chain A: E.140, W.162, K.230 Chain B: H.139 Ligands: EDO.14 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.139, A:E.140, A:K.230 IMD.16: 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.26: 5 residues within 4Å: Chain A: H.139 Chain B: E.140, W.162, K.230 Ligands: EDO.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.230 Water bridges: B:E.140, B:E.140 pi-Stacking: B:W.162 pi-Cation interactions: B:K.230 IMD.27: 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

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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