SMTL ID : 3q6q.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: Q.58, N.90, L.91, N.92, L.106 Ligand excluded by PLIP EDO.2: 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.3: 6 residues within 4Å: Chain A: R.80, G.81, V.142, S.160, T.161, W.162 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: P.24, P.61, T.62 Chain B: P.61, T.62 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: R.122, N.123, T.124, T.126, P.134 Chain B: N.235 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: S.196, T.202, L.203, N.204 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: K.6, Q.252, E.253 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: L.53, Q.58, L.59 Chain B: E.17 Ligand excluded by PLIP EDO.9: 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.10: 6 residues within 4Å: Chain A: H.139, E.140, W.162 Chain B: E.140, K.230 Ligands: IMD.19 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.13: 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.14: 5 residues within 4Å: Chain B: Q.58, N.90, L.91, N.92, L.106 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: F.226, I.227, P.228 Chain B: R.68, R.122, K.174 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: F.215, E.218, A.289, Y.314, T.315, L.316 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: E.36, A.38, D.190, W.192 Ligand excluded by PLIP

4 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.18: 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 Water bridges: B:L.53 IMD.19: 5 residues within 4Å: Chain A: H.139 Chain B: E.140, W.162, K.230 Ligands: EDO.10 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.20: 4 residues within 4Å: Chain B: D.50, G.51, E.52, S.254 1 PLIP interactions: 1 interactions with chain B 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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