SMTL ID : 3q3a.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

1 x NAG- GAL- FUL: beta-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-FUL.1: 13 residues within 4Å: Chain A: A.135, N.136, R.137, H.139, E.163, D.166 Chain B: R.80, W.162, K.230, G.231, G.232, Y.233 Ligands: IMD.16 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B 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:R.80, B:R.80, B:G.232, B:K.230 Water bridges: B:D.184, A:E.163, A:E.163, B:K.230 Salt bridges: A:H.139, B:K.230

5 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 5 residues within 4Å: Chain A: R.80, G.81, S.160, T.161, W.162 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.160 IMD.3: 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.4: 5 residues within 4Å: Chain A: E.140, W.162, K.230 Chain B: H.139 Ligands: EDO.26 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.139, A:K.230 pi-Stacking: A:W.162 IMD.15: 5 residues within 4Å: Chain B: L.53, Q.54, G.55, T.57, L.106 No protein-ligand interaction detected (PLIP) IMD.16: 6 residues within 4Å: Chain A: H.139 Chain B: E.140, W.162, K.230 Ligands: NAG-GAL-FUL.1, EDO.26 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.230, A:H.139 pi-Stacking: B:W.162

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

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 Ligand excluded by PLIP EDO.6: 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.7: 5 residues within 4Å: Chain A: Q.58, N.90, L.91, N.92, L.106 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: A.181, S.182, D.184, G.231, G.232 Ligand excluded by PLIP EDO.9: 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.10: 3 residues within 4Å: Chain A: K.6, Q.252, E.253 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: P.98, T.99, E.100, D.101, K.153, M.205, N.206 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: F.189, Q.191, R.224, P.236, A.237 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: P.24, P.61 Chain B: P.24, P.61, T.62 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: L.53, Q.58, L.59 Chain B: E.17 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: 3 residues within 4Å: Chain B: S.160, T.161, W.162 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: F.226, I.227, P.228 Chain B: R.68, R.122 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: K.6, Q.252, E.253 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: Q.58, N.90, L.91, N.92, L.106 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: K.153, T.202, L.203, M.205 Ligands: EDO.23 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain B: P.98, T.99, E.100, D.101, K.153, M.205, N.206 Ligands: EDO.22 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: F.189, Q.191, R.224, P.236, A.237 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: P.11, L.13, L.18, W.246, Y.303, F.304 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain A: E.140, K.230 Chain B: H.139, E.140, W.162 Ligands: IMD.4, IMD.16 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: T.193, L.194, S.196, N.204 Ligand excluded by PLIP

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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