SMTL ID : 6n08.1

Crystal structure of hemagglutinin from influenza virus A/Netherlands/209/1980 (H3N2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-trimer

Ligands

7 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.31, T.33, T.311 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: S.38, N.278, V.290, N.291, E.391 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.31, T.33, T.311 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.56, F.87 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: S.38, N.278, V.290, N.291, E.391 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.31, T.33, T.311 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain C: S.38, N.278, V.290, N.291, E.391 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: N.158 Chain C: S.212, P.214, W.215 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.215 NAG-NAG-BMA.6: 4 residues within 4Å: Chain A: S.212, P.214, W.215 Chain B: N.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.215 NAG-NAG-BMA.9: 5 residues within 4Å: Chain B: S.212, P.214, W.215 Chain C: N.158, I.235 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:W.215 Hydrophobic interactions: C:I.235 NAG-NAG-BMA.11: 2 residues within 4Å: Chain C: N.119, T.121 No protein-ligand interaction detected (PLIP)

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.12: 2 residues within 4Å: Chain A: N.15, T.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.15 Water bridges: A:T.30, A:N.31 NAG.13: 3 residues within 4Å: Chain A: K.55, N.56, F.87 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.55 Hydrogen bonds: A:N.56 Water bridges: A:K.85 NAG.14: 2 residues within 4Å: Chain A: N.119, T.121 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.121 Hydrogen bonds: A:T.121 NAG.15: 4 residues within 4Å: Chain B: N.15, T.17, T.30, N.31 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.17 Hydrogen bonds: B:N.15 NAG.16: 4 residues within 4Å: Chain C: N.15, T.17, T.30, N.31 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.17 Hydrogen bonds: C:N.15 NAG.17: 3 residues within 4Å: Chain C: K.55, N.56, F.87 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.55 Hydrogen bonds: C:N.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, Y.N. et al., Crystal structure of hemagglutinin from influenza virus A/Netherlands/209/1980 (H3N2). to be published

Release Date

2019-05-15

Peptides

Hemagglutinin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Hemagglutinin