SMTL ID : 7vdf.1

2.56 A structure of influenza hemagglutinin (HA) trimer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.1: 7 residues within 4Å: Chain A: S.45, S.46, S.47, N.285, V.297, N.298, E.398 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.297 NAG.2: 7 residues within 4Å: Chain A: N.165, T.167, V.244 Chain C: T.187, S.219, W.222 Ligands: NAG.11 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.165, A:T.167, C:S.219, C:W.222 NAG.3: 5 residues within 4Å: Chain A: Q.80, N.81, F.120, I.121, R.150 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.80 Hydrogen bonds: A:N.81 NAG.4: 8 residues within 4Å: Chain A: P.221, W.222 Chain B: T.167, R.207, V.242, V.244 Ligands: BMA.5, NAG.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.242 Hydrogen bonds: A:W.222 NAG.6: 7 residues within 4Å: Chain B: S.45, S.46, S.47, N.285, V.297, N.298, E.398 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.285, B:V.297 NAG.7: 8 residues within 4Å: Chain A: T.187, S.219, W.222, S.227 Chain B: N.165, T.167, V.244 Ligands: NAG.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.219, A:W.222, B:N.165 NAG.8: 5 residues within 4Å: Chain B: Q.80, N.81, F.120, I.121, R.150 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.81 NAG.9: 8 residues within 4Å: Chain B: P.221, W.222 Chain C: T.167, R.207, V.242, V.244 Ligands: BMA.10, NAG.14 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.242 Hydrogen bonds: B:W.222 NAG.11: 8 residues within 4Å: Chain A: T.167, R.207, V.242, V.244 Chain C: P.221, W.222 Ligands: NAG.2, BMA.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.242 Hydrogen bonds: C:W.222 NAG.13: 7 residues within 4Å: Chain C: S.45, S.46, S.47, N.285, V.297, N.298, E.398 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.297 Hydrogen bonds: C:N.285, C:V.297 NAG.14: 8 residues within 4Å: Chain B: T.187, S.219, W.222, S.227 Chain C: N.165, T.167, V.244 Ligands: NAG.9 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.219, B:S.219, B:W.222, C:N.165, C:T.167 NAG.15: 2 residues within 4Å: Chain C: Q.80, N.81 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Q.80 Hydrogen bonds: C:N.81

3 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.5: 2 residues within 4Å: Chain A: W.222 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) BMA.10: 2 residues within 4Å: Chain B: W.222 Ligands: NAG.9 No protein-ligand interaction detected (PLIP) BMA.12: 2 residues within 4Å: Chain C: W.222 Ligands: NAG.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, H. et al., A cryo-electron microscopy support film formed by 2D crystals of hydrophobin HFBI. Nat Commun (2021)

Release Date

2021-12-29

Peptides

Hemagglutinin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Hemagglutinin

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