SMTL ID : 8ur5.1

I53_dn5 nanoparticle displaying the trimeric HA heads with heptad domain, TH-1heptad-I53_dn5 (local refinement of TH-1heptad)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: Y.141, N.143, N.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.143 NAG.2: 2 residues within 4Å: Chain A: P.108, N.109 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.108 NAG.3: 2 residues within 4Å: Chain A: G.37, N.38 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain A: N.48, N.71, C.119, R.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.71, A:R.204 NAG.5: 3 residues within 4Å: Chain B: Y.141, N.143, N.228 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.143 NAG.6: 2 residues within 4Å: Chain B: P.108, N.109 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.108 NAG.7: 2 residues within 4Å: Chain B: G.37, N.38 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain B: N.48, N.71, C.119, R.204 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.71, B:R.204 NAG.9: 3 residues within 4Å: Chain C: Y.141, N.143, N.228 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.143 NAG.10: 2 residues within 4Å: Chain C: P.108, N.109 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.108 NAG.11: 2 residues within 4Å: Chain C: G.37, N.38 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain C: N.48, N.71, C.119, R.204 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.71, C:R.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ellis, D. et al., Antigen spacing on protein nanoparticles influences antibody responses to vaccination. Cell Rep (2023)

Release Date

2023-12-27

Peptides

Trimer head HA,Hemagglutinin HA1 chain: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Trimer head HA,Hemagglutinin HA1 chain