SMTL ID : 8ut6.1

CryoEM structure of A/Perth/16/2009 H3 in complex with polyclonal Fab from mice immunized with H3 stem nanoparticles-15 days post immunization

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-mer

Ligands

3 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: 9 residues within 4Å: Chain C: N.165, T.167, I.242, L.244 Chain D: S.219, R.220, P.221, R.222 Ligands: NAG.7 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.222 Hydrophobic interactions: C:I.242 NAG-NAG.2: 7 residues within 4Å: Chain D: N.165, T.167, I.242 Chain E: S.219, P.221, R.222 Ligands: NAG.13 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:R.222 Hydrophobic interactions: D:I.242 NAG-NAG.3: 8 residues within 4Å: Chain C: S.219, P.221, R.222 Chain E: N.165, T.167, I.242, L.244 Ligands: NAG.19 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:P.221, E:I.242 Hydrogen bonds: C:R.222, C:R.222

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

NAG.4: 2 residues within 4Å: Chain C: T.37, N.38 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain C: K.62, N.63, Q.75 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain C: Q.132, N.133, R.255 Ligand excluded by PLIP NAG.7: 7 residues within 4Å: Chain C: R.201, T.203, N.246, T.248 Chain D: I.217, G.218 Ligands: NAG-NAG.1 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain C: S.45, N.285, V.297, N.298, E.398 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain C: G.479, R.482, N.483 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: X.104 Chain D: N.38 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain D: K.62, N.63, Y.94 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain D: N.133, R.255 Ligand excluded by PLIP NAG.13: 8 residues within 4Å: Chain D: A.163, L.164, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG.2 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain D: S.45, N.285, V.297, N.298 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain D: A.476, G.479, S.480, N.483, T.485 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain E: T.37, N.38 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain E: K.62, N.63, Y.94 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain E: Q.132, N.133, R.255 Ligand excluded by PLIP NAG.19: 6 residues within 4Å: Chain C: I.217 Chain E: A.163, R.201, N.246, S.247 Ligands: NAG-NAG.3 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain E: S.45, N.285, V.297, N.298 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain E: A.476, G.479, N.483, T.485 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ray, R. et al., Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses. Immunity (2024)

Release Date

2024-05-08

Peptides

H3D15 pFab HC Fv_polyA: A
H3D15 pFab LC Fv_polyA: B
Hemagglutinin: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
A

D
C

E
E

H3D15 pFab HC Fv_polyA

H3D15 pFab LC Fv_polyA

Hemagglutinin

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