SMTL ID : 9ei9.1

Cryo-EM structure of 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.89 Å

Oligo State

hetero-3-3-2-2-mer

Ligands

4 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: 7 residues within 4Å: Chain A: A.163, R.201, N.246, S.247, T.248 Chain E: I.217, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.6, D.7, N.8 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: I.217, Y.219 Chain B: A.163, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-BMA.5 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: I.217 Chain E: A.163, R.201, N.246, S.247, T.248 No protein-ligand interaction detected (PLIP)

3 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: 7 residues within 4Å: Chain A: N.165, T.167, I.242, L.244 Chain E: Y.219, R.222, N.225 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:R.222, E:R.222, E:N.225 Hydrophobic interactions: A:I.242 NAG-NAG-BMA.5: 9 residues within 4Å: Chain A: Y.219, P.221, R.222, N.225 Chain B: N.165, T.167, L.244 Ligands: NAG-NAG.4, NAG-NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.222, A:R.222, A:R.222, A:N.225 NAG-NAG-BMA.7: 6 residues within 4Å: Chain B: Y.219, P.221, R.222 Chain E: N.165, T.167, L.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.222, B:R.222

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

NAG.8: 2 residues within 4Å: Chain A: N.285, V.297 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.122, N.133, R.255 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.22 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.38 Chain C: W.21 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: E.62, N.63, Y.94 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: N.285, V.297, N.298 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: Q.132, N.133, R.255 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.22 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.38, A.39 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: E.62, N.63, Y.94 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.126 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: G.150, N.154 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain D: A.147, G.150, S.151, N.154 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain E: N.285, V.297 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain E: N.133, R.255 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain E: N.22 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain E: N.38, T.40, T.318 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain E: E.62, N.63, Y.94 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain E: N.126 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain F: G.150, N.154 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rawi, R. et al., The N terminus of H3-influenza hemagglutinin as a site-of-vulnerability to neutralizing antibody. Structure (2025)

Release Date

2025-07-16

Peptides

Hemagglutinin HA1: ABE
Hemagglutinin HA2: CDF
5E10 Fab Heavy chain: GI
5E10 Fab Light chain: HJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

E
G

C
E

D
F

F
I

G
A

I
H

H
D

J
J

Hemagglutinin HA1

Hemagglutinin HA2

5E10 Fab Heavy chain

5E10 Fab Light chain

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