SMTL ID : 8veb.1

Cryo-EM structure of antibody T5-1E08 in complex with stabilized H1N1 Influenza Hemagglutinin Trimer (A/Kiev/1/57)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG-NAG.1: 5 residues within 4Å: Chain A: N.90, E.129, R.130, F.131, Q.185 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.131 Hydrogen bonds: A:Q.185 NAG-NAG.3: 5 residues within 4Å: Chain B: N.90, E.129, R.130, F.131, Q.185 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.131 Hydrogen bonds: B:Q.185 NAG-NAG.5: 5 residues within 4Å: Chain C: N.90, E.129, R.130, F.131, Q.185 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.131 Hydrogen bonds: C:Q.185

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.2: 5 residues within 4Å: Chain A: N.176, Y.214 Chain C: R.205, R.209, D.211 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.205, C:R.205, C:R.205 NAG-NAG-BMA-MAN-MAN-MAN.4: 3 residues within 4Å: Chain A: R.205, R.209 Chain B: N.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.205, A:R.205, A:R.205 NAG-NAG-BMA-MAN-MAN-MAN.6: 5 residues within 4Å: Chain B: R.205, R.209, D.211 Chain C: N.176, Y.214 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.205, B:R.205, B:R.205

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.7: 6 residues within 4Å: Chain A: N.81, E.83, E.103, N.104, C.107, R.237 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.83 Hydrogen bonds: A:N.81, A:E.83, A:E.83, A:E.103, A:N.104, A:R.237, A:R.237 NAG.8: 3 residues within 4Å: Chain A: N.28, S.29, T.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.28 NAG.9: 1 residues within 4Å: Chain A: N.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.40 NAG.10: 2 residues within 4Å: Chain A: N.497, T.499 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.497 NAG.11: 7 residues within 4Å: Chain B: N.81, E.83, E.103, N.104, C.107, P.153, R.237 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.83 Hydrogen bonds: B:E.83, B:E.83, B:E.103, B:N.104, B:R.237, B:R.237 NAG.12: 3 residues within 4Å: Chain B: N.28, S.29, T.30 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.28 NAG.13: 2 residues within 4Å: Chain B: K.39, N.40 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.39 Hydrogen bonds: B:N.40 NAG.14: 2 residues within 4Å: Chain B: N.497, T.499 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.497, B:T.499 NAG.15: 6 residues within 4Å: Chain C: N.81, E.83, E.103, N.104, C.107, R.237 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:E.83 Hydrogen bonds: C:N.81, C:E.83, C:E.83, C:E.103, C:N.104, C:R.237, C:R.237 NAG.16: 3 residues within 4Å: Chain C: N.28, S.29, T.30 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.31, C:N.28 NAG.17: 2 residues within 4Å: Chain C: K.39, N.40 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:K.39 NAG.18: 2 residues within 4Å: Chain C: N.497, T.499 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.497

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mantus, G.E. et al., Distinct binding modes drive the broad neutralization profile of two persistent influenza hemagglutinin stem-specific antibody lineages. Structure (2025)

Release Date

2025-03-19

Peptides

Hemagglutinin: ABC
T5-1E08 Fab heavy chain: DEG
T5-1E08 Fab light chain: FHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

E
H

G
J

F
I

H
K

I
L

Hemagglutinin

T5-1E08 Fab heavy chain

T5-1E08 Fab light chain

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