SMTL ID : 8ved.1

Cryo-EM structure of antibody T5-1E11 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

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

NAG-NAG.1: 7 residues within 4Å: Chain A: N.81, E.83, E.103, N.104, C.107, P.153, R.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.237 NAG-NAG.2: 5 residues within 4Å: Chain A: N.90, E.129, R.130, F.131, Q.185 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain D: N.81, E.83, E.103, N.104, C.107, P.153, R.237 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain G: N.81, E.83, E.103, N.104, C.107, P.153, R.237 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: Q.27 Chain G: N.40 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain G: N.90, E.129, R.130, F.131, Q.185 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.185

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]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-MAN.3: 3 residues within 4Å: Chain A: N.176, Y.214 Chain G: R.205 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.205, G:R.205, G:R.205 NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 3 residues within 4Å: Chain A: R.205, D.211 Chain D: 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-MAN.9: 2 residues within 4Å: Chain D: R.205 Chain G: N.176 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.205, D:R.205, D:R.205

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

NAG.10: 1 residues within 4Å: Chain A: N.28 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.40 Chain F: Q.27 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: P.141, N.142, R.179 Ligand excluded by PLIP NAG.13: 6 residues within 4Å: Chain A: E.51, S.53, H.54, N.55, A.301, N.303 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: E.490, E.493, N.497, T.499 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain D: N.40 Chain I: Q.27 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain D: N.90, E.129, R.130 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain D: P.141, N.142 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain D: S.53, H.54, N.55, N.303 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain D: N.27, N.28 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain D: E.490, N.497, T.499 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain G: P.141, N.142, A.170, N.171 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain G: P.141, N.142, R.179 Ligand excluded by PLIP NAG.23: 7 residues within 4Å: Chain G: E.51, S.53, H.54, N.55, A.301, I.302, N.303 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain G: N.28 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain G: E.490, N.497, T.499 Ligand excluded by PLIP

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: ADG
T5-1E11 Fab heavy chain: BEH
T5-1E11 Fab light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

G
E

B
H

E
G

H
J

C
L

F
I

I
K

Hemagglutinin

T5-1E11 Fab heavy chain

T5-1E11 Fab light chain

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