SMTL ID : 8ct6.1

1F8 mAb in complex with the computationally optimized broadly reactive H1 influenza hemagglutinin P1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

1 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.1: 7 residues within 4Å: Chain A: N.64, E.66, E.86, N.87, C.90, S.137, R.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.221

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 4 residues within 4Å: Chain A: N.127, T.129, K.130, T.152 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN: 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.3: 6 residues within 4Å: Chain B: N.64, E.66, E.86, N.87, C.90, R.221 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.221 NAG-NAG-BMA-MAN.4: 6 residues within 4Å: Chain C: N.64, E.66, E.86, N.87, C.90, R.221 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.221

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

NAG.5: 1 residues within 4Å: Chain A: N.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.287 NAG.6: 1 residues within 4Å: Chain A: N.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.11 NAG.7: 2 residues within 4Å: Chain A: K.22, N.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.22, A:K.22 NAG.8: 1 residues within 4Å: Chain A: N.269 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain B: N.269 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.269 NAG.10: 5 residues within 4Å: Chain B: H.126, N.127, T.129, K.130, K.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.127 NAG.11: 2 residues within 4Å: Chain B: N.276, N.287 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.287 NAG.12: 1 residues within 4Å: Chain C: N.23 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.23, C:N.23 NAG.13: 3 residues within 4Å: Chain C: C.275, N.276, N.287 No protein-ligand interaction detected (PLIP) NAG.14: 4 residues within 4Å: Chain C: N.127, T.129, K.130 Chain F: E.97 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:N.127, C:T.129, C:K.130, F:E.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dzimianski, J.V. et al., Structural insights into the broad protection against H1 influenza viruses by a computationally optimized hemagglutinin vaccine. Commun Biol (2023)

Release Date

2023-04-19

Peptides

COBRA P1 HA: ABC
1F8 light chain: DF
1F8 heavy chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
L

F
K

E
H

G
J

COBRA P1 HA

1F8 light chain

1F8 heavy chain