SMTL ID : 6fyt.1

Structure of H1 (A/solomon Islands/3/06) Influenza Hemagglutinin in complex with SD38

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-3-3-3-mer

Ligands

6 x NAG- FUC- NAG- FUC: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG-FUC.1: 1 residues within 4Å: Chain A: N.27 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG-FUC.5: 3 residues within 4Å: Chain B: N.154, T.156 Chain C: F.29 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.29 NAG-FUC-NAG-FUC.9: 1 residues within 4Å: Chain D: N.27 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG-FUC.13: 3 residues within 4Å: Chain E: N.154, T.156 Chain F: F.29 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.29 NAG-FUC-NAG-FUC.17: 1 residues within 4Å: Chain G: N.27 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG-FUC.21: 3 residues within 4Å: Chain H: N.154, T.156 Chain I: F.29 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:F.29

6 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.58, E.90 Ligands: NAG-NAG-BMA.3, NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.163, Y.201 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain D: N.58, E.90 Ligands: NAG-NAG-BMA.11, NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain D: N.163, Y.201 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain G: N.58, E.90 Ligands: NAG-NAG-BMA.19, NAG-NAG-BMA.19 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain G: N.163, Y.201 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.3: 9 residues within 4Å: Chain A: N.68, E.70, E.90, N.91, C.94, S.140, R.224 Ligands: NAG-NAG.2, NAG-NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.224 NAG-NAG-BMA.11: 9 residues within 4Å: Chain D: N.68, E.70, E.90, N.91, C.94, S.140, R.224 Ligands: NAG-NAG.10, NAG-NAG.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.224 NAG-NAG-BMA.19: 9 residues within 4Å: Chain G: N.68, E.70, E.90, N.91, C.94, S.140, R.224 Ligands: NAG-NAG.18, NAG-NAG.18 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.224

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

NAG.6: 1 residues within 4Å: Chain A: N.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.15 NAG.7: 1 residues within 4Å: Chain A: N.129 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain A: N.290, S.291, S.292, L.293 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.293 NAG.14: 1 residues within 4Å: Chain D: N.15 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.15 NAG.15: 1 residues within 4Å: Chain D: N.129 No protein-ligand interaction detected (PLIP) NAG.16: 4 residues within 4Å: Chain D: N.290, S.291, S.292, L.293 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.293 NAG.22: 1 residues within 4Å: Chain G: N.15 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.15 NAG.23: 1 residues within 4Å: Chain G: N.129 No protein-ligand interaction detected (PLIP) NAG.24: 4 residues within 4Å: Chain G: N.290, S.291, S.292, L.293 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laursen, N.S. et al., Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin. Science (2018)

Release Date

2018-11-07

Peptides

Hemagglutinin: ADG
Hemagglutinin: BEH
Single domain antibody SD38: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

B
B

E
B

H
B

C
I

F
I

I
I

Hemagglutinin

Hemagglutinin

Single domain antibody SD38

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