SMTL ID : 7qa4.1

Crystal structure of stabilized H3N2 A/Hong Kong/1/1968 Hemagglutinin at 2.2 Angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-trimer

Ligands

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.1: 4 residues within 4Å: Chain A: N.38, T.40, T.318, L.381 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain B: N.38, T.40, T.318, L.381 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain C: N.38, T.40, T.318, L.381 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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.2: 6 residues within 4Å: Chain A: N.165, T.167, V.242 Chain C: S.219, P.221, W.222 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:W.222 Hydrophobic interactions: A:V.242 NAG-NAG-BMA-MAN-MAN.8: 6 residues within 4Å: Chain A: S.219, P.221, W.222 Chain B: N.165, T.167, V.242 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.222 Hydrophobic interactions: B:V.242 NAG-NAG-BMA-MAN-MAN.14: 6 residues within 4Å: Chain B: S.219, P.221, W.222 Chain C: N.165, T.167, V.242 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.242 Hydrogen bonds: B:W.222

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.3: 5 residues within 4Å: Chain A: Q.80, N.81, E.119, F.120, I.121 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.121 NAG-NAG.4: 4 residues within 4Å: Chain A: S.45, N.285, V.297, N.298 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: Q.80, N.81, E.119, F.120, I.121 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.121 NAG-NAG.10: 4 residues within 4Å: Chain B: S.45, N.285, V.297, N.298 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain C: Q.80, N.81, E.119, F.120, I.121 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.121 NAG-NAG.16: 4 residues within 4Å: Chain C: S.45, N.285, V.297, N.298 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.22, G.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.22 NAG.11: 2 residues within 4Å: Chain B: N.22, G.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.22 NAG.17: 2 residues within 4Å: Chain C: N.22, G.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.22

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.6: 8 residues within 4Å: Chain A: L.431, H.435 Chain B: L.431, H.435 Chain C: L.431, H.435 Ligands: NO3.12, NO3.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.435 NO3.12: 8 residues within 4Å: Chain A: L.431, H.435 Chain B: L.431, H.435 Chain C: L.431, H.435 Ligands: NO3.6, NO3.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.435 NO3.18: 8 residues within 4Å: Chain A: L.431, H.435 Chain B: L.431, H.435 Chain C: L.431, H.435 Ligands: NO3.6, NO3.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.435

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Milder, F.J. et al., Universal stabilization of the influenza hemagglutinin by structure-based redesign of the pH switch regions. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-02-02

Peptides

Hemagglutinin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Hemagglutinin