SMTL ID : 6bkp.3 (2 other biounits)

Crystal structure of the A/Michigan/15/2014 (H3N2) influenza virus hemagglutinin apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-3-3-mer

Ligands

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.1: 4 residues within 4Å: Chain A: N.32, T.34, T.312 Chain B: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.32, T.34, T.312 Chain D: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain E: N.32, T.34, T.312 Chain F: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain E: N.39, N.279, V.291, N.292 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.2: 8 residues within 4Å: Chain A: N.159, T.161, I.236 Chain C: T.181, S.213, P.215, K.216 Ligands: NAG.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:I.236, C:P.215 Hydrogen bonds: C:K.216 NAG-NAG-BMA.8: 8 residues within 4Å: Chain C: N.159, T.161, I.236 Chain E: T.181, S.213, P.215, K.216 Ligands: NAG.12 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:P.215, C:I.236 Hydrogen bonds: E:K.216 NAG-NAG-BMA.14: 8 residues within 4Å: Chain A: T.181, S.213, P.215, K.216 Chain E: N.159, T.161, I.236 Ligands: NAG.18 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:P.215, E:I.236 Hydrogen bonds: A:K.216

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

NAG.4: 3 residues within 4Å: Chain A: E.56, N.57, Y.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.57, A:Y.88 Water bridges: A:N.57 NAG.5: 3 residues within 4Å: Chain A: Q.126, N.127, R.249 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.126 Hydrogen bonds: A:N.127, A:R.249 NAG.6: 8 residues within 4Å: Chain A: A.157, L.158, N.159, R.195, N.240, T.242 Chain C: I.211 Ligands: NAG-NAG-BMA.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.159 Hydrogen bonds: A:L.158, A:R.195, A:R.195 NAG.10: 3 residues within 4Å: Chain C: E.56, N.57, Y.88 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.57, C:Y.88 Water bridges: C:N.57 NAG.11: 3 residues within 4Å: Chain C: Q.126, N.127, R.249 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Q.126 Hydrogen bonds: C:N.127, C:R.249 NAG.12: 8 residues within 4Å: Chain C: A.157, L.158, N.159, R.195, N.240, T.242 Chain E: I.211 Ligands: NAG-NAG-BMA.8 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:N.159 Hydrogen bonds: C:L.158, C:R.195, C:R.195 NAG.16: 3 residues within 4Å: Chain E: E.56, N.57, Y.88 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.57, E:Y.88 Water bridges: E:N.57 NAG.17: 3 residues within 4Å: Chain E: Q.126, N.127, R.249 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:Q.126 Hydrogen bonds: E:N.127, E:R.249 NAG.18: 8 residues within 4Å: Chain A: I.211 Chain E: A.157, L.158, N.159, R.195, N.240, T.242 Ligands: NAG-NAG-BMA.14 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:N.159 Hydrogen bonds: E:L.158, E:R.195, E:R.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, N.C. et al., A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site. Nat Commun (2018)

Release Date

2018-02-28

Peptides

Hemagglutinin: ACE
Hemagglutinin: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Hemagglutinin

Hemagglutinin

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