SMTL ID : 6aot.1

Crystal structure of the A/Brisbane/10/2007 (H3N2) influenza virus hemagglutinin L194P mutant in complex with 6'-SLNLN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-3-3-mer

Ligands

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.1: 5 residues within 4Å: Chain A: N.32, T.34, D.285, T.312 Chain B: L.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.285 NAG-NAG-BMA-MAN-MAN.10: 5 residues within 4Å: Chain C: N.32, T.34, D.285, T.312 Chain D: L.52 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.285 NAG-NAG-BMA-MAN-MAN.19: 5 residues within 4Å: Chain E: N.32, T.34, D.285, T.312 Chain F: L.52 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.285

3 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: 5 residues within 4Å: Chain A: N.159 Chain C: S.213, P.215, R.216 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.216 NAG-NAG.11: 5 residues within 4Å: Chain C: N.159 Chain E: S.213, P.215, R.216 Ligands: NAG.17 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.216 NAG-NAG.20: 5 residues within 4Å: Chain A: S.213, P.215, R.216 Chain E: N.159 Ligands: NAG.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.216

3 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.3: 14 residues within 4Å: Chain A: Y.92, G.128, T.129, S.130, S.131, W.147, T.149, H.177, D.184, F.187, P.188, N.219, I.220, S.222 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.219, A:N.219, A:T.129, A:S.131, A:H.177, A:S.222 Hydrophobic interactions: A:W.147, A:T.149 Water bridges: A:T.129 GAL-SIA.12: 14 residues within 4Å: Chain C: Y.92, G.128, T.129, S.130, S.131, W.147, T.149, H.177, D.184, F.187, P.188, N.219, I.220, S.222 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.219, C:N.219, C:T.129, C:S.131, C:H.177, C:S.222 Hydrophobic interactions: C:W.147, C:T.149 Water bridges: C:T.129 GAL-SIA.21: 14 residues within 4Å: Chain E: Y.92, G.128, T.129, S.130, S.131, W.147, T.149, H.177, D.184, F.187, P.188, N.219, I.220, S.222 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.219, E:N.219, E:T.129, E:S.131, E:H.177, E:S.222 Hydrophobic interactions: E:W.147, E:T.149 Water bridges: E:T.129

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

NAG.4: 3 residues within 4Å: Chain A: N.16, T.18, T.31 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: E.56, N.57, Y.88 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: S.39, N.279, V.291, N.292 Chain B: E.69 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: Q.126, N.127 Ligand excluded by PLIP NAG.8: 8 residues within 4Å: Chain A: A.157, L.158, N.159, N.240, S.241, T.242 Chain C: I.211 Ligands: NAG-NAG.2 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain B: A.147, G.150, S.151, N.154, T.156 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain C: N.16, T.18, T.31 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain C: E.56, N.57, Y.88 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain C: S.39, N.279, V.291, N.292 Chain D: E.69 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain C: Q.126, N.127 Ligand excluded by PLIP NAG.17: 8 residues within 4Å: Chain C: A.157, L.158, N.159, N.240, S.241, T.242 Chain E: I.211 Ligands: NAG-NAG.11 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain D: A.147, G.150, S.151, N.154, T.156 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain E: N.16, T.18, T.31 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain E: E.56, N.57, Y.88 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain E: S.39, N.279, V.291, N.292 Chain F: E.69 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain E: Q.126, N.127 Ligand excluded by PLIP NAG.26: 8 residues within 4Å: Chain A: I.211 Chain E: A.157, L.158, N.159, N.240, S.241, T.242 Ligands: NAG-NAG.20 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain F: A.147, G.150, S.151, N.154, T.156 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, N.C. et al., A structural explanation for the low effectiveness of the seasonal influenza H3N2 vaccine. PLoS Pathog. (2017)

Release Date

2017-10-18

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

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