SMTL ID : 3whe.2 (3 other biounits)

A new conserved neutralizing epitope at the globular head of hemagglutinin in H3N2 influenza viruses

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.00 Å

Oligo State

hetero-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.1: 9 residues within 4Å: Chain A: N.277, V.289, K.291 Chain D: D.55, Q.57, T.58, R.103, G.104, M.106 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.57, D:T.58, D:Q.57 NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 10 residues within 4Å: Chain B: N.277, V.289, K.291 Chain E: Y.54, D.55, G.56, Q.57, T.58, R.103, G.104 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.57, E:T.58, E:Q.57 NAG-NAG-BMA-MAN-MAN-MAN-MAN.7: 10 residues within 4Å: Chain C: N.277, V.289, K.291 Chain F: Y.54, D.55, G.56, Q.57, R.103, G.104, M.106 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.57, F:Q.57

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.2: 6 residues within 4Å: Chain A: N.157, T.159 Chain C: S.211, W.214, S.219 Chain F: Q.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.214 NAG-NAG-BMA-MAN-MAN-MAN.5: 5 residues within 4Å: Chain A: S.211, W.214, S.219 Chain B: N.157, T.159 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.214 NAG-NAG-BMA-MAN-MAN-MAN.8: 7 residues within 4Å: Chain B: S.211, W.214, S.219 Chain C: N.157, T.159 Chain E: Q.1, Q.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.214, B:W.214

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: 3 residues within 4Å: Chain A: N.30, A.31, T.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain B: N.30, A.31, T.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 3 residues within 4Å: Chain C: N.30, A.31, T.32 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.310

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

NAG.10: 3 residues within 4Å: Chain A: N.73, F.112, R.142 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.73 Hydrogen bonds: A:F.112 NAG.11: 4 residues within 4Å: Chain A: E.471, S.472, N.475, T.477 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.475 NAG.12: 3 residues within 4Å: Chain B: N.73, F.112, R.142 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.73 Hydrogen bonds: B:F.112 NAG.13: 4 residues within 4Å: Chain B: E.471, S.472, N.475, T.477 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.475 NAG.14: 3 residues within 4Å: Chain C: N.73, F.112, R.142 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.73 Hydrogen bonds: C:F.112 NAG.15: 4 residues within 4Å: Chain C: E.471, S.472, N.475, T.477 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.475

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iba, Y. et al., Conserved neutralizing epitope at globular head of hemagglutinin in H3N2 influenza viruses. J.Virol. (2014)

Release Date

2014-04-23

Peptides

Hemagglutinin: ABC
immunoglobulin heavy chain: DEF
immunoglobulin light chain: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
S

E
U

F
W

G
T

H
V

I
X

Hemagglutinin

immunoglobulin heavy chain

immunoglobulin light chain

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