SMTL ID : 5br6.1 (1 other biounit)

Crystal structure of hemagglutinin of A/Taiwan/2/2013 (H6N1) in complex with LSTc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA.1: 13 residues within 4Å: Chain A: Y.91, R.129, V.131, T.132, N.133, W.150, V.152, H.181, V.188, L.192, G.223, Q.224, S.226 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.133, A:G.223, A:Q.224, A:Y.91, A:V.131, A:T.132, A:N.133, A:N.133, A:Q.224, A:Q.224, A:S.226, A:S.226 Hydrophobic interactions: A:L.192 NAG-GAL-SIA.7: 13 residues within 4Å: Chain C: Y.91, R.129, V.131, T.132, N.133, W.150, V.152, H.181, V.188, L.192, G.223, Q.224, S.226 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.133, C:G.223, C:Q.224, C:Y.91, C:V.131, C:T.132, C:N.133, C:N.133, C:Q.224, C:Q.224, C:S.226, C:S.226 Hydrophobic interactions: C:L.192 NAG-GAL-SIA.13: 13 residues within 4Å: Chain E: Y.91, R.129, V.131, T.132, N.133, W.150, V.152, H.181, V.188, L.192, G.223, Q.224, S.226 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:N.133, E:G.223, E:Q.224, E:Y.91, E:V.131, E:T.132, E:N.133, E:N.133, E:Q.224, E:Q.224, E:S.226, E:S.226 Hydrophobic interactions: E:L.192

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

NAG-NAG-BMA-MAN-MAN-FUC.2: 6 residues within 4Å: Chain B: E.147, E.150, S.151, N.154, T.156, K.161 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.147, B:E.147 NAG-NAG-BMA-MAN-MAN-FUC.8: 6 residues within 4Å: Chain D: E.147, E.150, S.151, N.154, T.156, K.161 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.147, D:E.147 NAG-NAG-BMA-MAN-MAN-FUC.14: 6 residues within 4Å: Chain F: E.147, E.150, S.151, N.154, T.156, K.161 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.147, F:E.147

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

NAG.3: 1 residues within 4Å: Chain A: N.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.11 Water bridges: A:N.11, A:T.13 NAG.4: 2 residues within 4Å: Chain A: Q.15, N.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.23 NAG.5: 4 residues within 4Å: Chain A: N.167, T.169, E.205, T.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.167, A:T.240 NAG.6: 1 residues within 4Å: Chain A: N.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.291, A:K.292 Water bridges: A:N.291 NAG.9: 1 residues within 4Å: Chain C: N.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.11 Water bridges: C:N.11, C:T.13 NAG.10: 2 residues within 4Å: Chain C: Q.15, N.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.23 NAG.11: 4 residues within 4Å: Chain C: N.167, T.169, E.205, T.240 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.167, C:T.240 NAG.12: 1 residues within 4Å: Chain C: N.291 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.291, C:K.292 Water bridges: C:N.291 NAG.15: 1 residues within 4Å: Chain E: N.11 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.11 Water bridges: E:N.11, E:T.13 NAG.16: 2 residues within 4Å: Chain E: Q.15, N.23 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.23 NAG.17: 4 residues within 4Å: Chain E: N.167, T.169, E.205, T.240 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.167, E:T.240 NAG.18: 1 residues within 4Å: Chain E: N.291 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.291, E:K.292 Water bridges: E:N.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, F. et al., Structural and Functional Studies of Influenza Virus A/H6 Hemagglutinin. Plos One (2015)

Release Date

2015-08-12

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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