SMTL ID : 3vun.1

Crystal structure of a influenza A virus (A/Aichi/2/1968 H3N2) hemagglutinin in C2 space group.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-3-3-mer

Ligands

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

NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.1: 7 residues within 4Å: Chain A: Q.80, N.81, E.119, F.120, I.121, T.122, G.124 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.119 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.4: 8 residues within 4Å: Chain C: Q.80, N.81, E.119, F.120, I.121, T.122, E.123, G.124 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.119 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.7: 7 residues within 4Å: Chain E: Q.80, N.81, E.119, F.120, I.121, T.122, G.124 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:E.119

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: 6 residues within 4Å: Chain A: N.165, T.167 Chain E: S.219, R.220, P.221, W.222 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:P.221, A:T.167 Hydrogen bonds: E:W.222 NAG-NAG.5: 5 residues within 4Å: Chain A: S.219, P.221, W.222 Chain C: N.165, T.167 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:W.222 Hydrophobic interactions: C:T.167 NAG-NAG.8: 6 residues within 4Å: Chain C: S.219, R.220, P.221, W.222 Chain E: N.165, T.167 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:T.167, C:P.221 Hydrogen bonds: C:W.222

3 x NAG- NAG- BMA- MAN: 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(Post Translational Modification)

NAG-NAG-BMA-MAN.3: 6 residues within 4Å: Chain A: S.45, N.285, V.297, N.298, K.299 Chain B: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.6: 6 residues within 4Å: Chain C: S.45, N.285, V.297, N.298, K.299 Chain D: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.9: 6 residues within 4Å: Chain E: S.45, N.285, V.297, N.298, K.299 Chain F: E.69 No protein-ligand interaction detected (PLIP)

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

NAG.10: 2 residues within 4Å: Chain A: N.38, T.318 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.38, A:T.318 NAG.11: 4 residues within 4Å: Chain B: A.147, E.150, N.154, T.156 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.156 Hydrogen bonds: B:A.147, B:E.150, B:T.156, B:T.156 NAG.12: 2 residues within 4Å: Chain C: N.38, T.318 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.38, C:T.318 NAG.13: 5 residues within 4Å: Chain D: A.147, E.150, S.151, N.154, T.156 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.147, D:E.150, D:T.156, D:T.156 NAG.14: 2 residues within 4Å: Chain E: N.38, T.318 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.38, E:T.318 NAG.15: 4 residues within 4Å: Chain F: A.147, E.150, N.154, T.156 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:T.156 Hydrogen bonds: F:A.147, F:E.150, F:N.154, F:T.156, F:T.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yasutake, Y. et al., Crystal structure of a influenza A virus (A/Aichi/2/1968 H3N2) hemagglutinin in C2 space group. To be Published

Release Date

2012-08-01

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

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