SMTL ID : 3ubn.1 (1 other biounit)

Influenza hemagglutinin from the 2009 pandemic in complex with ligand 6SLN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 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(Non-covalent)

NAG-GAL-SIA.1: 14 residues within 4Å: Chain A: Y.93, K.132, G.133, V.134, T.135, A.136, K.144, W.152, H.182, D.189, L.193, K.221, D.224, Q.225 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.221, A:D.224, A:Y.93, A:V.134, A:T.135, A:A.136, A:K.144, A:K.144, A:Q.225, A:Q.225, A:Q.225 Hydrophobic interactions: A:L.193 NAG-GAL-SIA.2: 14 residues within 4Å: Chain C: Y.93, K.132, V.134, T.135, A.136, K.144, W.152, H.182, D.189, S.192, L.193, K.221, D.224, Q.225 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.221, C:D.224, C:Q.225, C:D.189, C:D.189, C:V.134, C:T.135, C:A.136, C:K.144, C:K.144, C:H.182, C:Q.225, C:Q.225 Water bridges: C:E.226, C:D.189 Hydrophobic interactions: C:W.152, C:L.193 NAG-GAL-SIA.3: 15 residues within 4Å: Chain E: Y.93, K.132, G.133, V.134, T.135, A.136, K.144, W.152, H.182, D.189, S.192, L.193, K.221, D.224, Q.225 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:K.221, E:D.224, E:Q.225, E:D.189, E:D.189, E:Y.93, E:V.134, E:T.135, E:A.136, E:K.144, E:K.144, E:Q.225, E:Q.225, E:Q.225 Hydrophobic interactions: E:W.152 Water bridges: E:D.189 Salt bridges: E:K.144

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.4: 1 residues within 4Å: Chain A: N.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.13 NAG.5: 1 residues within 4Å: Chain A: N.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.25 NAG.6: 5 residues within 4Å: Chain A: N.66, E.68, N.89, C.92, R.223 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.68 Hydrogen bonds: A:N.66, A:E.68, A:N.89, A:R.223, A:R.223 NAG.7: 3 residues within 4Å: Chain A: G.48, N.278, T.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.278 NAG.8: 7 residues within 4Å: Chain C: N.66, E.68, D.88, N.89, C.92, P.139, R.223 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:E.68 Hydrogen bonds: C:N.66, C:D.88, C:D.88, C:N.89, C:R.223, C:R.223 Water bridges: C:D.88, C:D.88 NAG.9: 3 residues within 4Å: Chain C: D.276, C.277, N.278 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.278 NAG.10: 7 residues within 4Å: Chain E: N.66, E.68, D.88, N.89, C.92, P.139, R.223 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:E.68, E:P.139 Hydrogen bonds: E:N.66, E:D.88, E:N.89, E:R.223, E:R.223

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Xu, R. et al., Structural Characterization of the Hemagglutinin Receptor Specificity from the 2009 H1N1 Influenza Pandemic. J.Virol. (2012)

Release Date

2011-11-23

Peptides

Hemagglutinin HA1: ACE
Hemagglutinin HA2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin HA1

Hemagglutinin HA2

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