SMTL ID : 3ubj.2 (1 other biounit)

Influenza hemagglutinin from the 2009 pandemic in complex with ligand LSTa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-3-3-mer

Ligands

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

GAL-SIA.1: 12 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, Q.225 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.189, A:Y.93, A:V.134, A:T.135, A:A.136, A:K.144, A:Q.225, A:Q.225 Water bridges: A:D.189, A:S.185 Hydrophobic interactions: A:L.193 GAL-SIA.2: 12 residues within 4Å: Chain C: Y.93, K.132, G.133, V.134, T.135, A.136, K.144, W.152, H.182, D.189, L.193, Q.225 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:K.144, C:Q.225, C:V.134, C:T.135, C:A.136, C:H.182, C:Q.225, C:Q.225 Water bridges: C:K.221 Hydrophobic interactions: C:W.152 Salt bridges: C:K.144 GAL-SIA.3: 10 residues within 4Å: Chain E: Y.93, K.132, V.134, T.135, A.136, K.144, W.152, H.182, L.193, Q.225 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:Y.93, E:K.132, E:V.134, E:T.135, E:A.136, E:K.144, E:K.144, E:H.182, E:Q.225, E:Q.225

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 7 residues within 4Å: Chain E: N.66, E.68, D.88, N.89, C.92, P.139, R.223 No protein-ligand interaction detected (PLIP)

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

NAG.5: 1 residues within 4Å: Chain A: N.13 No protein-ligand interaction detected (PLIP) NAG.6: 7 residues within 4Å: Chain A: N.66, E.68, D.88, N.89, C.92, P.139, R.223 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.68 Hydrogen bonds: A:N.66, A:D.88, A:N.89, A:R.223, A:R.223 Water bridges: A:E.68 NAG.7: 3 residues within 4Å: Chain A: K.38, H.39, N.289 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.289 NAG.8: 1 residues within 4Å: Chain C: N.25 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.25 NAG.9: 7 residues within 4Å: Chain C: N.66, E.68, D.88, N.89, C.92, P.139, R.223 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:E.68 Hydrogen bonds: C:N.66, C:D.88, C:D.88, C:R.223, C:R.223 Water bridges: C:N.89 NAG.10: 4 residues within 4Å: Chain C: G.48, D.276, C.277, N.278 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.276 NAG.11: 1 residues within 4Å: Chain E: N.25 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.25 NAG.12: 3 residues within 4Å: Chain E: G.48, N.278, T.280 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.280 Water bridges: E:T.280, E:T.290 NAG.13: 2 residues within 4Å: Chain E: K.38, N.289 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.289 Water bridges: E:N.289

Links

RCSB   PDBe   PDBe-KB   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
G

C
I

E
K

B
H

D
J

F
L

Hemagglutinin HA1

Hemagglutinin HA2

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