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

Influenza hemagglutinin from the 2009 pandemic in complex with ligand LSTc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-3-3-mer

Ligands

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

GAL-NAG-GAL-SIA.1: 13 residues within 4Å: Chain A: Y.93, K.132, V.134, T.135, A.136, K.144, W.152, H.182, S.192, L.193, K.221, D.224, Q.225 12 PLIP interactions: 12 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:H.182, A:Q.225, A:Q.225 Water bridges: A:E.226, A:D.189 Hydrophobic interactions: A:L.193 Salt bridges: A:K.144 GAL-NAG-GAL-SIA.2: 16 residues within 4Å: Chain C: Y.93, K.132, G.133, V.134, T.135, A.136, K.144, W.152, H.182, A.188, D.189, S.192, L.193, K.221, D.224, Q.225 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.221, C:D.224, 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 Hydrophobic interactions: C:L.193, C:W.152, C:L.193

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

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 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:K.221, E:D.224, E:D.189, E:Y.93, E:V.134, E:T.135, E:A.136, E:K.144, E:K.144, E:H.182, E:Q.225, E:Q.225, E:Q.225 Water bridges: E:K.144, E:D.189 Hydrophobic interactions: E:L.193, E:W.152 Salt bridges: E:K.144

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

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: 6 residues within 4Å: Chain A: N.66, E.68, D.88, 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.6: 4 residues within 4Å: Chain A: R.47, G.48, N.278, T.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.278 NAG.7: 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.8: 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 Hydrogen bonds: E:N.66, E:D.88, E:N.89, E:R.223, E:R.223 Water bridges: E:E.68

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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