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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

hetero-3-3-mer

Ligands

1 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose(Non-covalent)

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, V.154, H.182, L.193, K.221, D.224, Q.225 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.221, A:K.221, A:D.224, A:Q.225, A:Y.93, A:V.134, A:T.135, A:A.136, A:K.144, A:H.182, A:Q.225, A:Q.225 Hydrophobic interactions: A:W.152, A:V.154 Water bridges: A:D.189

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.2: 8 residues within 4Å: Chain A: N.66, E.68, D.88, N.89, C.92, C.138, P.139, R.223 No protein-ligand interaction detected (PLIP)

2 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.3: 15 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, S.192, L.193, K.221, D.224, Q.225 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.221, C:K.221, C:D.224, C:K.132, C:V.134, C:T.135, C:A.136, C:K.144, C:Q.225, C:Q.225, C:Q.225, C:D.189 Hydrophobic interactions: C:L.193 Water bridges: C:D.189 Salt bridges: C:K.144 NAG-GAL-SIA.4: 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 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.221, E:K.221, E:Y.93, E:V.134, E:T.135, E:A.136, E:K.144, E:Q.225, E:Q.225, E:Q.225, E:D.189 Hydrophobic interactions: E:L.193

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

NAG.5: 3 residues within 4Å: Chain D: S.151, N.154, T.156 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.156 NAG.6: 3 residues within 4Å: Chain E: K.45, G.48, N.278 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:K.45 Hydrogen bonds: E:N.278, E:N.278

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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