SMTL ID : 4kdn.1

Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex with avian receptor analog LSTa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

hetero-3-3-mer

Ligands

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.1: 4 residues within 4Å: Chain A: N.166, N.237, A.239 Chain C: S.218 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain C: N.166, N.237, D.238, A.239 Chain E: S.218 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: S.218 Chain E: N.166, N.237, A.239 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: Q.16, N.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.24 NAG.6: 2 residues within 4Å: Chain C: Q.16, N.24 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.24 NAG.8: 3 residues within 4Å: Chain E: Q.16, K.23, N.24 No protein-ligand interaction detected (PLIP)

2 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.5: 13 residues within 4Å: Chain A: Y.92, L.130, G.131, V.132, S.133, S.134, W.150, I.152, H.180, E.187, K.190, L.191, L.223 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.150, A:I.152 Hydrogen bonds: A:V.132, A:S.134, A:H.180, A:K.190, A:K.190 SIA.7: 9 residues within 4Å: Chain C: Y.92, L.130, V.132, S.133, S.134, I.152, K.190, L.191, L.223 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.152, C:L.191 Hydrogen bonds: C:Y.92, C:Y.92, C:V.132, C:S.134, C:K.190, C:K.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, X. et al., Structure and receptor-binding properties of an airborne transmissible avian influenza A virus hemagglutinin H5 (VN1203mut). Protein Cell (2013)

Release Date

2013-07-24

Peptides

Hemagglutinin: ACE
Hemagglutinin: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin

Hemagglutinin

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