SMTL ID : 4kdo.1

Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex with human receptor analog LSTc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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, D.238, A.239 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain B: N.166, N.237, D.238, A.239 Chain C: S.218 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: S.218 Chain C: N.166, N.237, D.238, A.239 No protein-ligand interaction detected (PLIP)

1 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-GAL-SIA.3: 15 residues within 4Å: Chain B: Y.92, L.130, G.131, V.132, S.133, S.134, W.150, I.152, H.180, E.187, K.190, L.191, G.222, L.223, G.225 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.190, B:G.222, B:Y.92, B:V.132, B:S.134, B:E.187 Water bridges: B:K.219, B:G.225 Hydrophobic interactions: B:W.150, B:I.152

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

SIA.5: 14 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, G.225 8 PLIP interactions: 8 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 Water bridges: A:N.183, A:G.225

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

NAG.6: 2 residues within 4Å: Chain B: Q.16, N.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.16

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: ABC
Hemagglutinin: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
B

E
D

F
F

Hemagglutinin

Hemagglutinin

Related Entries With Identical Sequence