SMTL ID : 4bh3.1

Haemagglutinin from a Transmissible Mutant H5 Influenza Virus in Complex with Human Receptor Analogue 6'-SLN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA- BMA- MAN- FUC: beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA-BMA-MAN-FUC.1: 5 residues within 4Å: Chain A: N.167, N.238, D.239, A.240 Chain E: S.219 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA-MAN-FUC.6: 5 residues within 4Å: Chain A: S.219 Chain C: N.167, N.238, D.239, A.240 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA-MAN-FUC.11: 5 residues within 4Å: Chain C: S.219 Chain E: N.167, N.238, D.239, A.240 No protein-ligand interaction detected (PLIP)

3 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.2: 13 residues within 4Å: Chain A: Y.93, L.131, G.132, V.133, S.134, S.135, W.151, H.181, E.188, K.191, L.192, G.223, L.224 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.191, A:N.184 Salt bridges: A:K.191 Hydrogen bonds: A:G.223, A:Y.93, A:V.133, A:S.135, A:H.181, A:N.184 Hydrophobic interactions: A:W.151 NAG-GAL-SIA.7: 13 residues within 4Å: Chain C: Y.93, L.131, G.132, V.133, S.134, S.135, W.151, H.181, E.188, K.191, L.192, G.223, L.224 6 PLIP interactions: 6 interactions with chain C Water bridges: C:K.191, C:N.184 Salt bridges: C:K.191 Hydrogen bonds: C:G.223, C:Y.93, C:V.133, C:S.135, C:H.181, C:N.184 Hydrophobic interactions: C:W.151 NAG-GAL-SIA.12: 13 residues within 4Å: Chain E: Y.93, L.131, G.132, V.133, S.134, S.135, W.151, H.181, E.188, K.191, L.192, G.223, L.224 6 PLIP interactions: 6 interactions with chain E Water bridges: E:K.191, E:N.184 Salt bridges: E:K.191 Hydrogen bonds: E:G.223, E:Y.93, E:V.133, E:S.135, E:H.181, E:N.184 Hydrophobic interactions: E:W.151

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

NAG.3: 1 residues within 4Å: Chain A: N.13 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.13 NAG.4: 1 residues within 4Å: Chain A: N.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.25 NAG.8: 1 residues within 4Å: Chain C: N.13 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.13 NAG.9: 1 residues within 4Å: Chain C: N.25 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.25 NAG.13: 1 residues within 4Å: Chain E: N.13 1 PLIP interactions: 1 interactions with chain E Water bridges: E:N.13 NAG.14: 1 residues within 4Å: Chain E: N.25 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.25

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 5 residues within 4Å: Chain B: W.14, H.25, Y.34, N.135, C.137 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.14, B:Y.34, B:N.135 Salt bridges: B:H.25 EPE.10: 5 residues within 4Å: Chain D: W.14, H.25, Y.34, N.135, C.137 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:W.14, D:Y.34, D:N.135 Salt bridges: D:H.25 EPE.15: 5 residues within 4Å: Chain F: W.14, H.25, Y.34, N.135, C.137 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:W.14, F:Y.34, F:N.135 Salt bridges: F:H.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, X. et al., Receptor Binding by a Ferret-Transmissible H5 Avian Influenza Virus. Nature (2013)

Release Date

2013-04-24

Peptides

HEMAGGLUTININ: ACE
HEMAGGLUTININ: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

HEMAGGLUTININ

HEMAGGLUTININ

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