SMTL ID : 4d00.1

Haemagglutinin of H10N8 Influenza Virus Isolated from Humans in Complex with Human Receptor Analogue 6'SLN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-3-3-mer

Ligands

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)(Non-covalent)

NAG-GAL-SIA.1: 14 residues within 4Å: Chain A: Y.91, G.128, T.129, T.130, R.131, N.139, W.147, H.179, E.186, L.190, Q.218, G.221, Q.222, G.224 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.131, A:Q.218, A:G.221, A:R.131, A:T.129, A:R.131, A:H.179, A:Q.222, A:Q.222 Hydrophobic interactions: A:W.147 Water bridges: A:T.129, A:N.139, A:G.224 Salt bridges: A:R.131 NAG-GAL-SIA.3: 13 residues within 4Å: Chain C: Y.91, G.128, T.129, T.130, R.131, W.147, H.179, E.186, L.190, Q.218, G.221, Q.222, G.224 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Q.218, C:G.221, C:Y.91, C:T.129, C:R.131, C:H.179, C:Q.222, C:Q.222 Water bridges: C:R.131, C:N.139, C:T.129, C:T.129, C:N.139, C:G.224 Hydrophobic interactions: C:W.147 NAG-GAL-SIA.5: 13 residues within 4Å: Chain E: Y.91, G.128, T.129, T.130, R.131, N.139, W.147, H.179, E.186, L.190, G.221, Q.222, G.224 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:Q.218, E:G.221, E:N.139, E:T.129, E:R.131, E:N.139, E:H.179, E:Q.222, E:Q.222 Water bridges: E:Q.222, E:T.129, E:T.129, E:G.224 Salt bridges: E:R.131 Hydrophobic interactions: E:W.147

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.2: 7 residues within 4Å: Chain B: H.75, G.78, N.79, N.82 Chain C: E.107, R.259 Ligands: NI.10 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain D: H.75, N.79, N.82 Chain E: E.107 Ligands: NI.13 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: E.107, R.259 Chain E: R.296 Chain F: H.75, N.79, N.82 Ligands: NI.9 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.296 Water bridges: E:R.296

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

NAG.7: 5 residues within 4Å: Chain A: R.165, G.236, D.237, N.238 Chain E: P.217 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:R.165, A:G.236, A:D.237 Hydrophobic interactions: E:P.217 NAG.8: 3 residues within 4Å: Chain A: N.31, T.314 Chain B: L.52 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.52, A:T.314 Hydrogen bonds: A:T.314 NAG.11: 4 residues within 4Å: Chain C: R.165, G.236, D.237, N.238 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.165, C:G.236, C:D.237 NAG.12: 3 residues within 4Å: Chain C: N.31, T.314 Chain D: L.52 1 PLIP interactions: 1 interactions with chain C Water bridges: C:T.33 NAG.14: 5 residues within 4Å: Chain C: P.217 Chain E: R.165, G.236, D.237, N.238 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:R.165, E:G.236, E:N.238 Water bridges: C:Q.218 NAG.15: 3 residues within 4Å: Chain E: N.31, T.314 Chain F: L.52 No protein-ligand interaction detected (PLIP)

3 x NI: NICKEL (II) ION(Post Translational Modification)

NI.9: 4 residues within 4Å: Chain A: E.107 Chain B: E.64 Chain F: N.79 Ligands: NAG-NAG.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.64, B:E.64, A:E.107 NI.10: 4 residues within 4Å: Chain B: N.79 Chain C: E.107 Chain D: E.64 Ligands: NAG-NAG.2 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:E.64, D:E.64, C:E.107, C:E.107, H2O.9 NI.13: 4 residues within 4Å: Chain D: N.79 Chain E: E.107 Chain F: E.64 Ligands: NAG-NAG.4 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Metal complexes: E:E.107, F:E.64, F:E.64

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Vachieri, S.G. et al., Receptor Binding by H10 Influenza Viruses. Nature (2014)

Release Date

2014-06-11

Peptides

HAEMAGGLUTININ HA1: ACE
HAEMAGGLUTININ HA1: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

HAEMAGGLUTININ HA1

HAEMAGGLUTININ HA1

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