SMTL ID : 4hzz.1

Crystal structure of influenza neuraminidase N3-H274Y complexed with oseltamivir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

8 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 4 residues within 4Å: Chain A: N.64, S.355, K.387 Chain D: F.384 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.381, D:N.381 NAG-NAG-FUC.2: 4 residues within 4Å: Chain A: D.153, N.225, N.226, E.227 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.205 NAG-NAG-FUC.6: 4 residues within 4Å: Chain B: N.64, S.355, K.387 Chain C: F.384 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.381, C:N.381 NAG-NAG-FUC.7: 4 residues within 4Å: Chain B: D.153, N.225, N.226, E.227 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.205 NAG-NAG-FUC.11: 4 residues within 4Å: Chain A: F.384 Chain C: N.64, S.355, K.387 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.381, A:N.381 NAG-NAG-FUC.12: 4 residues within 4Å: Chain C: D.153, N.225, N.226, E.227 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.205 NAG-NAG-FUC.16: 4 residues within 4Å: Chain B: F.384 Chain D: N.64, S.355, K.387 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.381, B:N.381 NAG-NAG-FUC.17: 4 residues within 4Å: Chain D: D.153, N.225, N.226, E.227 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.205

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 5 residues within 4Å: Chain A: D.212, G.216, D.242, G.262, G.265 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.212, A:G.216, A:D.242, A:G.262, H2O.1 CA.4: 3 residues within 4Å: Ligands: CA.9, CA.14, CA.19 No protein-ligand interaction detected (PLIP) CA.8: 5 residues within 4Å: Chain B: D.212, G.216, D.242, G.262, G.265 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.212, B:G.216, B:D.242, B:G.262, H2O.20 CA.9: 3 residues within 4Å: Ligands: CA.4, CA.14, CA.19 No protein-ligand interaction detected (PLIP) CA.13: 5 residues within 4Å: Chain C: D.212, G.216, D.242, G.262, G.265 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.212, C:G.216, C:D.242, C:G.262, H2O.39 CA.14: 3 residues within 4Å: Ligands: CA.4, CA.9, CA.19 No protein-ligand interaction detected (PLIP) CA.18: 5 residues within 4Å: Chain D: D.212, G.216, D.242, G.262, G.265 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.212, D:G.216, D:D.242, D:G.262, H2O.58 CA.19: 3 residues within 4Å: Ligands: CA.4, CA.9, CA.14 No protein-ligand interaction detected (PLIP)

4 x G39: (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid(Non-covalent)

G39.5: 12 residues within 4Å: Chain A: R.36, E.37, D.69, R.70, W.97, R.143, E.196, E.197, R.211, N.213, R.288, Y.323 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.97 Hydrogen bonds: A:E.37, A:R.70 Water bridges: A:R.74, A:R.74, A:E.146, A:E.197 Salt bridges: A:R.36, A:R.211, A:R.288 G39.10: 12 residues within 4Å: Chain B: R.36, E.37, D.69, R.70, W.97, R.143, E.196, E.197, R.211, N.213, R.288, Y.323 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.97 Hydrogen bonds: B:E.37, B:R.70 Water bridges: B:R.74, B:R.74, B:E.146, B:E.197 Salt bridges: B:R.36, B:R.211, B:R.288 G39.15: 12 residues within 4Å: Chain C: R.36, E.37, D.69, R.70, W.97, R.143, E.196, E.197, R.211, N.213, R.288, Y.323 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.97 Hydrogen bonds: C:E.37, C:R.70 Water bridges: C:R.74, C:R.74, C:E.146, C:E.197 Salt bridges: C:R.36, C:R.211, C:R.288 G39.20: 12 residues within 4Å: Chain D: R.36, E.37, D.69, R.70, W.97, R.143, E.196, E.197, R.211, N.213, R.288, Y.323 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.97 Hydrogen bonds: D:E.37, D:R.70 Water bridges: D:R.74, D:R.74, D:E.146, D:E.197 Salt bridges: D:R.36, D:R.211, D:R.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Q. et al., Functional and structural analysis of influenza virus neuraminidase N3 offers further insight into the mechanisms of oseltamivir resistance. J.Virol. (2013)

Release Date

2013-11-06

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase