SMTL ID : 3ti8.1 (1 other biounit)

Crystal structure of influenza A virus neuraminidase N5 complexed with laninamivir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.213, G.217, D.243, Y.268, G.269 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.243, A:Y.268, H2O.1, H2O.1 CA.5: 5 residues within 4Å: Chain B: D.213, G.217, D.243, Y.268, G.269 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.243, B:Y.268, H2O.22, H2O.22 CA.9: 5 residues within 4Å: Chain C: D.213, G.217, D.243, Y.268, G.269 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.243, C:Y.268, H2O.44, H2O.44 CA.13: 5 residues within 4Å: Chain D: D.213, G.217, D.243, Y.268, G.269 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.243, D:Y.268, H2O.66, H2O.66

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

NAG.2: 4 residues within 4Å: Chain A: P.9, L.10, N.12, G.278 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.9 Hydrogen bonds: A:N.12 Water bridges: A:L.10, A:L.10, A:N.12, A:N.12 NAG.3: 2 residues within 4Å: Chain A: N.65, I.361 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.361 Hydrogen bonds: A:N.65 Water bridges: A:I.392 NAG.6: 4 residues within 4Å: Chain B: P.9, L.10, N.12, G.278 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.9 Hydrogen bonds: B:N.12 Water bridges: B:L.10, B:L.10, B:N.12, B:N.12 NAG.7: 2 residues within 4Å: Chain B: N.65, I.361 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.361 Hydrogen bonds: B:N.65 Water bridges: B:I.392 NAG.10: 4 residues within 4Å: Chain C: P.9, L.10, N.12, G.278 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:P.9 Hydrogen bonds: C:N.12 Water bridges: C:L.10, C:L.10, C:N.12, C:N.12 NAG.11: 2 residues within 4Å: Chain C: N.65, I.361 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.361 Hydrogen bonds: C:N.65 Water bridges: C:I.392 NAG.14: 4 residues within 4Å: Chain D: P.9, L.10, N.12, G.278 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:P.9 Hydrogen bonds: D:N.12 Water bridges: D:L.10, D:L.10, D:N.12, D:N.12 NAG.15: 2 residues within 4Å: Chain D: N.65, I.361 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.361 Hydrogen bonds: D:N.65 Water bridges: D:I.392

4 x LNV: 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-D-glycero-D-galacto-non-2-enonic acid(Non-covalent)

LNV.4: 17 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, N.214, Y.268, R.292, Y.326 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.98, A:I.142 Hydrogen bonds: A:R.71, A:W.98, A:W.98, A:R.144, A:E.197, A:R.212, A:R.212, A:Y.326 Water bridges: A:R.37, A:D.70, A:R.75, A:R.144, A:E.197 Salt bridges: A:R.37, A:E.38, A:D.70, A:E.147, A:R.212, A:R.292 LNV.8: 17 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, N.214, Y.268, R.292, Y.326 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:W.98, B:I.142 Hydrogen bonds: B:R.71, B:W.98, B:W.98, B:R.144, B:E.197, B:R.212, B:R.212, B:Y.326 Water bridges: B:R.37, B:D.70, B:R.75, B:R.144, B:E.197 Salt bridges: B:R.37, B:E.38, B:D.70, B:E.147, B:R.212, B:R.292 LNV.12: 17 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, N.214, Y.268, R.292, Y.326 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142 Hydrogen bonds: C:R.71, C:W.98, C:W.98, C:R.144, C:E.197, C:R.212, C:R.212, C:Y.326 Water bridges: C:R.37, C:D.70, C:R.75, C:R.144, C:E.197 Salt bridges: C:R.37, C:E.38, C:D.70, C:E.147, C:R.212, C:R.292 LNV.16: 17 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, N.214, Y.268, R.292, Y.326 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142 Hydrogen bonds: D:R.71, D:W.98, D:W.98, D:R.144, D:E.197, D:R.212, D:R.212, D:Y.326 Water bridges: D:R.37, D:D.70, D:R.75, D:R.144, D:E.197 Salt bridges: D:R.37, D:E.38, D:D.70, D:E.147, D:R.212, D:R.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vavricka, C.J. et al., Structural and functional analysis of laninamivir and its octanoate prodrug reveals group specific mechanisms for influenza NA inhibition. Plos Pathog. (2011)

Release Date

2011-11-16

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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