SMTL ID : 4qn5.1 (1 other biounit)

Neuraminidase N5 binds LSTa at the second SIA binding site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.1: 9 residues within 4Å: Chain A: S.288, S.290, S.291, S.293, N.320, K.321, N.322, W.323, E.356 8 PLIP interactions: 8 interactions with chain A Water bridges: A:S.290, A:N.320, A:I.289, A:S.290 Hydrophobic interactions: A:W.323 Hydrogen bonds: A:S.291, A:S.293, A:S.293, A:N.320, A:E.356 GAL-SIA.6: 9 residues within 4Å: Chain B: S.288, S.290, S.291, S.293, N.320, K.321, N.322, W.323, E.356 8 PLIP interactions: 8 interactions with chain B Water bridges: B:S.290, B:N.320, B:I.289, B:S.290 Hydrophobic interactions: B:W.323 Hydrogen bonds: B:S.291, B:S.293, B:S.293, B:N.320, B:E.356 GAL-SIA.11: 9 residues within 4Å: Chain C: S.288, S.290, S.291, S.293, N.320, K.321, N.322, W.323, E.356 8 PLIP interactions: 8 interactions with chain C Water bridges: C:S.290, C:N.320, C:I.289, C:S.290 Hydrophobic interactions: C:W.323 Hydrogen bonds: C:S.291, C:S.293, C:S.293, C:N.320, C:E.356 GAL-SIA.16: 9 residues within 4Å: Chain D: S.288, S.290, S.291, S.293, N.320, K.321, N.322, W.323, E.356 8 PLIP interactions: 8 interactions with chain D Water bridges: D:S.290, D:N.320, D:I.289, D:S.290 Hydrophobic interactions: D:W.323 Hydrogen bonds: D:S.291, D:S.293, D:S.293, D:N.320, D:E.356

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.7: 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.15, H2O.15 CA.12: 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.30, H2O.30 CA.17: 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.45, H2O.45

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

NAG.3: 3 residues within 4Å: Chain A: P.9, L.10, N.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.9 Hydrogen bonds: A:N.12 Water bridges: A:L.10, A:N.12, A:N.12 NAG.4: 1 residues within 4Å: Chain A: N.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.65 NAG.8: 3 residues within 4Å: Chain B: P.9, L.10, N.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.9 Hydrogen bonds: B:N.12 Water bridges: B:L.10, B:N.12, B:N.12 NAG.9: 1 residues within 4Å: Chain B: N.65 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.65 NAG.13: 3 residues within 4Å: Chain C: P.9, L.10, N.12 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:P.9 Hydrogen bonds: C:N.12 Water bridges: C:L.10, C:N.12, C:N.12 NAG.14: 1 residues within 4Å: Chain C: N.65 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.65 NAG.18: 3 residues within 4Å: Chain D: P.9, L.10, N.12 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:P.9 Hydrogen bonds: D:N.12 Water bridges: D:L.10, D:N.12, D:N.12 NAG.19: 1 residues within 4Å: Chain D: N.65 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.65

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

SIA.5: 14 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, W.98, R.144, 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 Hydrogen bonds: A:E.38, A:D.70, A:D.70, A:D.70, A:R.71, A:R.144, A:E.197, A:R.212, A:R.212, A:Y.326 Water bridges: A:R.71, A:R.75, A:E.147, A:E.147, A:E.147, A:E.197, A:E.197 Salt bridges: A:R.37, A:R.212, A:R.292 SIA.10: 14 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, W.98, R.144, 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 Hydrogen bonds: B:E.38, B:D.70, B:D.70, B:D.70, B:R.71, B:R.144, B:E.197, B:R.212, B:R.212, B:Y.326 Water bridges: B:R.71, B:R.75, B:E.147, B:E.147, B:E.147, B:E.197, B:E.197 Salt bridges: B:R.37, B:R.212, B:R.292 SIA.15: 14 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, W.98, R.144, 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 Hydrogen bonds: C:E.38, C:D.70, C:D.70, C:D.70, C:R.71, C:R.144, C:E.197, C:R.212, C:R.212, C:Y.326 Water bridges: C:R.71, C:R.75, C:E.147, C:E.147, C:E.147, C:E.197, C:E.197 Salt bridges: C:R.37, C:R.212, C:R.292 SIA.20: 14 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, W.98, R.144, 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 Hydrogen bonds: D:E.38, D:D.70, D:D.70, D:D.70, D:R.71, D:R.144, D:E.197, D:R.212, D:R.212, D:Y.326 Water bridges: D:R.71, D:R.75, D:E.147, D:E.147, D:E.147, D:E.197, D:E.197 Salt bridges: D:R.37, D:R.212, D:R.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, X. et al., Structure of influenza virus N7: the last piece of the neuraminidase "jigsaw" puzzle. J.Virol. (2014)

Release Date

2014-07-30

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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