SMTL ID : 4wa5.1

The crystal structure of neuraminidase from a H3N8 influenza virus isolated from New England harbor seals in complex with zanamivir

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 4 residues within 4Å: Chain A: N.64, T.66, I.356, I.387 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.356 Hydrogen bonds: A:N.64 NAG-FUC.4: 4 residues within 4Å: Chain B: N.64, T.66, I.356, I.387 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.356 Hydrogen bonds: B:N.64 NAG-FUC.7: 4 residues within 4Å: Chain C: N.64, T.66, I.356, I.387 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.356 Hydrogen bonds: C:N.64 NAG-FUC.10: 4 residues within 4Å: Chain D: N.64, T.66, I.356, I.387 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.356 Hydrogen bonds: D:N.64

4 x ZMR: ZANAMIVIR(Non-covalent)

ZMR.2: 17 residues within 4Å: Chain A: R.36, E.37, D.69, R.70, R.74, W.97, I.141, R.143, E.146, A.165, E.195, E.196, R.211, N.213, Y.264, R.288, Y.322 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.97, A:I.141 Hydrogen bonds: A:R.70, A:R.74, A:W.97, A:W.97, A:R.143, A:E.196, A:R.211, A:Y.264 Water bridges: A:E.196 Salt bridges: A:R.36, A:E.37, A:E.146, A:R.211, A:R.288 ZMR.5: 17 residues within 4Å: Chain B: R.36, E.37, D.69, R.70, R.74, W.97, I.141, R.143, E.146, A.165, E.195, E.196, R.211, N.213, Y.264, R.288, Y.322 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.97, B:I.141 Hydrogen bonds: B:R.70, B:R.74, B:W.97, B:W.97, B:R.143, B:E.196, B:R.211, B:Y.264 Water bridges: B:E.196 Salt bridges: B:R.36, B:E.37, B:E.146, B:R.211, B:R.288 ZMR.8: 17 residues within 4Å: Chain C: R.36, E.37, D.69, R.70, R.74, W.97, I.141, R.143, E.146, A.165, E.195, E.196, R.211, N.213, Y.264, R.288, Y.322 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:W.97, C:I.141 Hydrogen bonds: C:R.70, C:R.74, C:W.97, C:W.97, C:R.143, C:E.196, C:R.211, C:Y.264 Water bridges: C:E.196 Salt bridges: C:R.36, C:E.37, C:E.146, C:R.211, C:R.288 ZMR.11: 17 residues within 4Å: Chain D: R.36, E.37, D.69, R.70, R.74, W.97, I.141, R.143, E.146, A.165, E.195, E.196, R.211, N.213, Y.264, R.288, Y.322 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:W.97, D:I.141 Hydrogen bonds: D:R.70, D:R.74, D:W.97, D:W.97, D:R.143, D:E.196, D:R.211, D:Y.264 Water bridges: D:E.196 Salt bridges: D:R.36, D:E.37, D:E.146, D:R.211, D:R.288

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.212, G.216, D.242, G.263, Y.264 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.212, A:G.216, A:D.242, A:Y.264 CA.6: 5 residues within 4Å: Chain B: D.212, G.216, D.242, G.263, Y.264 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.212, B:G.216, B:D.242, B:Y.264 CA.9: 5 residues within 4Å: Chain C: D.212, G.216, D.242, G.263, Y.264 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.212, C:G.216, C:D.242, C:Y.264 CA.12: 5 residues within 4Å: Chain D: D.212, G.216, D.242, G.263, Y.264 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.212, D:G.216, D:D.242, D:Y.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, H. et al., Structural and Functional Analysis of Surface Proteins from an A(H3N8) Influenza Virus Isolated from New England Harbor Seals. J.Virol. (2015)

Release Date

2015-01-14

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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