SMTL ID : 5huk.1

The crystal structure of neuraminidase from A/Northern pintail/Washington/40964/2014 influenza virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: N.79, W.370, I.402 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.167, Y.217 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.79, W.370, I.402 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.79, W.370, I.402 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: N.79, W.370, I.402 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.3: 9 residues within 4Å: Chain A: N.133 Chain D: D.263, Q.324, V.325, N.326, R.327, Y.386, G.387, T.388 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.326, D:N.326, D:R.327, D:N.326, D:R.327 Water bridges: D:N.326, D:Y.386 NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 10 residues within 4Å: Chain B: N.133, Q.153 Chain C: D.263, Q.324, V.325, N.326, R.327, Y.386, G.387, T.388 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.326, C:N.326, C:R.327, C:N.326, C:R.327, C:N.326 Water bridges: C:R.311 NAG-NAG-BMA-MAN-MAN-MAN-MAN.7: 9 residues within 4Å: Chain A: Q.324, V.325, N.326, R.327, Y.386, G.387, T.388 Chain C: N.133, Q.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.326, A:N.326, A:R.327, A:N.326, A:R.327 Water bridges: A:Y.386 NAG-NAG-BMA-MAN-MAN-MAN-MAN.9: 10 residues within 4Å: Chain B: D.263, Q.324, V.325, N.326, R.327, Y.386, G.387, T.388 Chain D: N.133, Q.153 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.326, B:N.326, B:R.327, B:V.325, B:N.326, B:R.327 Water bridges: B:N.326, B:Y.386

4 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain A: D.226, G.230, D.257, G.278, G.281 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.226, A:G.230, A:D.257, A:G.278, H2O.2 CA.11: 5 residues within 4Å: Chain B: D.226, G.230, D.257, G.278, G.281 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.226, B:G.230, B:D.257, B:G.278 CA.13: 6 residues within 4Å: Chain C: D.226, G.230, S.231, D.257, G.278, G.281 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.226, C:G.230, C:D.257, C:G.278 CA.15: 5 residues within 4Å: Chain D: D.226, G.230, D.257, G.278, G.281 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.226, D:G.230, D:D.257, D:G.278, H2O.13

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

NAG.12: 2 residues within 4Å: Chain B: N.19, N.167 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Chain C: N.167 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.167 NAG.16: 3 residues within 4Å: Chain D: N.19, N.167, Y.217 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.19 Hydrogen bonds: D:Y.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, H. et al., Molecular Characterizations of Surface Proteins Hemagglutinin and Neuraminidase from Recent H5Nx Avian Influenza Viruses. J.Virol. (2016)

Release Date

2016-04-13

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Neuraminidase