SMTL ID : 6n4d.1 (1 other biounit)

The crystal structure of neuramindase from A/canine/IL/11613/2015 (H3N2) influenza virus.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 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: 2 residues within 4Å: Chain A: N.74, W.365 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: N.74, W.365 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: N.74, W.365 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain D: N.74, W.365 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.2: 9 residues within 4Å: Chain A: N.128 Chain B: D.258, Q.319, V.320, N.321, R.322, Y.381, G.382, T.383 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.321, B:N.321, B:R.322, B:V.320, B:N.321, B:R.322 Water bridges: B:N.321, B:Y.381 NAG-NAG-BMA-MAN-MAN-MAN.4: 9 residues within 4Å: Chain B: N.128 Chain C: D.258, Q.319, V.320, N.321, R.322, Y.381, G.382, T.383 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.321, C:N.321, C:R.322, C:V.320, C:N.321, C:R.322 Water bridges: C:N.321, C:Y.381 NAG-NAG-BMA-MAN-MAN-MAN.10: 9 residues within 4Å: Chain C: N.128 Chain D: D.258, Q.319, V.320, N.321, R.322, Y.381, G.382, T.383 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.321, D:N.321, D:R.322, D:V.320, D:N.321, D:R.322 Water bridges: D:N.321, D:Y.381 NAG-NAG-BMA-MAN-MAN-MAN.12: 9 residues within 4Å: Chain A: D.258, Q.319, V.320, N.321, R.322, Y.381, G.382, T.383 Chain D: N.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.321, A:N.321, A:R.322, A:V.320, A:N.321, A:R.322 Water bridges: A:N.321, A:Y.381

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: D.221, G.225, D.252, G.273, P.275, G.276 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.221, A:G.225, A:D.252, A:G.273, A:P.275, H2O.2 CA.7: 6 residues within 4Å: Chain B: D.221, G.225, D.252, G.273, P.275, G.276 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.221, B:G.225, B:D.252, B:G.273, B:P.275, H2O.5 CA.13: 6 residues within 4Å: Chain C: D.221, G.225, D.252, G.273, P.275, G.276 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.221, C:G.225, C:D.252, C:G.273, C:P.275, H2O.9 CA.15: 6 residues within 4Å: Chain D: D.221, G.225, D.252, G.273, P.275, G.276 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.221, D:G.225, D:D.252, D:G.273, D:P.275, H2O.13

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

NAG.6: 2 residues within 4Å: Chain A: N.162, Y.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.162 NAG.8: 2 residues within 4Å: Chain B: N.162, Y.212 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.162 Water bridges: B:R.186, B:R.186 NAG.14: 2 residues within 4Å: Chain C: N.162, Y.212 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.162 NAG.16: 2 residues within 4Å: Chain D: N.162, Y.212 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.162 Water bridges: D:R.186, D:R.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pulit-Penaloza, J.A. et al., Assessment of Molecular, Antigenic, and Pathological Features of Canine Influenza A(H3N2) Viruses That Emerged in the United States. J. Infect. Dis. (2017)

Release Date

2019-01-30

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
A

D
D

Neuraminidase

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