SMTL ID : 4h52.1

Wild-type influenza N2 neuraminidase covalent complex with 3-fluoro-Neu5Ac

Coordinates

PDB Format Compare

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: 5 residues within 4Å: Chain A: K.62, N.65, V.68, W.356 Chain D: F.385 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.349 NAG-NAG.3: 3 residues within 4Å: Chain A: F.385 Chain B: N.65, W.356 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.349 NAG-NAG.9: 5 residues within 4Å: Chain B: F.385 Chain C: K.62, N.65, V.68, W.356 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.349 NAG-NAG.11: 3 residues within 4Å: Chain C: F.385 Chain D: N.65, W.356 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.349

4 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA-MAN.2: 9 residues within 4Å: Chain A: N.119 Chain D: D.249, Q.310, V.311, N.312, R.313, Y.372, G.373, T.374 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.312, D:N.312, D:R.313, D:N.312, D:R.313, D:D.249 Water bridges: D:Y.372, D:Y.372, D:Q.310, D:R.283, D:Q.310, D:Q.310, D:R.313 NAG-NAG-BMA-MAN.4: 8 residues within 4Å: Chain A: Q.310, V.311, N.312, R.313, Y.372, G.373, T.374 Chain B: N.119 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.312, A:N.312, A:R.313, A:N.312, A:R.313 Water bridges: A:Y.372, A:Y.372, A:Q.310, A:Q.310, A:D.249, A:R.283, A:E.294, A:Q.310, A:Q.310, A:R.313, A:R.313 NAG-NAG-BMA-MAN.10: 9 residues within 4Å: Chain B: D.249, Q.310, V.311, N.312, R.313, Y.372, G.373, T.374 Chain C: N.119 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.312, B:N.312, B:R.313, B:N.312, B:R.313, B:D.249, B:D.249 Water bridges: B:Y.372, B:Q.310, B:R.283, B:Q.310, B:Q.310, B:R.313 NAG-NAG-BMA-MAN.12: 8 residues within 4Å: Chain C: Q.310, V.311, N.312, R.313, Y.372, G.373, T.374 Chain D: N.119 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.312, C:N.312, C:R.313, C:N.312, C:R.313 Water bridges: C:Y.372, C:Q.310, C:Q.310, C:D.249, C:R.283, C:E.294, C:Q.310, C:Q.310, C:R.313, C:R.313

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.212, G.216, D.243, G.264, Q.266 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.212, A:G.216, A:D.243, A:G.264, A:Q.266, H2O.1 CA.7: 5 residues within 4Å: Chain B: D.212, G.216, D.243, G.264, Q.266 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.212, B:G.216, B:D.243, B:G.264, B:Q.266, H2O.19 CA.13: 5 residues within 4Å: Chain C: D.212, G.216, D.243, G.264, Q.266 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.212, C:G.216, C:D.243, C:G.264, C:Q.266, H2O.36 CA.15: 5 residues within 4Å: Chain D: D.212, G.216, D.243, G.264, Q.266 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.212, D:G.216, D:D.243, D:G.264, D:Q.266, H2O.54

4 x FSI: 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid(Post Translational Modification)

FSI.6: 13 residues within 4Å: Chain A: R.37, E.38, R.71, W.97, I.141, R.143, A.165, E.195, E.196, R.211, N.213, R.290, Y.325 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.97, A:I.141, A:R.143 Hydrogen bonds: A:E.38, A:R.71, A:R.143, A:E.196, A:R.211 Water bridges: A:R.75, A:E.146, A:E.196, A:E.196, A:E.196, A:R.211, A:R.211, A:R.290 Salt bridges: A:R.37, A:R.211, A:R.290 FSI.8: 13 residues within 4Å: Chain B: R.37, E.38, R.71, W.97, I.141, R.143, A.165, E.195, E.196, R.211, N.213, R.290, Y.325 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.97, B:I.141, B:R.143 Hydrogen bonds: B:E.38, B:R.71, B:R.143, B:E.196, B:R.211, B:R.211 Water bridges: B:R.75, B:E.146, B:E.196, B:R.290 Salt bridges: B:R.37, B:R.211, B:R.290 FSI.14: 13 residues within 4Å: Chain C: R.37, E.38, R.71, W.97, I.141, R.143, A.165, E.195, E.196, R.211, N.213, R.290, Y.325 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:W.97, C:I.141, C:R.143 Hydrogen bonds: C:E.38, C:R.71, C:R.143, C:E.196, C:R.211 Water bridges: C:R.75, C:E.146, C:E.196, C:E.196, C:R.211, C:R.211, C:R.290 Salt bridges: C:R.37, C:R.211, C:R.290 FSI.16: 13 residues within 4Å: Chain D: R.37, E.38, R.71, W.97, I.141, R.143, A.165, E.195, E.196, R.211, N.213, R.290, Y.325 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:W.97, D:I.141, D:R.143 Hydrogen bonds: D:E.38, D:R.71, D:R.143, D:E.196, D:R.211, D:R.211 Water bridges: D:R.75, D:E.146, D:E.196, D:E.196 Salt bridges: D:R.37, D:R.211, D:R.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vavricka, C.J. et al., Influenza neuraminidase operates via a nucleophilic mechanism and can be targeted by covalent inhibitors. Nat Commun (2013)

Release Date

2013-02-20

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Neuraminidase

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