SMTL ID : 4h53.1

Influenza N2-Tyr406Asp neuraminidase in complex with beta-Neu5Ac

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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(Non-covalent)

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 11 residues within 4Å: Chain A: N.119 Chain B: D.249, I.299, S.309, Q.310, V.311, N.312, R.313, Y.372, G.373, T.374 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.312, B:R.313, B:D.249, B:N.312, B:N.312, B:R.313 Water bridges: B:R.283, B:R.283, B:Q.310, B:Q.310, B:R.313, B:Y.372, B:Y.372

3 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.2: 8 residues within 4Å: Chain A: S.286, E.288, S.289, S.291, N.319, N.320, N.321, W.322 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.288, A:S.286, A:S.286, A:S.289, A:S.291, A:S.291, A:N.319 Water bridges: A:N.319, A:K.287, A:N.319, A:N.320, A:Q.351, A:Q.351 Salt bridges: A:K.287 Hydrophobic interactions: A:W.322 GAL-SIA.5: 7 residues within 4Å: Chain B: S.286, S.289, S.291, N.319, N.320, N.321, W.322 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.322 Hydrogen bonds: B:S.286, B:S.286, B:S.289, B:S.289, B:S.291, B:S.291, B:N.319 Water bridges: B:K.287, B:N.319, B:N.320, B:Q.351, B:Q.351 GAL-SIA.8: 8 residues within 4Å: Chain C: S.286, S.289, S.291, N.319, N.320, N.321, W.322, Q.351 12 PLIP interactions: 12 interactions with chain C Water bridges: C:N.319, C:K.287, C:N.319, C:N.320, C:Q.351, C:Q.351 Hydrophobic interactions: C:W.322 Hydrogen bonds: C:S.286, C:S.286, C:S.289, C:S.291, C:S.291, C:N.319

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(Non-covalent)

NAG-NAG-BMA-MAN.3: 3 residues within 4Å: Chain B: N.65, W.356, I.388 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.4: 8 residues within 4Å: Chain B: N.119 Chain D: 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:R.313, D:N.312, D:N.312, D:R.313 Water bridges: D:Q.310, D:D.249, D:E.294, D:E.294, D:Q.310, D:Q.310, D:R.313, D:Y.372, D:Y.372 NAG-NAG-BMA-MAN.6: 3 residues within 4Å: Chain C: N.65, W.356, I.388 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.356 NAG-NAG-BMA-MAN.7: 9 residues within 4Å: Chain A: D.249, Q.310, V.311, N.312, R.313, Y.372, G.373, T.374 Chain C: N.119 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.311, A:N.312, A:R.313, A:D.249, A:D.249, A:N.312, A:N.312, A:R.313 Water bridges: A:R.283, A:R.283, A:E.294, A:Q.310, A:Q.310, A:R.313, A:R.313, A:Y.372, A:Y.372

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

NAG-NAG.9: 3 residues within 4Å: Chain D: N.65, W.356, I.388 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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(Non-covalent)

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

3 x CA: CALCIUM ION(Non-covalent)

CA.11: 5 residues within 4Å: Chain A: D.212, G.216, D.243, G.264, Q.266 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.212, A:G.216, A:D.243, A:G.264, A:Q.266 CA.14: 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.21 CA.16: 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.43

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

NAG.12: 3 residues within 4Å: Chain A: N.65, W.356, I.388 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.388 Hydrogen bonds: A:N.65, A:W.356

3 x SLB: N-acetyl-beta-neuraminic acid(Non-covalent)

SLB.13: 12 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, W.97, I.141, R.143, A.165, E.195, E.196, R.211, R.290 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:D.70, A:R.71, A:R.143, A:E.196, A:R.211 Water bridges: A:R.37, A:E.38, A:R.75, A:E.196, A:R.290, A:R.290, A:D.325 Salt bridges: A:R.37, A:R.211, A:R.290 SLB.15: 13 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, W.97, I.141, R.143, A.165, E.195, E.196, R.211, N.213, R.290 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:W.97, B:I.141, B:R.143 Hydrogen bonds: B:E.38, B:D.70, B:R.71, B:R.143, B:E.196, B:R.211, B:R.211 Water bridges: B:E.38, B:R.75, B:E.146, B:E.196, B:E.196, B:E.196, B:R.290, B:R.290, B:D.325 Salt bridges: B:R.37, B:R.211, B:R.290 SLB.17: 13 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, W.97, I.141, R.143, A.165, E.195, E.196, R.211, N.213, R.290 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:W.97, C:I.141, C:R.143 Hydrogen bonds: C:E.38, C:D.70, C:D.70, C:R.71, C:R.143, C:E.196, C:R.211, C:R.211 Water bridges: C:R.37, C:E.38, C:E.146, C:E.196, C:E.196, C:R.290, C:R.290 Salt bridges: C:R.37, C:R.211, C:R.290

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 6 residues within 4Å: Chain D: E.38, D.70, R.143, E.196, R.211, Q.266 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:E.38, D:E.38, D:R.143, D:R.211, D:Q.266 Water bridges: D:R.143, D:E.146, D:E.196, D:E.196, D:R.211, D:R.211

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
C

D
D

Neuraminidase