SMTL ID : 5l18.1

The crystal structure of neuraminidase in complex with sialic acid from A/Shanghai/2/2013 (H7N9) influenza virus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN.1: 18 residues within 4Å: Chain A: N.128, N.129 Chain D: R.256, N.258, D.259, R.292, I.294, T.296, E.303, L.305, P.318, I.319, Q.320, G.321, F.381, L.382, G.383, Q.384 5 PLIP interactions: 5 interactions with chain D Water bridges: D:G.321, D:Q.322, D:Q.320, D:Q.320, D:Q.384 Hydrophobic interactions: D:F.381 Hydrogen bonds: D:G.321 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.5: 18 residues within 4Å: Chain B: N.128, N.129 Chain C: R.256, N.258, D.259, R.292, I.294, T.296, E.303, L.305, P.318, I.319, Q.320, G.321, F.381, L.382, G.383, Q.384 5 PLIP interactions: 5 interactions with chain C Water bridges: C:G.321, C:Q.322, C:Q.320, C:Q.320, C:Q.384 Hydrophobic interactions: C:F.381 Hydrogen bonds: C:G.321 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.9: 18 residues within 4Å: Chain A: R.256, N.258, D.259, R.292, I.294, T.296, E.303, L.305, P.318, I.319, Q.320, G.321, F.381, L.382, G.383, Q.384 Chain C: N.128, N.129 5 PLIP interactions: 5 interactions with chain A Water bridges: A:G.321, A:Q.322, A:Q.320, A:Q.320, A:Q.384 Hydrophobic interactions: A:F.381 Hydrogen bonds: A:G.321 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.13: 18 residues within 4Å: Chain B: R.256, N.258, D.259, R.292, I.294, T.296, E.303, L.305, P.318, I.319, Q.320, G.321, F.381, L.382, G.383, Q.384 Chain D: N.128, N.129 5 PLIP interactions: 5 interactions with chain B Water bridges: B:G.321, B:Q.322, B:Q.320, B:Q.320, B:Q.384 Hydrophobic interactions: B:F.381 Hydrogen bonds: B:G.321

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

NAG.2: 2 residues within 4Å: Chain A: N.74, W.366 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.74, A:W.366 Water bridges: D:Y.395 NAG.6: 2 residues within 4Å: Chain B: N.74, W.366 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.74, B:W.366 Water bridges: C:Y.395 NAG.10: 2 residues within 4Å: Chain C: N.74, W.366 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.74, C:W.366 Water bridges: A:Y.395 NAG.14: 2 residues within 4Å: Chain D: N.74, W.366 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Water bridges: B:Y.395 Hydrogen bonds: D:N.74, D:W.366

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.222, G.226, D.253, N.275, G.276 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.222, A:G.226, A:D.253, A:N.275, H2O.7, H2O.10 CA.7: 5 residues within 4Å: Chain B: D.222, G.226, D.253, N.275, G.276 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.222, B:G.226, B:D.253, B:N.275, H2O.27, H2O.30 CA.11: 5 residues within 4Å: Chain C: D.222, G.226, D.253, N.275, G.276 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.222, C:G.226, C:D.253, C:N.275, H2O.47, H2O.50 CA.15: 5 residues within 4Å: Chain D: D.222, G.226, D.253, N.275, G.276 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.222, D:G.226, D:D.253, D:N.275, H2O.67, H2O.70

4 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.4: 14 residues within 4Å: Chain A: R.46, E.47, D.79, R.80, W.107, I.151, R.153, A.175, E.205, E.206, R.221, N.223, R.299, Y.333 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:W.107, A:I.151, A:R.153 Hydrogen bonds: A:E.47, A:D.79, A:R.80, A:R.153, A:E.206, A:R.221, A:R.221, A:Y.333 Water bridges: A:R.46, A:D.79, A:R.80, A:R.84, A:R.84, A:E.156, A:E.156, A:E.206, A:E.206 Salt bridges: A:R.46, A:R.221, A:R.299 SIA.8: 14 residues within 4Å: Chain B: R.46, E.47, D.79, R.80, W.107, I.151, R.153, A.175, E.205, E.206, R.221, N.223, R.299, Y.333 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:W.107, B:I.151, B:R.153 Hydrogen bonds: B:E.47, B:D.79, B:R.80, B:R.153, B:E.206, B:R.221, B:R.221, B:Y.333 Water bridges: B:R.46, B:D.79, B:R.80, B:R.84, B:R.84, B:E.156, B:E.156, B:E.206, B:E.206 Salt bridges: B:R.46, B:R.221, B:R.299 SIA.12: 14 residues within 4Å: Chain C: R.46, E.47, D.79, R.80, W.107, I.151, R.153, A.175, E.205, E.206, R.221, N.223, R.299, Y.333 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:W.107, C:I.151, C:R.153 Hydrogen bonds: C:E.47, C:D.79, C:R.80, C:R.153, C:E.206, C:R.221, C:R.221, C:Y.333 Water bridges: C:R.46, C:D.79, C:R.80, C:R.84, C:R.84, C:E.156, C:E.156, C:E.206, C:E.206 Salt bridges: C:R.46, C:R.221, C:R.299 SIA.16: 14 residues within 4Å: Chain D: R.46, E.47, D.79, R.80, W.107, I.151, R.153, A.175, E.205, E.206, R.221, N.223, R.299, Y.333 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:W.107, D:I.151, D:R.153 Hydrogen bonds: D:E.47, D:D.79, D:R.80, D:R.153, D:E.206, D:R.221, D:R.221, D:Y.333 Water bridges: D:R.46, D:D.79, D:R.80, D:R.84, D:R.84, D:E.156, D:E.156, D:E.206, D:E.206 Salt bridges: D:R.46, D:R.221, D:R.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gubareva, L.V. et al., Drug Susceptibility Evaluation of an Influenza A(H7N9) Virus by Analyzing Recombinant Neuraminidase Proteins. J. Infect. Dis. (2017)

Release Date

2017-08-09

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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