SMTL ID : 2bat.1

THE STRUCTURE OF THE COMPLEX BETWEEN INFLUENZA VIRUS NEURAMINIDASE AND SIALIC ACID, THE VIRAL RECEPTOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- NAG- NGK- FUL: 2-acetamido-2-deoxy-4-O-sulfo-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA-MAN-NAG-NGK-FUL.1: 4 residues within 4Å: Chain A: N.65, W.356, I.388 Chain D: N.382 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.382 NAG-NAG-BMA-MAN-NAG-NGK-FUL.7: 4 residues within 4Å: Chain B: N.65, W.356, I.388 Chain C: N.382 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.382 NAG-NAG-BMA-MAN-NAG-NGK-FUL.13: 4 residues within 4Å: Chain A: N.382 Chain C: N.65, W.356, I.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.382 NAG-NAG-BMA-MAN-NAG-NGK-FUL.19: 4 residues within 4Å: Chain B: N.382 Chain D: N.65, W.356, I.388 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.382

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: 8 residues within 4Å: Chain A: N.119 Chain D: Q.310, I.311, N.312, R.313, Y.372, G.373, T.374 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:I.311, D:N.312, D:R.313, D:N.312, D:N.312, D:R.313 Water bridges: D:Y.372 NAG-NAG-BMA-MAN-MAN-MAN.8: 8 residues within 4Å: Chain B: N.119 Chain C: Q.310, I.311, N.312, R.313, Y.372, G.373, T.374 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.311, C:N.312, C:R.313, C:N.312, C:N.312, C:R.313 Water bridges: C:Y.372 NAG-NAG-BMA-MAN-MAN-MAN.14: 8 residues within 4Å: Chain A: Q.310, I.311, N.312, R.313, Y.372, G.373, T.374 Chain C: N.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.311, A:N.312, A:R.313, A:N.312, A:N.312, A:R.313 Water bridges: A:Y.372 NAG-NAG-BMA-MAN-MAN-MAN.20: 8 residues within 4Å: Chain B: Q.310, I.311, N.312, R.313, Y.372, G.373, T.374 Chain D: N.119 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.311, B:N.312, B:R.313, B:N.312, B:N.312, B:R.313 Water bridges: B:Y.372

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

NAG.3: 5 residues within 4Å: Chain A: E.2, N.5, S.7, Y.203 Ligands: NAG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.2, A:N.5, A:S.7 Water bridges: A:E.2, A:E.2 NAG.4: 5 residues within 4Å: Chain A: I.152, N.153, Y.203, E.227 Ligands: NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.152 Hydrogen bonds: A:N.153, A:Y.203 NAG.9: 5 residues within 4Å: Chain B: E.2, N.5, S.7, Y.203 Ligands: NAG.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.2, B:N.5, B:S.7 Water bridges: B:E.2, B:E.2 NAG.10: 5 residues within 4Å: Chain B: I.152, N.153, Y.203, E.227 Ligands: NAG.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.152 Hydrogen bonds: B:N.153, B:Y.203 NAG.15: 5 residues within 4Å: Chain C: E.2, N.5, S.7, Y.203 Ligands: NAG.16 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.2, C:N.5, C:S.7 Water bridges: C:E.2, C:E.2 NAG.16: 5 residues within 4Å: Chain C: I.152, N.153, Y.203, E.227 Ligands: NAG.15 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.152 Hydrogen bonds: C:N.153, C:Y.203 NAG.21: 5 residues within 4Å: Chain D: E.2, N.5, S.7, Y.203 Ligands: NAG.22 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.2, D:N.5, D:S.7 Water bridges: D:E.2, D:E.2 NAG.22: 5 residues within 4Å: Chain D: I.152, N.153, Y.203, E.227 Ligands: NAG.21 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.152 Hydrogen bonds: D:N.153, D:Y.203

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

SIA.5: 14 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, N.213, R.290, Y.325 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.97, A:I.141 Hydrogen bonds: A:E.38, A:D.70, A:D.70, A:R.71, A:E.196, A:R.211, A:R.211 Water bridges: A:R.37, A:E.146, A:E.146 Salt bridges: A:R.37, A:R.211, A:R.290 SIA.11: 14 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, Y.325 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.97, B:I.141 Hydrogen bonds: B:E.38, B:D.70, B:D.70, B:R.71, B:E.196, B:R.211, B:R.211 Water bridges: B:R.37, B:E.146, B:E.146 Salt bridges: B:R.37, B:R.211, B:R.290 SIA.17: 14 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, Y.325 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:W.97, C:I.141 Hydrogen bonds: C:E.38, C:D.70, C:D.70, C:R.71, C:E.196, C:R.211, C:R.211 Water bridges: C:R.37, C:E.146, C:E.146 Salt bridges: C:R.37, C:R.211, C:R.290 SIA.23: 14 residues within 4Å: Chain D: 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, Y.325 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:W.97, D:I.141 Hydrogen bonds: D:E.38, D:D.70, D:D.70, D:R.71, D:E.196, D:R.211, D:R.211 Water bridges: D:R.37, D:E.146, D:E.146 Salt bridges: D:R.37, D:R.211, D:R.290

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: D.212, G.216, D.243, G.264, T.265, 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.12: 6 residues within 4Å: Chain B: D.212, G.216, D.243, G.264, T.265, Q.266 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.212, B:G.216, B:D.243, B:G.264, B:Q.266 CA.18: 6 residues within 4Å: Chain C: D.212, G.216, D.243, G.264, T.265, Q.266 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.212, C:G.216, C:D.243, C:G.264, C:Q.266 CA.24: 6 residues within 4Å: Chain D: D.212, G.216, D.243, G.264, T.265, Q.266 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.212, D:G.216, D:D.243, D:G.264, D:Q.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varghese, J.N. et al., The structure of the complex between influenza virus neuraminidase and sialic acid, the viral receptor. Proteins (1992)

Release Date

1994-01-31

Peptides

NEURAMINIDASE N2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

NEURAMINIDASE N2