SMTL ID : 4qn6.1 (1 other biounit)

Crystal structure of Neuraminidase N6 complexed with Laninamivir

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA: 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.1: 4 residues within 4Å: Chain A: R.64, N.67, L.360 Chain D: Y.389 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain B: R.64, N.67, L.360 Chain C: Y.389 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain A: Y.389 Chain C: R.64, N.67, L.360 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain B: Y.389 Chain D: R.64, N.67, L.360 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA- MAN- MAN- MAN: 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.2: 18 residues within 4Å: Chain A: N.121, N.122 Chain D: S.16, S.17, I.243, D.252, R.286, E.297, L.299, P.312, I.313, S.314, H.315, V.317, R.375, L.376, G.377, S.378 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.315, D:H.315, D:H.315, D:H.315, D:R.375, D:R.286 Water bridges: D:D.252, D:D.252, D:E.297 NAG-NAG-BMA-MAN-MAN-MAN.6: 18 residues within 4Å: Chain B: N.121, N.122 Chain C: S.16, S.17, I.243, D.252, R.286, E.297, L.299, P.312, I.313, S.314, H.315, V.317, R.375, L.376, G.377, S.378 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.315, C:H.315, C:H.315, C:H.315, C:R.375, C:R.286 Water bridges: C:D.252, C:D.252, C:E.297 NAG-NAG-BMA-MAN-MAN-MAN.10: 18 residues within 4Å: Chain A: S.16, S.17, I.243, D.252, R.286, E.297, L.299, P.312, I.313, S.314, H.315, V.317, R.375, L.376, G.377, S.378 Chain C: N.121, N.122 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.315, A:H.315, A:H.315, A:H.315, A:R.375, A:R.286 Water bridges: A:D.252, A:D.252, A:E.297 NAG-NAG-BMA-MAN-MAN-MAN.14: 18 residues within 4Å: Chain B: S.16, S.17, I.243, D.252, R.286, E.297, L.299, P.312, I.313, S.314, H.315, V.317, R.375, L.376, G.377, S.378 Chain D: N.121, N.122 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.315, B:H.315, B:H.315, B:H.315, B:R.375, B:R.286 Water bridges: B:D.252, B:D.252, B:E.297

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.215, G.219, D.246, P.269 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.215, A:G.219, A:D.246, A:P.269, H2O.1, H2O.2 CA.7: 4 residues within 4Å: Chain B: D.215, G.219, D.246, P.269 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.215, B:G.219, B:D.246, B:P.269, H2O.17, H2O.18 CA.11: 4 residues within 4Å: Chain C: D.215, G.219, D.246, P.269 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.215, C:G.219, C:D.246, C:P.269, H2O.32, H2O.33 CA.15: 4 residues within 4Å: Chain D: D.215, G.219, D.246, P.269 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.215, D:G.219, D:D.246, D:P.269, H2O.48, H2O.49

4 x LNV: 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-D-glycero-D-galacto-non-2-enonic acid(Non-covalent)

LNV.4: 16 residues within 4Å: Chain A: R.39, E.40, D.72, R.73, R.77, W.100, I.144, R.146, E.149, A.168, E.198, E.199, R.214, N.216, R.293, Y.327 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:W.100, A:I.144, A:R.146 Hydrogen bonds: A:R.73, A:W.100, A:W.100, A:R.146, A:E.199, A:R.214, A:R.214 Water bridges: A:R.39, A:D.72, A:R.77, A:R.77, A:R.146, A:E.199, A:E.199 Salt bridges: A:R.39, A:E.40, A:D.72, A:E.149, A:R.214, A:R.293 LNV.8: 16 residues within 4Å: Chain B: R.39, E.40, D.72, R.73, R.77, W.100, I.144, R.146, E.149, A.168, E.198, E.199, R.214, N.216, R.293, Y.327 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:W.100, B:I.144, B:R.146 Hydrogen bonds: B:R.73, B:W.100, B:W.100, B:R.146, B:E.199, B:R.214, B:R.214 Water bridges: B:R.39, B:D.72, B:R.77, B:R.77, B:R.146, B:E.199, B:E.199 Salt bridges: B:R.39, B:E.40, B:D.72, B:E.149, B:R.214, B:R.293 LNV.12: 16 residues within 4Å: Chain C: R.39, E.40, D.72, R.73, R.77, W.100, I.144, R.146, E.149, A.168, E.198, E.199, R.214, N.216, R.293, Y.327 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:W.100, C:I.144, C:R.146 Hydrogen bonds: C:R.73, C:W.100, C:W.100, C:R.146, C:E.199, C:R.214, C:R.214 Water bridges: C:R.39, C:D.72, C:R.77, C:R.77, C:R.146, C:E.199, C:E.199 Salt bridges: C:R.39, C:E.40, C:D.72, C:E.149, C:R.214, C:R.293 LNV.16: 16 residues within 4Å: Chain D: R.39, E.40, D.72, R.73, R.77, W.100, I.144, R.146, E.149, A.168, E.198, E.199, R.214, N.216, R.293, Y.327 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:W.100, D:I.144, D:R.146 Hydrogen bonds: D:R.73, D:W.100, D:W.100, D:R.146, D:E.199, D:R.214, D:R.214 Water bridges: D:R.39, D:D.72, D:R.77, D:R.77, D:R.146, D:E.199, D:E.199 Salt bridges: D:R.39, D:E.40, D:D.72, D:E.149, D:R.214, D:R.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, X. et al., Structure of influenza virus N7: the last piece of the neuraminidase "jigsaw" puzzle. J.Virol. (2014)

Release Date

2014-07-30

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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