SMTL ID : 4hzx.1

Crystal structure of influenza A neuraminidase N3 complexed with oseltamivir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 3 residues within 4Å: Chain A: N.65, S.356, K.388 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.6: 3 residues within 4Å: Chain B: N.65, S.356, K.388 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.11: 3 residues within 4Å: Chain C: N.65, S.356, K.388 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.16: 3 residues within 4Å: Chain D: N.65, S.356, K.388 No protein-ligand interaction detected (PLIP)

4 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 4 residues within 4Å: Chain A: D.154, N.226, N.227, E.228 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.228 Hydrogen bonds: A:T.156, A:N.227, A:E.228, A:E.228 Water bridges: A:D.154, A:R.178, A:R.178 NAG-FUC.7: 4 residues within 4Å: Chain B: D.154, N.226, N.227, E.228 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:E.228 Hydrogen bonds: B:T.156, B:N.227, B:E.228, B:E.228 Water bridges: B:D.154, B:R.178, B:R.178 NAG-FUC.12: 4 residues within 4Å: Chain C: D.154, N.226, N.227, E.228 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:E.228 Hydrogen bonds: C:T.156, C:N.227, C:E.228, C:E.228 Water bridges: C:D.154, C:R.178, C:R.178 NAG-FUC.17: 4 residues within 4Å: Chain D: D.154, N.226, N.227, E.228 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:E.228 Hydrogen bonds: D:T.156, D:N.227, D:E.228, D:E.228 Water bridges: D:D.154, D:R.178, D:R.178

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 6 residues within 4Å: Chain A: D.213, G.217, D.243, G.263, P.265, G.266 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.243, A:G.263, A:P.265, H2O.1 CA.4: 3 residues within 4Å: Ligands: CA.9, CA.14, CA.19 No protein-ligand interaction detected (PLIP) CA.8: 6 residues within 4Å: Chain B: D.213, G.217, D.243, G.263, P.265, G.266 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.243, B:G.263, B:P.265, H2O.14 CA.9: 3 residues within 4Å: Ligands: CA.4, CA.14, CA.19 No protein-ligand interaction detected (PLIP) CA.13: 6 residues within 4Å: Chain C: D.213, G.217, D.243, G.263, P.265, G.266 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.243, C:G.263, C:P.265, H2O.27 CA.14: 3 residues within 4Å: Ligands: CA.4, CA.9, CA.19 No protein-ligand interaction detected (PLIP) CA.18: 6 residues within 4Å: Chain D: D.213, G.217, D.243, G.263, P.265, G.266 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.243, D:G.263, D:P.265, H2O.40 CA.19: 3 residues within 4Å: Ligands: CA.4, CA.9, CA.14 No protein-ligand interaction detected (PLIP)

4 x G39: (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid(Non-covalent)

G39.5: 14 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.197, E.198, R.212, N.214, R.289, Y.324 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.98, A:I.142, A:A.166 Hydrogen bonds: A:E.38, A:D.70, A:R.71, A:Y.324 Water bridges: A:R.75, A:E.147 Salt bridges: A:R.37, A:R.212, A:R.289 G39.10: 14 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.197, E.198, R.212, N.214, R.289, Y.324 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.98, B:I.142, B:A.166 Hydrogen bonds: B:E.38, B:D.70, B:R.71, B:Y.324 Water bridges: B:R.75, B:E.147 Salt bridges: B:R.37, B:R.212, B:R.289 G39.15: 14 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.197, E.198, R.212, N.214, R.289, Y.324 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142, C:A.166 Hydrogen bonds: C:E.38, C:D.70, C:R.71, C:Y.324 Water bridges: C:R.75, C:E.147 Salt bridges: C:R.37, C:R.212, C:R.289 G39.20: 14 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.197, E.198, R.212, N.214, R.289, Y.324 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142, D:A.166 Hydrogen bonds: D:E.38, D:D.70, D:R.71, D:Y.324 Water bridges: D:R.75, D:E.147 Salt bridges: D:R.37, D:R.212, D:R.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Q. et al., Functional and structural analysis of influenza virus neuraminidase N3 offers further insight into the mechanisms of oseltamivir resistance. J.Virol. (2013)

Release Date

2013-11-06

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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