SMTL ID : 4b7j.1

H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-tetramer

Ligands

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 2 residues within 4Å: Chain A: N.88, S.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.88 NAG.2: 3 residues within 4Å: Chain A: K.143, N.146, I.436 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.436 Hydrogen bonds: A:N.146 NAG.3: 3 residues within 4Å: Chain A: K.84, N.235, Q.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.84, A:N.235 NAG.6: 2 residues within 4Å: Chain B: N.88, S.89 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.88 NAG.7: 3 residues within 4Å: Chain B: K.143, N.146, I.436 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.436 Hydrogen bonds: B:N.146 NAG.8: 3 residues within 4Å: Chain B: K.84, N.235, Q.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.84, B:N.235 NAG.11: 2 residues within 4Å: Chain C: N.88, S.89 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.88 NAG.12: 3 residues within 4Å: Chain C: K.143, N.146, I.436 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.436 Hydrogen bonds: C:N.146 NAG.13: 3 residues within 4Å: Chain C: K.84, N.235, Q.308 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.84, C:N.235 NAG.16: 2 residues within 4Å: Chain D: N.88, S.89 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.88 NAG.17: 3 residues within 4Å: Chain D: K.143, N.146, I.436 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.436 Hydrogen bonds: D:N.146 NAG.18: 3 residues within 4Å: Chain D: K.84, N.235, Q.308 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.84, D:N.235

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: D.294, G.298, D.324, G.342, N.344, G.345 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.294, A:D.324, A:G.342, A:N.344, H2O.7 CA.9: 6 residues within 4Å: Chain B: D.294, G.298, D.324, G.342, N.344, G.345 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.294, B:D.324, B:G.342, B:N.344, H2O.16 CA.14: 6 residues within 4Å: Chain C: D.294, G.298, D.324, G.342, N.344, G.345 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.294, C:D.324, C:G.342, C:N.344, H2O.24 CA.19: 6 residues within 4Å: Chain D: D.294, G.298, D.324, G.342, N.344, G.345 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.294, D:D.324, D:G.342, D:N.344, H2O.33

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.118, E.119, D.151, R.152, W.179, R.223, R.225, S.247, E.277, E.278, R.293, N.295, R.368, Y.402 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.179 Hydrogen bonds: A:E.119, A:D.151, A:R.152, A:Y.402 Water bridges: A:D.151, A:R.156, A:E.278 Salt bridges: A:R.118, A:R.293, A:R.368 G39.10: 14 residues within 4Å: Chain B: R.118, E.119, D.151, R.152, W.179, R.223, R.225, S.247, E.277, E.278, R.293, N.295, R.368, Y.402 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.179 Hydrogen bonds: B:E.119, B:D.151, B:R.152, B:Y.402 Water bridges: B:D.151, B:R.156, B:E.278 Salt bridges: B:R.118, B:R.293, B:R.368 G39.15: 14 residues within 4Å: Chain C: R.118, E.119, D.151, R.152, W.179, R.223, R.225, S.247, E.277, E.278, R.293, N.295, R.368, Y.402 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.179 Hydrogen bonds: C:E.119, C:D.151, C:R.152, C:Y.402 Water bridges: C:D.151, C:R.156, C:E.278 Salt bridges: C:R.118, C:R.293, C:R.368 G39.20: 14 residues within 4Å: Chain D: R.118, E.119, D.151, R.152, W.179, R.223, R.225, S.247, E.277, E.278, R.293, N.295, R.368, Y.402 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.179 Hydrogen bonds: D:E.119, D:D.151, D:R.152, D:Y.402 Water bridges: D:D.151, D:R.156, D:E.278 Salt bridges: D:R.118, D:R.293, D:R.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Der Vries, E. et al., H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis. Plos Pathog. (2012)

Release Date

2012-10-03

Peptides

NEURAMINIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

NEURAMINIDASE

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