SMTL ID : 4b7r.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 1.90 Å

Oligo State

homo-tetramer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain A: K.61, N.64 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.212, G.216, D.242, G.260, N.262, G.263 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.212, A:G.216, A:D.242, A:G.260, A:N.262, H2O.7 CA.3: 4 residues within 4Å: Chain A: D.294, N.296, D.302, N.304 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.294, A:D.302, A:N.304, H2O.8, H2O.8 CA.8: 5 residues within 4Å: Chain B: D.212, G.216, D.242, G.260, N.262 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.212, B:G.216, B:D.242, B:G.260, B:N.262, H2O.15 CA.9: 4 residues within 4Å: Chain B: D.294, N.296, D.302, N.304 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.294, B:D.302, B:N.304, H2O.17, H2O.17 CA.15: 5 residues within 4Å: Chain C: D.212, G.216, D.242, G.260, N.262 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.212, C:G.216, C:D.242, C:G.260, C:N.262, H2O.25 CA.16: 4 residues within 4Å: Chain C: D.294, N.296, D.302, N.304 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.294, C:D.302, C:N.304, H2O.27, H2O.27 CA.23: 6 residues within 4Å: Chain D: D.212, G.216, D.242, G.260, N.262, G.263 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.212, D:G.216, D:D.242, D:G.260, D:N.262, H2O.34 CA.24: 4 residues within 4Å: Chain D: D.294, N.296, D.302, N.304 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.294, D:D.302, D:N.304, H2O.36, H2O.36

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

G39.4: 15 residues within 4Å: Chain A: R.36, E.37, D.69, R.70, W.97, I.141, R.143, S.165, E.195, E.196, R.211, N.213, R.286, Y.320 Ligands: EPE.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.97, A:I.141, A:I.141 Hydrogen bonds: A:E.37, A:R.70, A:Y.320 Water bridges: A:D.69, A:R.70, A:E.196 Salt bridges: A:R.36, A:R.211, A:R.286 G39.10: 14 residues within 4Å: Chain B: R.36, E.37, D.69, R.70, W.97, R.143, S.165, E.195, E.196, R.211, N.213, R.286, Y.320 Ligands: EPE.11 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.97, B:E.195 Hydrogen bonds: B:E.37, B:R.70 Water bridges: B:D.69, B:R.74, B:E.196 Salt bridges: B:R.36, B:R.211, B:R.286 G39.17: 15 residues within 4Å: Chain C: R.36, E.37, D.69, R.70, W.97, I.141, R.143, S.165, E.195, E.196, R.211, N.213, R.286, Y.320 Ligands: EPE.18 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.97, C:I.141, C:E.195, C:N.213 Hydrogen bonds: C:E.37, C:R.70, C:Y.320 Water bridges: C:D.69, C:R.74, C:E.196, C:R.211 Salt bridges: C:R.36, C:R.211, C:R.286 G39.25: 14 residues within 4Å: Chain D: R.36, E.37, D.69, R.70, W.97, R.143, S.165, E.195, E.196, R.211, N.213, R.286, Y.320 Ligands: EPE.26 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.97 Hydrogen bonds: D:E.37, D:R.70, D:Y.320 Water bridges: D:D.69, D:D.69, D:R.74, D:E.196, D:E.196 Salt bridges: D:R.36, D:R.211, D:R.286

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 6 residues within 4Å: Chain A: I.67, K.68, D.69, R.286, P.349 Ligands: G39.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.69, A:D.69 Water bridges: A:R.70, A:R.70, A:R.286, A:R.286, A:K.350 Salt bridges: A:D.69 EPE.11: 6 residues within 4Å: Chain B: I.67, K.68, D.69, R.286, P.349 Ligands: G39.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.69, B:D.69, B:D.69 Water bridges: B:R.70, B:R.70, B:R.286 Salt bridges: B:D.69, B:D.69 EPE.18: 6 residues within 4Å: Chain C: I.67, K.68, D.69, R.286, P.349 Ligands: G39.17 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.69, C:D.69, C:D.69 Water bridges: C:R.70, C:R.70, C:R.286, C:R.286 Salt bridges: C:D.69 EPE.26: 6 residues within 4Å: Chain D: I.67, K.68, D.69, R.286, P.349 Ligands: G39.25 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.69, D:D.69 Water bridges: D:R.70, D:R.70, D:R.286, D:K.350 Salt bridges: D:D.69

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

NAG.6: 1 residues within 4Å: Chain A: N.6 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain A: K.2, N.153, Q.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.2, A:N.153, A:Q.226 NAG.12: 2 residues within 4Å: Chain B: N.6, S.7 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain B: K.61, N.64, I.354, I.385 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.354 Hydrogen bonds: B:N.64 NAG.14: 2 residues within 4Å: Chain B: K.2, N.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.2 NAG.19: 1 residues within 4Å: Chain C: N.6 No protein-ligand interaction detected (PLIP) NAG.20: 3 residues within 4Å: Chain C: N.64, I.354, I.385 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.354 Hydrogen bonds: C:N.64 NAG.21: 2 residues within 4Å: Chain C: K.2, N.153 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.153 NAG.22: 2 residues within 4Å: Chain C: D.302, N.304 No protein-ligand interaction detected (PLIP) NAG.27: 1 residues within 4Å: Chain D: N.6 No protein-ligand interaction detected (PLIP) NAG.28: 3 residues within 4Å: Chain D: N.64, I.354, I.385 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.354 Hydrogen bonds: D:N.64 NAG.29: 2 residues within 4Å: Chain D: K.2, N.153 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.153

Links

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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
B

C
C

D
D

NEURAMINIDASE