SMTL ID : 5nzf.1

Complex of H275Y/I223V mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: 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.1: 1 residues within 4Å: Chain C: N.65 No protein-ligand interaction detected (PLIP)

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.2: 2 residues within 4Å: Chain A: E.381 Chain D: N.65 No protein-ligand interaction detected (PLIP)

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

CA.3: 5 residues within 4Å: Chain A: D.213, G.217, D.243, G.261, N.263 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.261, A:N.263, H2O.2 CA.4: 4 residues within 4Å: Chain A: D.295, N.297, D.303, N.305 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.295, A:D.303, A:N.305, H2O.3, H2O.4 CA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.9: 6 residues within 4Å: Chain B: D.213, G.217, D.243, G.261, N.263, G.264 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.261, B:N.263, H2O.14 CA.10: 4 residues within 4Å: Chain B: D.295, N.297, D.303, N.305 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.295, B:D.303, B:N.305, H2O.13, H2O.14 CA.18: 5 residues within 4Å: Chain C: D.213, G.217, D.243, G.261, N.263 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.261, C:N.263, H2O.27 CA.19: 4 residues within 4Å: Chain C: D.295, N.297, D.303, N.305 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.295, C:D.303, C:N.305, H2O.26, H2O.29 CA.25: 6 residues within 4Å: Chain D: D.213, G.217, D.243, G.261, N.263, G.264 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.261, D:N.263, H2O.39 CA.26: 4 residues within 4Å: Chain D: D.295, N.297, D.303, N.305 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.295, D:D.295, D:D.303, H2O.38, H2O.39

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, V.142, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.98, A:V.142 Hydrogen bonds: A:E.38, A:R.71, A:Y.321 Water bridges: A:D.70, A:R.75, A:R.75, A:E.197, A:E.197, A:R.212 Salt bridges: A:R.37, A:R.212, A:R.287 G39.11: 14 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, W.98, V.142, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.98, B:V.142 Hydrogen bonds: B:E.38, B:R.71 Water bridges: B:D.70, B:R.75, B:E.147, B:E.147, B:R.212 Salt bridges: B:R.37, B:R.212, B:R.287 G39.20: 14 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, W.98, V.142, R.144, E.196, E.197, R.212, N.214, R.287, Y.321 Ligands: EDO.24 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.98, C:V.142 Hydrogen bonds: C:E.38, C:R.71, C:Y.321 Water bridges: C:D.70, C:E.197 Salt bridges: C:R.37, C:R.212, C:R.287 G39.27: 14 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, W.98, V.142, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.98 Hydrogen bonds: D:E.38, D:R.71, D:Y.321 Water bridges: D:R.75, D:E.147 Salt bridges: D:R.37, D:R.212, D:R.287

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

NAG.6: 1 residues within 4Å: Chain A: N.7 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain A: N.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.65 NAG.12: 1 residues within 4Å: Chain B: N.7 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain B: K.62, N.65, I.355 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.355 Hydrogen bonds: B:N.65 NAG.14: 2 residues within 4Å: Chain B: K.3, N.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.154 NAG.21: 1 residues within 4Å: Chain C: N.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.7 NAG.22: 2 residues within 4Å: Chain C: K.3, N.154 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.154 Water bridges: C:Q.227, C:Q.227 NAG.28: 1 residues within 4Å: Chain D: N.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.7 NAG.29: 2 residues within 4Å: Chain D: K.3, N.154 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.154

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.15: 5 residues within 4Å: Chain A: N.128 Chain B: Y.19, L.46, E.47, C.48 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:C.48, B:C.48 Water bridges: B:L.46, B:I.82, A:N.128, A:N.128 EDO.16: 2 residues within 4Å: Chain B: E.178, K.181 No protein-ligand interaction detected (PLIP) EDO.17: 2 residues within 4Å: Chain B: K.69, D.70 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.70, B:D.70 Water bridges: B:R.71, B:R.71 EDO.23: 5 residues within 4Å: Chain C: Y.89, N.90, S.91, R.92 Chain D: E.84 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Y.89, D:E.84 Water bridges: C:S.91 EDO.24: 3 residues within 4Å: Chain C: I.68, P.350 Ligands: G39.20 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.287, C:R.287, C:R.349 EDO.30: 3 residues within 4Å: Chain A: S.375 Chain D: P.73, Y.74 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Water bridges: A:S.375, A:S.375 Hydrogen bonds: D:Y.74, D:Y.74 EDO.31: 7 residues within 4Å: Chain C: N.128, G.129, I.130 Chain D: Y.19, L.46, E.47, C.48 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:N.128, D:C.48, D:C.48 Water bridges: D:E.47 EDO.32: 3 residues within 4Å: Chain D: D.133, T.134, I.182 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.133 Water bridges: D:T.134, D:I.182 EDO.33: 5 residues within 4Å: Chain D: D.118, N.119, N.140, N.141, V.142 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.141 Water bridges: D:N.140 EDO.34: 4 residues within 4Å: Chain D: E.178, K.179, K.181, V.183 2 PLIP interactions: 2 interactions with chain D Water bridges: D:K.181, D:K.181 EDO.35: 2 residues within 4Å: Chain D: K.69, D.70 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.70, D:D.70 Water bridges: D:R.71

1 x NA: SODIUM ION(Non-functional Binders)

NA.36: 5 residues within 4Å: Chain D: I.346, G.348, R.349, P.350, K.351 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.348, D:K.351 Water bridges: D:G.348

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pokorna, J. et al., Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Viruses (2018)

Release Date

2018-07-04

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Neuraminidase