SMTL ID : 5nze.1 (1 other biounit)

Complex of S247N mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-tetramer

Ligands

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.1: 4 residues within 4Å: Chain A: K.62, N.65, I.355, I.386 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.12: 4 residues within 4Å: Chain B: K.62, N.65, I.355, I.386 No protein-ligand interaction detected (PLIP)

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

CA.2: 6 residues within 4Å: Chain A: D.213, G.217, D.243, G.261, N.263, G.264 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.4 CA.3: 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.1, H2O.2 CA.13: 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.19 CA.14: 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.16, H2O.17 CA.23: 6 residues within 4Å: Chain C: D.213, G.217, D.243, G.261, N.263, G.264 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.34 CA.24: 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.295, C:D.303, H2O.32, H2O.32 CA.37: 1 residues within 4Å: Ligands: CA.52 No protein-ligand interaction detected (PLIP) CA.38: 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.49 CA.39: 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.47, H2O.48 CA.52: 1 residues within 4Å: Ligands: CA.37 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)

G39.4: 13 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, W.98, R.144, N.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:N.166, A:E.196 Hydrogen bonds: A:E.38, A:R.71 Water bridges: A:D.70, A:D.70, A:R.71, A:R.75, A:E.197, A:R.212 Salt bridges: A:R.37, A:R.212, A:R.287 G39.15: 13 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, W.98, R.144, N.166, E.196, E.197, R.212, N.214, R.287, Y.321 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.98, B:N.166, B:E.196 Hydrogen bonds: B:E.38, B:R.71, B:Y.321 Water bridges: B:R.71, B:R.75, B:E.197, B:E.197, B:R.212 Salt bridges: B:R.37, B:R.212, B:R.287 G39.25: 13 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, W.98, R.144, N.166, E.196, E.197, R.212, N.214, R.287, Y.321 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.98, C:N.166, C:E.196 Hydrogen bonds: C:E.38, C:R.71 Water bridges: C:R.71, C:R.75, C:R.75, C:N.166, C:E.197 Salt bridges: C:R.37, C:R.212, C:R.287 G39.40: 13 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, W.98, R.144, N.166, E.196, E.197, R.212, N.214, R.287, Y.321 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:W.98, D:N.166, D:E.196 Hydrogen bonds: D:E.38, D:R.71, D:Y.321 Water bridges: D:D.70, D:R.71, D:R.75, D:N.166, D:E.197, D:E.197 Salt bridges: D:R.37, D:R.212, D:R.287

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

NAG.5: 2 residues within 4Å: Chain A: A.5, N.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.7 NAG.16: 2 residues within 4Å: Chain B: A.5, N.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.7 NAG.26: 1 residues within 4Å: Chain C: N.7 No protein-ligand interaction detected (PLIP) NAG.27: 1 residues within 4Å: Chain C: N.65 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.65 NAG.28: 2 residues within 4Å: Chain C: K.3, N.154 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.3, C:N.154 Water bridges: C:Q.227 NAG.41: 1 residues within 4Å: Chain D: N.7 No protein-ligand interaction detected (PLIP) NAG.42: 1 residues within 4Å: Chain D: N.65 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.65 NAG.43: 2 residues within 4Å: Chain D: K.3, N.154 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.3, D:N.154 Water bridges: D:Q.227

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

EDO.6: 7 residues within 4Å: Chain A: N.65, G.66, T.67, K.69, S.72, Y.74 Chain D: R.26 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: I.68, K.69, D.70 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: Y.89, N.90, S.91 Chain D: E.84 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: K.271, G.273, T.300 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: E.206, S.224, F.225, N.226, E.230, Y.231, Q.232 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: Y.19, L.46, E.47, C.48 Chain C: N.128, G.129, I.130 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain B: N.65, G.66, T.67, K.69, S.72, Y.74 Chain C: R.26 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain B: I.68, K.69, D.70 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: Y.89, N.90, S.91 Chain C: E.84 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: K.271, G.273, T.300 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: E.206, S.224, F.225, N.226, E.230, Y.231, Q.232 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: Y.19, L.46, E.47, C.48 Chain D: N.128, G.129, I.130 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain A: R.26 Chain C: N.65, G.66, T.67, K.69, S.72, Y.74 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain C: I.68, K.69, D.70 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain A: W.16, A.17, I.18, Q.310, T.371, V.372, W.376 Chain C: V.124 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain C: I.182, K.184, S.185 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain C: E.187, N.189, A.190 Ligand excluded by PLIP EDO.34: 2 residues within 4Å: Chain C: N.189, P.191 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain C: D.203, K.271, Y.272, G.273 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain B: N.128, I.130 Chain C: Y.19, L.46, E.47, C.48 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain B: R.26 Chain D: N.65, G.66, T.67, K.69, S.72, Y.74 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain D: I.68, K.69, D.70 Ligand excluded by PLIP EDO.46: 8 residues within 4Å: Chain B: W.16, A.17, I.18, Q.310, T.371, V.372, W.376 Chain D: V.124 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain D: I.182, K.184, S.185 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain D: E.187, N.189, A.190 Ligand excluded by PLIP EDO.49: 2 residues within 4Å: Chain D: N.189, P.191 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain D: D.203, K.271, Y.272, G.273 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain A: N.128, I.130 Chain D: Y.19, L.46, E.47, C.48 Ligand excluded by PLIP

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
B

B
B

C
A

D
A

Neuraminidase

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