SMTL ID : 3ro5.1

Crystal structure of influenza A virus nucleoprotein with ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

homo-hexamer

Ligands

6 x LGH: [4-(2-chloro-4-nitrophenyl)piperazin-1-yl][3-(2-methoxyphenyl)-5-methyl-1,2-oxazol-4-yl]methanone(Non-covalent)

LGH.1: 13 residues within 4Å: Chain A: Y.282, E.287, Y.289, D.295, R.298, L.299, N.302 Chain B: Y.45, E.46, R.92, W.97, Y.306, S.369 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.45, B:Y.306, A:Y.282, A:Y.282, A:R.298 Hydrogen bonds: B:S.369 pi-Stacking: B:W.97, B:Y.306, A:Y.282 Halogen bonds: B:Y.45 LGH.2: 15 residues within 4Å: Chain A: Y.45, E.46, L.49, R.92, W.97, Y.306, S.369 Chain B: Y.282, F.284, E.287, Y.289, D.295, R.298, L.299, N.302 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.45, A:Y.45, A:L.49, A:W.97, A:Y.306, B:Y.282, B:Y.282, B:R.298, B:L.299 Hydrogen bonds: A:S.369 pi-Stacking: A:W.97, B:Y.282 Halogen bonds: A:Y.45 LGH.3: 13 residues within 4Å: Chain C: Y.282, E.287, Y.289, D.295, R.298, L.299, N.302 Chain D: Y.45, E.46, R.92, W.97, Y.306, S.369 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.45, D:Y.306, C:Y.282, C:Y.282, C:R.298 Hydrogen bonds: D:S.369 pi-Stacking: D:W.97, D:Y.306, C:Y.282 Halogen bonds: D:Y.45 LGH.4: 15 residues within 4Å: Chain C: Y.45, E.46, L.49, R.92, W.97, Y.306, S.369 Chain D: Y.282, F.284, E.287, Y.289, D.295, R.298, L.299, N.302 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:Y.45, C:Y.45, C:L.49, C:W.97, C:Y.306, D:Y.282, D:Y.282, D:R.298, D:L.299 Hydrogen bonds: C:S.369 pi-Stacking: C:W.97, D:Y.282 Halogen bonds: C:Y.45 LGH.5: 13 residues within 4Å: Chain E: Y.282, E.287, Y.289, D.295, R.298, L.299, N.302 Chain F: Y.45, E.46, R.92, W.97, Y.306, S.369 10 PLIP interactions: 4 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:Y.282, E:Y.282, E:R.298, F:Y.45, F:Y.306 pi-Stacking: E:Y.282, F:W.97, F:Y.306 Hydrogen bonds: F:S.369 Halogen bonds: F:Y.45 LGH.6: 15 residues within 4Å: Chain E: Y.45, E.46, L.49, R.92, W.97, Y.306, S.369 Chain F: Y.282, F.284, E.287, Y.289, D.295, R.298, L.299, N.302 13 PLIP interactions: 5 interactions with chain F, 8 interactions with chain E Hydrophobic interactions: F:Y.282, F:Y.282, F:R.298, F:L.299, E:Y.45, E:Y.45, E:L.49, E:W.97, E:Y.306 pi-Stacking: F:Y.282, E:W.97 Hydrogen bonds: E:S.369 Halogen bonds: E:Y.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gerritz, S.W. et al., Inhibition of influenza virus replication via small molecules that induce the formation of higher-order nucleoprotein oligomers. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-09-14

Peptides

Nucleocapsid protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Nucleocapsid protein

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