Integration of the human immunodeficiency virus (HIV-1) DNA into the host genome is catalysed by a virus-encoded protein integrase. Here, we report some of the structural and functional properties of two synthetic peptides: integrase-(147–175)-peptide reproducing the residues 147–175 (SQGVVESMNKELK159KIIGQVRDQAEHLKTAY) of the HIV-1 integrase, and [Pro159] integrase-(147–175)-peptide where the lysine 159 is substituted for a proline. Circular dichroism revealed that both peptides are mostly under unordered conformation in aqueous solution, contrasting with the α-helix exhibited by residues 147–175 in the protein crystal structure. In a weak α-helix-promoting environment, integrase-(147–175)-peptide self-associated into stable coiled-coil oligomers, while [Pro159] integrase-(147–175)-peptide did not. This property was further confirmed by cross-linking experiments. In our in vitro experiments, only integrase-(147–175)-peptide was able to reduce the integration activity of the enzyme. We propose that the inhibitory activity shown by integrase-(147–175)-peptide is dependent on its ability to bind to its counterpart in integrase through a peptide-protein coiled-coil structure disturbing the catalytic properties of the enzyme.