I applied homology modelling approaches as well as threading approaches on CDKN2A (132 a.a) protein to model its structure but i failed to get a proper structure ... need help any structural bioinformatican to sort out the problem ???
Are you talking about Uniprot entry https://www.uniprot.org/uniprot/P42771 (Cyclin-dependent kinase inhibitor 2A), one of its isoforms/splicing variants or orthologs in another species? if so, there are 3 NMR (1A5E, 1DC2, 2A5E) and one low resolution (1B17, 3.4Å) X-ray structure available, the x-ray structure is in complex with Cyclin-dependent kinase 6. Isoform 1 has 156 amino acids, but there are several other isoforms. Isoform https://www.uniprot.org/uniprot/Q8N726 Tumor suppressor ARF has a length of 132 amino acids.
If it is a different protein, do a blast search of UniProt and return the UniProt ID corresponding to your gene/protein. According to the NMR structures, both the N- and the C-terminus appear to be intrinsically disordered, while the core consists of four ankyrin repeats. In the X-ray structure, the disordered termini are not visible.
The closest template is the NMR structure of the N-terminal 37 amino acids of murine ARF (pdb entry 1HN3, https://www.rcsb.org/structure/1hn3), which is intrinsically disordered, but forms two helices in trifluoroethanol
"Circular dichroism and NMR spectroscopy show that mArfN37 is largely unstructured under aqueous conditions; however, the peptide adopts two alpha-helices (helix 1, residues 4-14; and helix 2, residues 20-29) in 2,2,2-trifluoroethanol (TFE). Each helix contains an amino acid motif that is repeated twice in mArfN37, once in each helix. The two helices, however, do not interact but are connected by an apparently flexible linker." https://pubmed.ncbi.nlm.nih.gov/11327858/
The sequence past residue 60 also very much looks like an intrinsically unfolded protein, with very few large hydrophobic residues, but many Pro, Gly and Ala. and a strong net positive charge. The whole protein may be intrinsically unfolded in isolation, and only assume a defined structure upon complex formation with a partner domain.