Sandbox Reserved 467: Difference between revisions

Currently, no crystal structure for human CDK-3 had been resolved. There is only a theoretical molecular model available, based on analysis of 39 binary complexes of CDK-3:inhibitors. Data showed that 74.18% of CDK-3 structure is sequentially identical with CDK-2, thus making CDK-2 a perfect template model for CDK-3 protein. The Parmodel web server was used for comparative modeling and evaluation of protein structure, and molecular dynamics (5 ns) simulation was done with GROMACS.  

Based on the molecular model, the overall structure of human CDK-3 was found to contain 305 amino acid residues, with a total molecular weight of 35,045.74 Da, and a theoretical pI of 8.86. Many features of secondary structure and molecular fork was found to very much resemble CDK-2.  

Human CDK-3 proteins was found to have alpha and beta structures. Its fold contains two alpha and two beta domains, with a larger C-terminal that is mostly alpha helical (this is characteristic of a typical protein kinase fold). CDK-3 is found to be folded into a bilobal structure, with smaller N-terminal lobe that is mostly β-sheet structure.  

The N-terminal lobe is found in a sheet of 5 antiparallel β-strands (β1-β5), and in one, large alpha helix (α-1). The C-terminal domain contains pseudo-4-helical bundle (α-2 to α-3, α-6), small β-ribbon (β-6 to β-8), and 2 alpha helices (α-5, α-7).  

The ATP binding pocket is found in the cleft in between the bilobal structure. Most residues found in the ATP binding pocket is hydrophobic. The hydrophobic pocket can fit in different geometries of residues, like adenine derivatives and flavonoids.