Sandbox Reserved 467: Difference between revisions
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{{Sandbox_Reserved_Robert_B_Rose_1}} | {{Sandbox_Reserved_Robert_B_Rose_1}} | ||
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=Cyclin-Dependent Kinase 3= | =Cyclin-Dependent Kinase 3= | ||
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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 <ref name="model">PMID: 19152876</ref>. | 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 <ref name="model">PMID: 19152876</ref>. | ||
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 <ref name="model" | 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 <ref name="model">. | ||
<scene name='Sandbox_Reserved_467/Secondary_structures/1'>Secondary structures</scene> | <scene name='Sandbox_Reserved_467/Secondary_structures/1'>Secondary structures</scene> | ||
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 <ref name="model" | 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 <ref name="model">. | ||
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) <ref name="model" | 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) <ref name="model">. | ||
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 <ref name="model" | 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 <ref name="model">. | ||
==BINDING== | ==BINDING== | ||