It seems researchers have chopped this protein in 100 pieces and all there is to download from RCSB are confusing PDB files with chunks, bits and pieces of PKC ...always in complex with something else...
Is there a site where I can download a PDB of just the simple, plain, isolated protein?, (in complex with nothing, ALONE) :-D
You may use moleuclar visualization software like pymol to optimize structures like 4RA4 to get it isolated on a separate PBD file to study.
If there are only structures of parts of the protein available, it means that either the full length protein does not crystallize, or that part of the protein is too flexible and does not diffract well enough to determine a structure. A pdb file may contain multiple copies of your protein in the asymmetric unit - in this case you can download the biological unit from the pdb or just delete or undisplay the additional chains in your molecular viewer.
Do a blast search of the PDB (advanced search) with the full-length protein sequences of the different isotypes ( e.g. from UniProt, www.expasy.org), that way you get the most relevant largest fragments first in the list of hits (the kinase domain).The UniProt record will also list the PDB structures available for exactly this protein. Compare the sequences of the hits with your full length sequence to find overlapping fragments that might allow to model a larger part of the structure. This will make the different fragments less confusing. Look at the publications associated with the structures and at recent review articles citing the main structural hits to learn more about the protein..
Most kinase domain structure will be complexes with various small-molecule inhibitors, and/or with non-cleavable ATP analogs, because from these structures you can learn how the enzyme works and how to build more specific inhibitors as a base for drugs targeted to this enzyme. Binding of an inhibitor also makes the kinase more rigid, facilitating crystallization.
Depending on what you want to learn from the molecule, you may want to do a least-square superposition of the kinase in complex with different ligands to learn about how these affect the conformation on the protein. On the other hand, you can delete/undisplay the ligands to show only the protein for an illustration.
Thank you Tathyana.
I'm an undergrad student and the protein is for an academic excercise, required for a veey particular short research on how this protein docks with a specific peptide.
Most open source public PDB models will do just fine for now.
Thank you for your offer.
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