Protein 3D structure

Protein Data Bank

It is a repository for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This data is obtained open source to all the people around the world. The structures are obtained by two major methods which are X-ray crystallography and NMR spectroscopy.

• Structures in PDB have respective id's (identifiers) by which we can access them this could be done by typing there id's in PDB search engine.
• My pet gene is CYP2C9 the protein associated to this gene is having a respective PDB id 1OG5 but on further research regarding my protein I found  that even 1OG2 also corresponds to my pet gene but ligands bound to protein vary. 
• 1OG5 has two ligands associated to it S-WARFARIN and Heme C group (the one which I am considering right now).
• 1OG2 has Heme C group. 
• 1OG5 belongs to homo sapiens and S-WARFARIN is the perfect ligand which is bound to it.

                                                               3D structure of 1OG5

Cn3D Protein Visualization Tool:

• Cn3D ("see in 3D") is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez Structure database. Cn3D is provided for Windows and MCn3D ("see in 3D") is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez Structure database.
•  Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.
• From structure module in NCBI we obtained our Cn3D structure and we visualize using this tool.
• We can change the type of view by going to Style menu ----> Rendering shortcuts ------> Space fill.
• We select the disease causing site ILE at 359th position select the site in the sequence window.

 Fig represents Molecule(pink color) in space fill format and ILE at 359th position is represented in the sequence window (yellow color) 

• For showing the particular site 359th position in "Worms" view Style menu ----> Rendering shortcuts ------> Worms. 

 Fig represents ILE site 359th position in "Worms" view

• Then Select menu ------> Show selected residues.

 Fig represents ILE (specifically) site 359th position in "Worms" view

Secondary Structures:

The secondary structure associated to the site (ILE at 359th protein) according to PDB secondary structure prediction which uses CATH and SCOP to calculate.

         Fig represents ILE at position 359 has an Alpha helix

DNA STAR Protein Secondary Structure Analysis:

Protean software was used from DNA STAR to view secondary structures of protein which uses 2 algorithms Garnier Robson and Chou Fasman. Both these algorithms state that this site is a Beta sheet.

 Fig representing that ILE at 359th position is a Beta sheet

We could see that there is a contrast in the prediction DNA STAR algorithms predicts the site as sheet were in PDB (SCOP) predict it to a Helix.