PDB

Assalamualaikum everyone..

Have you ever heard about PDB?? I'm sure that pretty much of you never heard about it right??

So, let me explain to you about it.. =)

PDB is the short form from Protein Data Bank. For those who love biology, you must be very excited to learn about PDB right?

PDB is a repository for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. As we know, long time ago, scientists have determined the atomic structures of thousands of the biomolecular components of cells. These structures allow us to understand cell biology at the atomic level. The secrets of protein synthesis have been revealed, starting with the structure of DNA half a century ago, revealing the atomic basis of genetic information, to the recent structures of working ribosomes, caught in the act of translating this information into new proteins. The enzymes of glycolysis, citric acid cycle, and electron transport have all been studied and their structures have been determined.

So, PDB is important to many important biological questions, and also allow scientists to pose many new ones as it is a key resource in areas of structural biology, such as structural genomics. The PDB data is typically obtained by X-ray crystallography or NMR Spectroscopy. Then, it was submitted by biologist and biochemist from all aroud the world, as it is freely accesible to everyone on the internet via the website of its member organisations.The PDB is overseen by an organization called the wwPDB ( Worldwide Protein Data Bank ).

So, you might be wondering what is the important of PDB right?

Function	Explanation
To discover new drugs	When we know the structure of a protein, we can attempt to design small drug molecules to bind to it and block its function. The power of this approach has been shown in the battle against HIV and AIDS. Many of the anti-HIV drugs that are currently saving lives were discovered with the help of knowing the structures of HIV proteins (Figure 1)                                                             Figure 1
Reveals the atomic details of life	For instance, structures of oxy and deoxy hemoglobin revealed the atomic basis of allostery for control of oxygen binding, and structures of sickle cell hemoglobin revealed the atomic basis of a disease-causing mutation (Figure 2). With an atomic structure, it has been possible to explore the detailed mechanism of enzymes, and understand how they stabilize transition states. Atomic structures have revealed the complex motions of motor proteins and the basis of immune system function.                                                             Figure 2
For scientists to design new molecular machines	Biomolecular structures have also opened up a new discipline of biomolecular engineering and bionanotechnology. With understanding comes control, and researchers are currently modifying existing biomolecules for new functions, or even designing entirely new biomolecules. For instance, scientists are designing and building nanoscale structures with DNA (Figure 3)                                                                 Figure 3

             

The PDB is an exciting database to explore, but since it includes actual data from scientists, one needs to be a bit careful. PDB structure files include a few idiosyncracies that are related to the complex processes used to solve the structures. For instance, X-ray crystallographers will do almost anything to get their molecules to crystallize, so the structures may have pieces missing or sulfur atoms replaced by selenium. The file may also include only part of a whole molecule, as in the case of symmetrical molecules solved by crystallography, or many copies of the same molecule, as in the multiple models often generated in NMR spectroscopy. If you run into these challenges when you're exploring, you can consult the "Understanding PDB Data" pages at the RCSB PDB. It describes the experimental details of structure determination, how they are manifested in PDB files, and how to deal with them when exploring atomic structures.

Hope you have fun!