Protein Data Bank (database)
L’archivio del PDB Ã¨ un database di coordinate atomiche e altre informazioni che descrivono proteine e altre importanti macromolecole.
I biologi strutturali usano metodi come: cristallografia ai raggi X, spettroscopia NMR , (Homology Modeling) e microscropio crio-elettronico per determinare l’esatta posizione di ciascun atomo rispetto agli altri nella molecola.
Successivamente queste informazioni, vengono trascritte e rilasciate pubblicamente negli archivi elettronici (wwPDB) del Protein Data Bank.
La crescita costante del PDB Ã¨ un’azione riflessa dalla ricerca sviluppata nei laboratori in tutti il mondo.
Questo puÃ² rendere il database avvincente e una sfida nell’utilizzo di ricerca e di insegnamento.
Le strutture sono disponibili per molte proteine e acidi nucleici, coinvolti in processi centrali della vita; Si puÃ² andare negli archivi del PDB per trovare le strutture di ribosomi, oncogeni, drug targets, ed anche alcuni virus.
In ogni caso, puÃ² essere una sfida trovare le informazioni che interessano, da quando gli archivi del PDB hanno inserito diverse strutture.
Si possono spesso trovare strutture multiple, di una data molecola, o solo strutture parziali, o strutture modificate o inattivate dalla loro forma nativa.
Looking at Structures is designed to help you get started with charting a path through this material, and help you avoid a few common pitfalls. These chapters are intertwined with one another. To begin, select a topic from the right menu, or select a topic from below:
The primary information stored in the PDB archive consists of coordinate files for biological molecules. These files list the atoms in each protein, and their 3D location in space. These files are available in several formats (PDB, mmCIF, XML). A typical PDB formatted file includes a large “header” section of text that summarizes the protein, citation information, and the details of the structure solution, followed by the sequence and a long list of the atoms and their coordinates. The archive also contains the experimental observations that are used to determine these atomic coordinates.
While you can view PDB files directly using a text editor, it is often most useful to use a browsing or visualization program to look at them. Online tools, such as the ones on the RCSB PDB website, allow you to search and explore the information under the PDB header, including information on experimental methods and the chemistry and biology of the protein. Once you have found the PDB entries that you are interested in, you may use visualization programs to allow you to read in the PDB file, display the protein structure on your computer, and create custom pictures of it. These programs also often include analysis tools that allow you to measure distances and bond angles, and identify interesting structural features.
Reading Coordinate Files
When you start exploring the structures in the PDB archive, you will need to know a few things about the coordinate files. In a typical entry, you will find a diverse mixture of biological molecules, small molecules, ions, and water. Often, you can use the names and chain IDs to help sort these out. In structures determined from crystallography, atoms are annotated with temperature factors that describe their vibration and occupancies that show if they are seen in several conformations. NMR structures often include several different models of the molecule.
You may run into several challenges as you explore the PDB archive. For example, many structures, particular those determined by crystallography, only include information about part of the functional biological assembly. Fortunately the PDB can help with this. Also, many PDB entries are missing portions of the molecule that were not observed in the experiment. These include structures that include only alpha carbon positions, structures with missing loops, structures of individual domains, or subunits from a larger molecule. In addition, most of the crystallographic structure entries do not have information on hydrogen atoms.