Lesson 3 : PDB - Protein Data Bank

Bismillahirrahmanirrahim...

     Alhamdulillah, for our today's KOS1110 class, we had learned about Protein Data Bank, aka PDB. What is PDB? PDB basically means is a repository for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. These proteins and nucleic acids are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape of a molecule deduce a structure's role in human health and disease, and in drug development. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome. All of these proteins and nucleic acids structures are commonly obtained by X ray Crystallography, NMP spectroscopy, and so on.

     The PDB archive is available at no cost to users. The PDB archive is updated each week at the target time of Wednesday 00:00 UTC (Coordinated Universal Time).

     The PDB was established in 1971 at Brookhaven National Laboratory under the leadership of Walter Hamilton and originally contained 7 structures. After Hamilton's untimely death, Tom Koetzle began to lead the PDB in 1973, and then Joel Sussman in 1994.  In 1998, the Research Collaboratory for Structural Bioinformatics (RCSB) became responsible for the management of the PDB. In 2003, the wwPDB was formed to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community. It consists of organizations that act as deposition, data processing and distribution centers for PDB data.

     In addition, the RCSB PDB supports a website where visitors can perform simple and complex queries on the data, analyze, and visualize the results. For more details about PDB, all of us can find it at this website.

     The PDB data format is made to contain coordinate. The main data format of PDB is mmCIF. mmCIF is a dictionary containing 2500 definitions. Furthermore, it also contain syntax such as "_chem_comp_link.details". And finally PDB which confirmed by syntax can be loaded by the system.

     The examples of software for PDB is pdb_extract, ADIT, and Validation Suite. The details of the softwares are as follows :

pdf_extract	Extract info from output of crystallographic, and merge it into mmCIF
ADIT	It has two types, which is web-based and standalone tools. Its function is to assemble, edit, validate, and deposition structural data
Validation Suite	Create reports

     For more information about PDB you can go to the website http://www.rcsb.org/. All the PDB datas are stored in this website.

     RasMol is a program for molecular graphics visualisation. It is a sophisticated, yet user-friendly, molecular graphics program for viewing molecules. The program is provided as freeware,available for internet downloading, by Roger Sayle in 1992 at the BioMolecular Structures Group of Glaxo Research & Development (UK). It is used by hundreds of thousands of users world-wide to view macromolecules and to prepare publication-quality images. Rasmol can be obtained by downloading from the internet as it is programmed as an open source program. 

     Difference between Rasmol and RASWIN. When the RasMol is compiled for use by Microsoft Windows users, it is called RASWIN.

     Then, we will show 5 types of proteins which we had got them from the RCSB PDB website  The 5 types of proteins are :

• Amylase
• Trypsin
• Pepsin
• Protease
• Lipase

 The details of the 5 proteins are as follows :

• Amylase (1BAG)

Classification: Alpha Amylase 

Structure Weight: 48016.77 

Molecule: ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE 

Polymer: 1 

Type: protein 

Length: 425 

Chains: A EC#: 3.2.1.1 

Mutation: E208Q 

Details: COMPLEXED WITH MALTOPENTAOSE 

Organism: Bacillus subtilis 

Gene Names: amyE amyA BSU03040 

• Pepsin (3PSG)

 

 

Classification: Hydrolase(acid Proteinase Zymogen) 

Structure Weight: 39551.90 

Molecule: PEPSINOGEN 

Polymer: 1 

Type: protein 

Length: 370 

Chains: A EC#: 3.4.23.1 

Organism: Sus scrofa 

Gene Name: PGA 

• Trypsin (7PTI)

 

Classification: Proteinase Inhibitor (trypsin) 

Structure Weight: 6558.45 

Molecule: BOVINE PANCREATIC TRYPSIN INHIBITOR 

Polymer: 1 

Type: protein 

Length: 58 

Chains: A 

Organism: Bos taurus 

• Protease (3B4R)

Classification: Hydrolase 

Structure Weight: 50019.76 

Molecule: Putative zinc metalloprotease MJ0392 

Polymer: 1 

Type: protein 

 Length: 224 

Chains: A, B EC#: 3.4.24 

Fragment: Site-2 Protease residues 1-224 

Organism: Methanocaldococcus jannaschii 

Gene Name: MJ0392 

• Lipase (1GT6)

Classification: Lipase 

Structure Weight: 59218.33 

Molecule: LIPASE 

Polymer: 1 

Type: protein 

Length: 269 

Chains: A, B EC#: 3.1.1.3 

Mutation: YES 

Details: OLEIC ACID 

Organism: Thermomyces lanuginosus 

Gene Name: LIP