PDB

PDB

Aim

To retrieve structure information for a protein sequence

Description

PDB is a worldwide central repository of structural information of biological macromolecules and is currently managed by the Research Collaboratory for Structural Bioinformatics (RCSB). In addition, the PDB website provides a number of services for structure submission and data searching and retrieval. PDB is one centralized database for three-dimensional structures of biological macromolecules. This database archives atomic coordinates of macromolecules (both proteins and nucleic acids) determined by x-ray crystallography and NMR. It uses a flat file format to represent protein name, authors, experimental details, secondary structure, cofactors, and atomic coordinates. The web interface of PDB also provides viewing tools for simple image manipulation. The coordinate information is required to be deposited in the Protein Data Bank (PDB, www.rcsb.org/pdb/) as a condition of publication of a journal paper. Protein Data Bank (PDB) is a well known   primary database.

Procedure

 

STEP 1: Access https://www.rcsb.org/pdb

STEP 2: Enter the PDB ID in the keyword and search

STEP 3: Note down the title, compound, residues, source organism, chemical composition etc from summary information.

STEP 4: Note down the bond angle and bond lines of the respective chains,

STEP 5: Click on the sequence detail and save the sequence

STEP 6: Close the window

Result

Structural information of 10D5 retrieved from PDB.                


Comments

Post a Comment

Popular posts from this blog

Cell membrane /Plasma membrane

Image
    Plasma membrane or cell membrane Plasma membrane or cell membrane is a dynamic , fluid structure and forms external boundary of the cell. It acts as a selective permeable membrane and regulates molecular traffic across the boundary. Plasma membrane behaves as a capacitor. In absence of integral membrane proteins, plasma membrane have similar electrical properties. The non conductive lipid bilayer of the membrane separates the conductive extracellular and intracellular electrolyte solutions. This results in the separation of charge across the lipid bilayer and this charge separation   brings about an electrical potential difference across the bilayer which is referred to as membrane potential. Different models are: Overton model The Overton model, (1899)  proposed by Charles Overton, suggests that the plasma membrane is primarily composed of lipids, and its permeability is largely determined by the lipid solubility of substances. This model is based...
Read more

Bovine Spongiform Encephalopathy (BSE)

Image
  Bovine Spongiform Encephalopathy (BSE) Spongiform encephalopathies (SEs) are degenerative disorders of the brain that occur in a number of species. They are recognized by the clinical appearance of the affected animal and the characteristic histological changes they produce in the brain.  One of the common Spongiform encephalopathy is Bovine Spongiform Encephalopathy (BSE),which mainly affect cattle. Bovine Spongiform Encephalopathy (BSE), widely referred to as “mad cow disease,” is a progressive and fatal neurologic disease of cattle. It is caused by  an unconventional transmissible agent, an abnormal prion protein . "Bovine" means that the disease affects cows, "spongiform" refers to the way the brain from a sick cow looks spongy under a microscope, and "encephalopathy" indicates that it is a disease of the brain. The infection spreads to cattle by the practice of feeding them abattoir waste and offal which may have contained scrapie infected meat. ...
Read more

Biological databases

 Biological databases A database is a computerized archive used to store and organize data in such a way that information can be retrieved easily via a variety of search criteria. Databases are composed of computer hardware and software for data management. The chief objective of the development of a database is to organize data in a set of structured records to enable easy retrieval of information. Each record, also called an entry, should contain a number of fields that hold the actual data items, for example, fields for names, phone numbers, addresses, dates. To retrieve a particular record from the database, a user can specify a particular piece of information, called value , to be found in a particular field and expect the computer to retrieve the whole data record. This process is called making a query. Biological databases are  libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and compu...
Read more