PDB

PDB

Aim

To retrieve structure information for a protein sequence

Description

PDB is a primary biological database that contains raw structural data obtained from experiments. 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  NMR and cryo-electron microscopy. 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.                


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