Protein Structure and Protein Structure Databases

BioCodeKb - Bioinformatics Knowledgebase

progressivaey, drug developers are looking to large molecules, especially proteins, as a therapeutic option. Formulation of a protein drug product is a quite challenge, and without a good understanding of the nature of protein structure and the conformational characteristics of the specific protein being formulated, the results can be unfavourable.

Structure of Proteins


The building blocks of proteins are amino acids, which are small organic molecules that consist of an alpha (central) carbon atom linked to an amino group, a carboxyl group, a hydrogen atom, and a variable component called a side chain. Within a protein, multiple amino acids are linked together by peptide bonds to form a long chain. Peptide bonds are formed by a biochemical reaction that removes a water molecule as it joins the amino group of one amino acid to the carboxyl group of a neighboring amino acid.


Protein has 4 levels of Structure conformation;


Primary Structure is the unique straight chain with specific order of amino acids that are linked together to form a protein. The three-dimensional shape of a protein is determined by its primary structure.


Secondary Structure is the coiling or folding of a polypeptide chain that gives the protein its 3-D shape, alpha (α) helix structure and beta (β) chains. One method used to characterize the secondary structure of a protein is circular dichroism spectroscopy (CD) pleated sheet.


Tertiary Structure refers to the comprehensive 3-D structure of the polypeptide chain of a protein. There are many types of bonds and forces that hold a protein in its tertiary structure.

  • Hydrophobic interactions

  • Hydrogen bonding

  • ionic bonding

  • covalent bonding

  • van der Waals forces


Quaternary Structure is the structure of a protein macromolecule formed by interactions between multiple polypeptide chains. Each polypeptide chain is referred to as a subunit. Proteins with quaternary structure may consist of more than one of the same type of protein subunit.


The complexities of protein structure make the explanation of a complete protein structure extremely difficult even with the most advanced analytical equipment.  An amino acid analyzer can be used to determine which amino acids are present and the molar ratios of each. The sequence of the protein can then be analyzed by means of peptide mapping and the use of Edman degradation or mass spectroscopy.


Proteins are frequently described as consisting of many structural units. These units include domains, motifs, and folds that make protein more conserved.


Methods used to determine the 3D structure of proteins include X-ray crystallography, NMR spectroscopy and electron microscopy.


A protein structure database is a database that is modeled around the many experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way.


Once the structure of a particular protein is solved, a table of (x, y, z) coordinates representing the spatial position of each atom of the structure is created. The coordinate information is required to be deposited in the Protein structure databases.


Protein structure Databases

  • Database of Macromolecular Movements

  • JenaLib

  • ModBase

  • PDB

  • PDBsum

  • Sacch3D

  • Cambridge Structural Database (CSD)

  • MMDB

  • SCOP

  • CATH

  • Cn3D

  • Structural Biology Knowledgebase (SBKB)

  • PISA (Protein Interfaces, Surfaces and Assemblies)

  • mmCIF

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