Tutorials –

1. Finding structures in MMDB
NCBI's Molecular Modeling Database contains over 20,000 structures of proteins, DNA, RNA, and other molecules. Learn how to use Entrez to find structures in MMDB.

You can follow along and do the activities shown in the tutorials below, by opening Cn3D and using Cn3D to open structure file.

2. Properties of amino acids and the primary structure of proteins
The primary structure of a protein is the sequence of amino acids. Identify different amino acids within a protein chain and compare their properties.

• Open Cn3D, then download and open a structure for a drug-resistant form of HIV protease.

3. Identifying types of secondary structure
The secondary structure of a protein is determined by interactions between amino acids that are located near each other in a protein chain. Learn how to identify different types of secondary structure.

• Open Cn3D, then download and open a structure for Human hemoglobin .

4. Protein domains and tertiary structure
Tertiary structure is determined by interactions between amino acids that are farther apart. When secondary structure elements form compact units, these structures are called "domains". Domains can range in size from 50 to 350 amino acids.

• Open Cn3D, then download and open a structure for HIV-1 Reverse Transcriptase.

5. Understanding quaternary structure
Some proteins contain multiple polypeptide chains. How many genes does it take to make an enzyme?

• Open Cn3D, then download and open a structure for Lactate Synthase.

6. Compare the structures of proteins and DNA    
Compare the structures of proteins and DNA to learn how they differ. Cro repressor is a phage protein that binds to DNA and prevents gene expression.

• Download the structure for Cro Repressor (Cro Repressor).

7. Identifying an enzyme's active site
Enzymes bind to substrates and catalyze chemical reactions. Drug companies use compounds that bind to the active site to inhibit or promote activity. Learn how to find an enzyme's active site and determine which amino acids are binding to the substrate.

• Download the structure for EcoRI bound to single-stranded DNA.

Handouts and worksheets –

• Amino acid abbreviations ( 24kb)
• Amino acid structures (36kb)

Programs and databases

• National Center of Biotechnology Information (NCBI)
• PDB

Before you begin, here are some helpful hints: