Structures
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View a structure with Cn3D

  Sample User Question
Analysis/Comments
Flow Chart
Step By Step Guide 		 

Sample User Question back to top

View the molecular structure of HIV-1 reverse transcriptase, wild-type.

Analysis/Comments back to top

The ability to view and manipulate the molecular structure of a protein can provide a researcher with a great deal of valuable information including the conformation and location of the active site of an enzyme, binding sites for ligands and other cofactors, relationships between protein chains, amino acid content, hydrophobicity and charge, and potential alterations in structure based on mutation or environmental changes. Often, the MMDB will contain multiple structures for a particular protein which include specific mutations, structures determined under particular buffer, pH or salt conditions, and structures bound to a drug or other substrate.

Flow Chart back to top

  1. NCBI Entrez Structure Division - Search MMDB using standard Entrez searching techniques.

  2. Cn3D Molecular Structure Viewer - This program should be pre-installed so that it will be automatically launched following clicking on the "View 3D structure" button.

Step By Step Guide back to top

Entrez Structures

(Note: The PDB ID for wild type HIV reverse transcriptase is 1REV which can also be used to search.)

  • Try two searches: one for "HIV reverse transcriptase" and one for "1REV."
  • Look at the other records found in the former search. Scroll through the results until you find 1REV. How far down is it? What other types of structure records do you find in this search? How might you create a more effective search strategy?
  • Click on the 1REV link to view the structure summary. Read through it. What kind of information is provided to signal you that this is the wild type structure? How might you check this?
Cn3D

  • Click on the View 3D Structure button in the structure summary. Use the default settings.
  • Cn3D should activate automatically if it was properly installed.
  • View structure.

Structures Return to Slides (*.html or *.mht format)
Return to Exercises List		 Revised 08/08/2007