How To Use the Molecular Modeling Database (MMDB): search by gene or protein product

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3D Macromolecular Structures

How to find 3D structures for a gene or protein product of interest

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Search method 1 will work if a 3D structure has already been resolved for your protein of interest. However, the number of resolved structures is far smaller than the number of protein sequences, so it's possible you might not find 3D structures for the exact protein of interest. In that case, you can use method 2 or method 3 to retrieve the 3D structures of homologous proteins.


Method 1:	Search the Entrez Structure database directly for terms(s) of interest	example: retrieve neurofibromin 3D structures

Method 2:	Search the Entrez Protein database for terms(s) of interest, open the Links menu for protein sequence record(s) of interest, and select the Related Structures option	example: start with neurofibromin protein sequences

Method 3:	Search the Entrez Gene database for a gene of interest, view its protein translation in the Entrez Protein database, then follow the link from the protein sequence record to Related Structures	example: start with the human neurofibromin gene record

Illustration showing how to retrieve 3D structures for a gene or protein product of interest, in this case the human PTGS1 gene, which produces the prostaglandin-endoperoxide synthase 1 protein.

Additional details are provided in: How to align a query protein to a similar sequence from a 3D structure and interactively view sequence/structure relationships.

| Revised 12 November 2009 |