Protein Structure Availability

Question

[joaopdinis.to]

Hi everyone,

How do I check if a certain protein as a known 3D structure?

I have a list of Entrez IDs and I want to check if the proteins this genes encodes are available or not.

Thanks,

Joao Dinis

[User000]

All the 3D structures of proteins are kept in Protein Data Bank database..I guess what you need is PDB ID, to see if the protein structure is in the data bank. You might use UniProt ID mapper to find UniProt ID's from Gene ID, then from UniProt you can find PDB ID. There might be easier ways..I need to think and check

[User000]

Actually, you dont even need PDB ID, if you know UniProtKB ID you can find out from Protein Data Bank, if protein has a structure. Otherwise, if you have a lot of Entrez IDs you might want to write a script using Biopython..

Answer 1

[David Westergaard]

It depends, really. Do you want exactly the structure for the given protein encoded by the gene, or are you satisfied with a structure of a protein which may be homologous to a protein encoded by the query gene? Others have already suggested a solution for the first case, so I'll outline some solutions for the second case:

1. You can try simply BLASTing (either BLAST or PSI-BLAST) the sequence against the PDB database. This can be done directly on the PDB site.
2. If you're not interesting in the full structure of the protein, but just curious about which domains it contains, you can try searching it against the Pfam database instead. The Pfam database has links to proteins which matches the Hidden Markov Model of a given entry

Answer 2

[Elisabeth Gasteiger]

To complete the answer given by User000:

You can use the UniProt ID mapping service (http://www.uniprot.org/mapping/) to upload your Entrez identifiers and map them to UniProtKB. You will have to specify either EMBL CDS, RefSeq or GeneID as the source database, depending on the type of your identifiers.

Once you have your result, You can follow the link "UniProtKB (xx)" (where "xx" is the number of protein entries), and then refine your query by adding "database:pdb" to it. This will result in a URL like http://www.uniprot.org/uniprot/?query=job%3A20140324428MW6BLCK+database%3Apdb&sort=score (note that job identifiers are temporary and the corresponding data will only be kept for 7 days, i.e. this URL will only be valid for 7 days).