Question: How to get the PDB ID of a viral protein?
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gravatar for kschaf012
3.0 years ago by
kschaf0120
kschaf0120 wrote:

How can I obtain the PDB ID for a protein from a Genbank flat file? I want to use PdbEfold for a putative ankyrin repeat protein (Accession #: ANB50278) from a Megavirus genome and I need the PDB ID in order to do the search, or to do other searches to find structurally-related genes (such as VAST or DALI).

I have the GenBank flat file with the protein accession number and the FASTA sequence for the protein, but when I searched the PDB Databank I found no results for this protein. I also tried performing a BLAST search against the PDB database with no luck. Is it possible that the protein does not have a PDB ID? And if it is possible, is there a way to use PdbEfold, VAST or DALI for my protein without the PDB ID? If you can't already tell, I am a bit of an amateur in this field and would appreciate any help!!

Thank you!

protein sequence alignment pdb • 1.1k views
ADD COMMENTlink written 3.0 years ago by kschaf0120

That looks like a pretty new entry submitted just earlier this year. There are many ankyrin repear proteins in PDB (not sure if this search link will work when you click on it) see if one of those would work.

ADD REPLYlink written 3.0 years ago by genomax73k
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