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6.8 years ago
nishyanand
•
0
In order to find the PDB structure of the gene, I used Entrez Gene (GeneID) to PDBid mapping through the UNIPROT, however the mapping is not unique, I need the main 3D structure(PDBid) for the specific gene, how to find out which is main structure?
For ex: Mapping Ongo gene > with Entrez Gene (GeneID) as "367" http://www.uniprot.org/uniprot/?query=yourlist:M2018020283C3DD8CE55183C76102DC5D3A26728B04E94B8&sort=yourlist:M2018020283C3DD8CE55183C76102DC5D3A26728B04E94B8
It totally mapped to 81 different PDBids, so how to find the main structure(direct mapping from GeneID) among them to the gene. http://www.uniprot.org/mapping/M20180202F725F458AC8690F874DD868E4ED79B88E99245M
I would go to this page: http://www.uniprot.org/mapping/M20180202F725F458AC8690F874DD868E4ED79B88E99245M open every abbreviation on the right and look at the protein length (on the left side) - (if it's a fragment or not), if it is a complex structure or not, if all the necessary ligands are present, if all the chain are present in case of multimer, etc.
But see this professional opinion below:
Question about UniProt Isoforms
A: isoforms and the definition of a protein
Protein Sequence identifier to use after annotating variants (Swissprot or Uniparc) ?
A: Protein database for TCGA MAF files - see the answer in the middle
A: What Is Rationale Behind Ucsc Canonical Transcripts?
http://www.jalview.org/help/html/features/siftsmapping.html
http://www.cureffi.org/2013/03/15/mapping-proteomics-data-to-uniprot-refseq-and-gene-symbol/
https://www.biostars.org/t/uniprot/