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I have two kinds of interactions: transient and stable. We are supposed to work on stable interaction, like interactions between two monomers in a heterodimer.

In a heterodimer there are two chains in which there are some residues between monomers which take part in the interaction of monomers and building the structure of heterodimer, and there are other residues interacting inside each monomer for building the structure of that monomer. There are some PDB IDs related to heterodimers in PDB.

Now imagine that we are trying to show which residues are physically interacting between two monomers in a heterodimer, and then we are trying two show the site of these physically interacting residues in the sequence related to that special structure. For that, we need to find the sequence related to that structure and we can download it from PDB.

But if we want to make a multiple sequence alignment of that sequence, first we need to find the refseq sequence of that and then we must blast the sequence and find homologues of that sequence.

Here there are some challenges:

  1. we must find residues interacting in the structure of heterodimer between two monomers.
  2. we must find the sequences of monomer chains of the heterodimer and map the interacting residues in the structure to the sequence.
  3. we know that when a structure is solved and its monomers are sequenced, may be they are not able to completely sequence the heterodimer and residue numbers are maybe different from the related refseq sequence.

I would like to know how can we find the related refseq sequence (or sequences, in the case of heterodimer) and then how can we map the physically interacting residues in the structure of PDB ID to refseq sequence (finding the sites of these interacting residues in that refseq sequence) regarding three challenges mentioned above.

Imagine that I have 100 PDB IDs of 100 nonredundant heterodimers and I would like to find and download the structures, sequence and finally refseq sequence. What should I do?

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    $\begingroup$ So you want to map IDs to RefSeq IDs? Do you want protein or gene IDs? Have you tried anything? If so, please edit and tell us what you tried and how it failed so we don't just give you the same solutions. What species are the PDBs from? What to PPIs have to do with it? PDB isn't a database of interactions. Could you edit your question and add a bit more detail so we can understand what you need, please? $\endgroup$
    – terdon ♦
    Commented Jun 11, 2017 at 14:01
  • $\begingroup$ You can find mappings PDB <-> Uniprot and Uniprot <-> RefSeq, but if you just want to use Blast, can't you use the sequence from PDB? $\endgroup$
    – marcin
    Commented Jun 11, 2017 at 23:48
  • $\begingroup$ That works but I do not just want to do blast. I want to do multiple sequence alignment after that (after finding homologous sequences by running blast). The main challenge is mapping residue-residue interaction in PDB structure to refseq sequences and finding residues sites which participate in interaction. what can I do for that? $\endgroup$
    – Sara
    Commented Jun 12, 2017 at 0:40
  • $\begingroup$ I think you could use the sequence from PDB also in MSA, and the alignment will show what the residues of interest correspond to in other sequences (but take what I write with a grain of salt, I don't have first-hand experience here) $\endgroup$
    – marcin
    Commented Jun 12, 2017 at 11:48

2 Answers 2

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You can download seqs and structures based on a list of PDB ids using http://www.rcsb.org/pdb/download/download.do#FASTA

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The post might seem old, but I wish to share my thaughts based on how I solved similar problem. Here it goes:

I will use an example to illustrate. Other posts have already explained how you could get the protein ID from PDB and so on. I used the database PDBSUM (www.ebi.ac.uk/pdbsum/) and with protein PDB ID: 1KJF.

By following these steps I got to the results below: Go to --> www.ebi.ac.uk/pdbsum/ -->(put in PDB ID) or (others e.g UniProt ID) --> Enter --> Click on "Ligands" -->(a LIGPLOT appears at the botoom of the page). You can as well search just by pasting in the sequence.

Results: You can see that 1KJF is made up of 3 chains A, B & P and both chains have clearly anntated and interacting residues. You can now see clearly read inidividual types of interactions.

Another good option is http://protein.bio.unipd.it/ring. It shows you a graph plot of all inteacting residues and how they are linked to each other. You can adjust the default result settings to meet your needs.

Hope it helps. :)

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  • $\begingroup$ Yes. 'pdbsum' and 'ring' are definitely two useful tools for fast analytical work. $\endgroup$
    – Aalawlx
    Commented Jan 2, 2018 at 0:24

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