<p>The UniProt website offers an <a href="http://www.uniprot.org/uploadlists/" rel="nofollow noreferrer">ID mapping tool</a> that tends to work pretty well:</p>

<p><a href="https://i.sstatic.net/VXN4K.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/VXN4K.png" alt="UniProt ID mapping tool screenshot"></a></p>

<p>Then, hit "submit" and you will get the list of corresponding PDB IDs:</p>

<p><a href="https://i.sstatic.net/n7SIH.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/n7SIH.png" alt="UniProt ID mapping tool results screenshot"></a></p>

CC BY-SA 3.0
2017-12-29T12:50:17.443Z
Thank you, it worked.
Please aid a PDB-Noob like myself to understand the results: https://ibb.co/jTMGmb
How come each of the UNIPROT ID received several different PDB IDs?
https://ibb.co/b5fRmb
Adrian Smith
CC BY-SA 3.0
2017-12-29T13:14:52.793Z
@AdrianSmith that's how PDB works. You'll have one structure for the active site, another for the active site bound by foo, one for the active site bound by bar, another structure for the protein in complex with something else. . . This should be clear enough if you just click on the results you got and see their descriptions.
terdon
CC BY-SA 3.0
2017-12-29T14:31:42.697Z
Thanks for the explanation. I'm looking for a specific protein-target structure (I have a list of ligand-protein interactions and i'm looking for the 3d structure of the binding site if available). Is there any way to search through all of the different "structures"? Does the PDB site offer such a curated database?
Adrian Smith
CC BY-SA 3.0
2017-12-29T16:20:46.413Z
@AdrianSmith no idea, I'm afraid. I've almost never used PDB. I suggest you ask a new question explaining what you need in more detail. Ideally, give an example UniProt ID and explain what you would want to see from it.
terdon
CC BY-SA 3.0
2017-12-29T10:12:19.040Z
2017-12-29T10:12:19.040Z
terdon
<p>You can use the SIFTS mapping: <a href="http://www.ebi.ac.uk/pdbe/docs/sifts/" rel="nofollow noreferrer">http://www.ebi.ac.uk/pdbe/docs/sifts/</a></p>

<p>From <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531078/" rel="nofollow noreferrer">an article</a>:</p>

<blockquote>
  <p>The Structure Integration with Function, Taxonomy and Sequences
  resource (SIFTS; <a href="http://pdbe.org/sifts" rel="nofollow noreferrer">http://pdbe.org/sifts</a>) is a close collaboration
  between the Protein Data Bank in Europe (PDBe) and UniProt. The two
  teams have developed a semi-automated process for maintaining
  up-to-date cross-reference information to UniProt entries, for all
  protein chains in the PDB entries present in the UniProt database.
  This process is carried out for every weekly PDB release and the
  information is stored in the SIFTS database.</p>
</blockquote>

<p>It has no web interface for querying. You just download CSV (or TSV) file with all the mapping data.</p>

CC BY-SA 3.0
2017-12-29T12:55:53.287Z
Thank you. I'll try it if the ID mapping tool won't provide.
Adrian Smith
CC BY-SA 3.0
2017-12-29T10:42:52.390Z
2017-12-29T10:42:52.390Z
marcin
<p>I have a list of several thousand proteins and their UNIPROT IDs. I'm looking for an efficient method of cross-referencing it against the PDB tertiary structure database, and get a list of those proteins with a tertiary structure in the PDB database.</p>

<p>I've tried to BLASTP the list of UNIPROT IDs against the PDB database, using the NCBI BLAST portal but encountered too many errors of "Error: Failed to read the Blast query: Sequence ID not found", making the process of manual filtering not convenient and not efficient.</p>

<p>Any ideas?</p>

<p>Thank you!</p>

<proteins><protein-structure><pdb><uniprot>
Cross-reference with PDB database
# Cross-reference with PDB database

(Asked by: username_0 on 2017-12-29)

I have a list of several thousand proteins and their UNIPROT IDs. I'm looking for an efficient method of cross-referencing it against the PDB tertiary structure database, and get a list of those proteins with a tertiary structure in the PDB database.

I've tried to BLASTP the list of UNIPROT IDs against the PDB database, using the NCBI BLAST portal but encountered too many errors of "Error: Failed to read the Blast query: Sequence ID not found", making the process of manual filtering not convenient and not efficient.

Any ideas?

Thank you!

**Tags:** proteins, protein-structure, pdb, uniprot

---

## 2 answers

### Answer by username_1 on 2017-12-29. Score: 2

The UniProt website offers an [ID mapping tool](http://www.uniprot.org/uploadlists/) that tends to work pretty well:

[![UniProt ID mapping tool screenshot](https://i.sstatic.net/VXN4K.png)](https://i.sstatic.net/VXN4K.png)

Then, hit "submit" and you will get the list of corresponding PDB IDs:

[![UniProt ID mapping tool results screenshot](https://i.sstatic.net/n7SIH.png)](https://i.sstatic.net/n7SIH.png)

> **Comments:**
> **username_0**: Thank you, it worked. Please aid a PDB-Noob like myself to understand the results: https://ibb.co/jTMGmb How come each of the UNIPROT ID received several different PDB IDs? https://ibb.co/b5fRmb  
> **username_1**: @AdrianSmith that's how PDB works. You'll have one structure for the active site, another for the active site bound by foo, one for the active site bound by bar, another structure for the protein in complex with something else. . . This should be clear enough if you just click on the results you got and see their descriptions.  
> **username_0**: Thanks for the explanation. I'm looking for a specific protein-target structure (I have a list of ligand-protein interactions and i'm looking for the 3d structure of the binding site if available). Is there any way to search through all of the different "structures"? Does the PDB site offer such a curated database?  
> **username_1**: @AdrianSmith no idea, I'm afraid. I've almost never used PDB. I suggest you ask a new question explaining what you need in more detail. Ideally, give an example UniProt ID and explain what you would want to see from it.  

---

### Answer by username_2 on 2017-12-29. Score: 2

You can use the SIFTS mapping: <http://www.ebi.ac.uk/pdbe/docs/sifts/>

From [an article](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531078/):

> The Structure Integration with Function, Taxonomy and Sequences
> resource (SIFTS; <http://pdbe.org/sifts>) is a close collaboration
> between the Protein Data Bank in Europe (PDBe) and UniProt. The two
> teams have developed a semi-automated process for maintaining
> up-to-date cross-reference information to UniProt entries, for all
> protein chains in the PDB entries present in the UniProt database.
> This process is carried out for every weekly PDB release and the
> information is stored in the SIFTS database.

It has no web interface for querying. You just download CSV (or TSV) file with all the mapping data.

> **Comments:**
> **username_0**: Thank you. I'll try it if the ID mapping tool won't provide.  

---

