Missing data link?

[Melanie Vollmar]

Hello,

Can you please have a look at PMC11533991? Or here the full website link: https://journals.iucr.org/m/issues/2024/06/00/jt5078/index.html

My query to get the linked protein structures is here:

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC/PMC11533991/datalinks?category=Protein%20Structures&format=json

It returns the following PDB IDs:

4f55

8yoa

However, from reading the paper there should also be:

2r1f

4iiw

Can someone please have a look and check whether the structure links are missing?

Thanks

Melanie

[Zunaira Shafique]

Hi Melanie,

Thanks for your message.

I've checked the paper (PMC11533991) and the linked structures via our data links service. The current response includes the PDB IDs 4f55 and 8yoa:
🔗 https://www.ebi.ac.uk/europepmc/webservices/rest/PMC/PMC11533991/datalinks?category=Protein%20Structures&format=json

For the PDB IDs 2r1f and 4iiw mentioned in the paper, we validate all identifiers using the EBISearch service before including them in the data links. When we query EBISearch:
🔗 https://www.ebi.ac.uk/ebisearch/ws/rest/pdbe?query=acc:%222r1f%22%20OR%20id:%222r1f%22
🔗 https://www.ebi.ac.uk/ebisearch/ws/rest/pdbe?query=acc:%224iiw%22%20OR%20id:%224iiw%22

Both return no results, which is why they are currently excluded from the data links.

We've informed the PDBe team about this, and they are investigating further. We will update our API accordingly based on their response.

Thanks again for bringing this to our attention.

Regards,

Zunaira