Structure

The Structure Tool allows you to visualize and compare the structures of both class I and class II MHC alleles. This page features data generated using ESMFold, providing structural insights into alleles that have never been experimentally resolved. By leveraging advanced computational methods, this tool offers a unique opportunity to explore the detailed architecture of MHC molecules, facilitating a deeper understanding of their function and role in immune response.

Structures of complete CDS for both MHC class I and class II are calculated using a customized pipeline to ensure accurate modelling. The predicted structures include a poly-A peptide within the binding pocket, which helps to properly orient the residues involved in peptide recognition and binding. This approach enhances the reliability of the predicted structures, making them more relevant for functional and comparative studies.

Structures

8815

Class I molecules

6419

Class II molecules

2396

Please click on the statistics to show the list of alleles

The modelled structure includes the predicted local distance difference test (pLDDT) score generated by ESMFold in the pdb temperature factor column. The pLDDT indicates a per-residue confidence score between 0 and 100 and is visualised in the IPD-MHC structure comparison tool using a gradient colour

Available structures are visualised using a custom Molstar interface, allowing users to visualise, explore, and compare the predicted structures directly within the database.

Additional details about the Structure tool and how structures are generated can be found on the Structure help page.

The predicted structure of allele Gogo-B*04:01:01:01 [NHP00188]

References

Please check the following references for further details:

  • Maccari G, Robinson J, Barker DJ, Yates AD, Hammond JA, Marsh SGE, The 2024 IPD-MHC database update: a comprehensive resource for major histocompatibility complex studies Nucleic Acids Research, 2024;, gkae932, DOI: 10.1093/nar/gkae932
  • Lin Z, Akin H, Rao R, Hie B, Zhu Z, Lu W, Smetanin N, Verkuil R, Kabeli O, Shmueli Y, dos Santos Costa A. Evolutionary-scale prediction of atomic-level protein structure with a language model. Science. 2023 Mar 17;379(6637):1123-30. DOI: 10.1126/science.ade2574