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| - | | + | #REDIRECT [[5vcn]] This PDB entry is obsolete and replaced by 5vcn |
| - | ==The crystal structure of Der p 1 allergen complexed with Fab fragment of mAb 5H8==
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| - | <StructureSection load='4pp1' size='340' side='right'caption='[[4pp1]], [[Resolution|resolution]] 3.00Å' scene=''>
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| - | == Structural highlights ==
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| - | <table><tr><td colspan='2'>[[4pp1]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Dermatophagoides_pteronyssinus Dermatophagoides pteronyssinus] and [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PP1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PP1 FirstGlance]. <br>
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| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rvw|3rvw]], [[3rvv|3rvv]], [[3rvx|3rvx]], [[4poz|4poz]], [[4pp2|4pp2]]</div></td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptidase_1_(mite) Peptidase 1 (mite)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.65 3.4.22.65] </span></td></tr>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4pp1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pp1 OCA], [https://pdbe.org/4pp1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pp1 RCSB], [https://www.ebi.ac.uk/pdbsum/4pp1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pp1 ProSAT]</span></td></tr>
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| - | </table>
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| - | == Function ==
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| - | [[https://www.uniprot.org/uniprot/PEPT1_DERPT PEPT1_DERPT]] Thiol protease, with a preference for substrates with a large hydrophobic side chain in the P2 position, or with basic residues.
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| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | Der p 1 is a major allergen from the house dust mite, Dermatophagoides pteronyssinus, that belongs to the papain-like cysteine protease family. To investigate the antigenic determinants of Der p 1, we determined two crystal structures of Der p 1 in complex with the Fab fragments of mAbs 5H8 or 10B9. Epitopes for these two Der p 1-specific Abs are located in different, nonoverlapping parts of the Der p 1 molecule. Nevertheless, surface area and identity of the amino acid residues involved in hydrogen bonds between allergen and Ab are similar. The epitope for mAb 10B9 only showed a partial overlap with the previously reported epitope for mAb 4C1, a cross-reactive mAb that binds Der p 1 and its homolog Der f 1 from Dermatophagoides farinae. Upon binding to Der p 1, the Fab fragment of mAb 10B9 was found to form a very rare alpha helix in its third CDR of the H chain. To provide an overview of the surface properties of the interfaces formed by the complexes of Der p 1-10B9 and Der p 1-5H8, along with the complexes of 4C1 with Der p 1 and Der f 1, a broad analysis of the surfaces and hydrogen bonds of all complexes of Fab-protein or Fab-peptide was performed. This work provides detailed insight into the cross-reactive and specific allergen-Ab interactions in group 1 mite allergens. The surface data of Fab-protein and Fab-peptide interfaces can be used in the design of conformational epitopes with reduced Ab binding for immunotherapy.
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| - | Structural Analysis of Der p 1-Antibody Complexes and Comparison with Complexes of Proteins or Peptides with Monoclonal Antibodies.,Osinski T, Pomes A, Majorek KA, Glesner J, Offermann LR, Vailes LD, Chapman MD, Minor W, Chruszcz M J Immunol. 2015 Jul 1;195(1):307-16. doi: 10.4049/jimmunol.1402199. Epub 2015 May, 29. PMID:26026055<ref>PMID:26026055</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 4pp1" style="background-color:#fffaf0;"></div>
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| - | == References ==
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| - | <references/>
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| - | __TOC__
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| - | </StructureSection>
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| - | [[Category: Dermatophagoides pteronyssinus]]
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| - | [[Category: Large Structures]]
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| - | [[Category: Lk3 transgenic mice]]
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| - | [[Category: Chapman, M D]]
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| - | [[Category: Chruszcz, M]]
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| - | [[Category: Glesner, J]]
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| - | [[Category: Majorek, K A]]
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| - | [[Category: Minor, W]]
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| - | [[Category: Offermann, L R]]
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| - | [[Category: Osinski, S]]
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| - | [[Category: Osinski, T]]
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| - | [[Category: Pomes, A]]
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| - | [[Category: Vailes, L D]]
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| - | [[Category: Allergen]]
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| - | [[Category: Antibody]]
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| - | [[Category: Immune system]]
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