6TRW image
Deposition Date 2019-12-19
Release Date 2021-01-13
Last Version Date 2024-01-24
Entry Detail
PDB ID:
6TRW
Keywords:
Title:
Crystal structure of DPP8 in complex with the EIL peptide (SLRFLFEGQRIADNH)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Dipeptidyl peptidase 8
Gene (Uniprot):DPP8
Chain IDs:A, B, C
Chain Length:903
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:SER-LEU-ARG-PHE-LEU-PHE-GLU-GLY-GLN-ARG
Chain IDs:D, E, F
Chain Length:15
Number of Molecules:3
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Aerosol-based ligand soaking of reservoir-free protein crystals.
J.Appl.Crystallogr. 54 895 902 (2021)
PMID: 34188616 DOI: 10.1107/S1600576721003551

Abstact

Soaking of macromolecular crystals allows the formation of complexes via diffusion of molecules into a preformed crystal for structural analysis. Soaking offers various advantages over co-crystallization, e.g. small samples and high-throughput experimentation. However, this method has disadvantages, such as inducing mechanical stress on crystals and reduced success rate caused by low affinity/solubility of the ligand. To bypass these issues, the Picodropper was previously developed in the authors' laboratory. This technique aimed to deliver small volumes of compound solution in response to crystal dehydration supported by the Free Mounting System humidity control or by IR-laser-induced protein crystal transformation. Herein, a new related soaking development, the Aerosol-Generator, is introduced. This device delivers compounds onto the solution-free surface of protein crystals using an ultrasonic technique. The produced aerosol stream enables an easier and more accurate control of solution volumes, reduced crystal handling, and crystal-size-independent soaking. The Aerosol-Generator has been used to produce complexes of DPP8 crystals, where otherwise regular soaking did not achieve complex formation. These results demonstrate the potential of this device in challenging ligand-binding scenarios and contribute to further understanding of DPP8 inhibitor binding.

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Primary Citation of related structures