This page describes validity of the proposed binding structure at the catalytic triad of the DPP-4 protein. There are a variety of ligands that were tested using electron density clashes and real space R-values to flag potential clashes in the current model.
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You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
What is a Validation Report?
A validation report (see linked image) [[1]] is an analysis of a molecular dataset model and the real space electron density of the proposed model. There are several factors that affect the validity of the model. Perhaps the most important is the resolution in Angstroms. A low resolution of less than 2 will likely have few electron density clashes, while a resolution of above 3 will have several clashes due to overlapping atomic radii.
Validaton report guidelines.
Rfree - measures the fit of the model using a subset of the data available.
RSRZ outliers - Real Space R values, measures fit of atomic model vs. the collected data in real space.
Clashscore - Derived from number of atoms in the model that are unusually close together.
Ramachandran outliers - Measures φ (phi) and ψ (psi) angle irregularities.
Sidechain outliers - Measures protein sidechain outliers and deviations from expected backbone angles.
JMol Images
This page will allow the user to view Jmol renderings of each protein along with the ligand in the binding pocket. The validation report will also identify the clashes in the model, which will be indicated as follows:
Red atoms indicate that there are significant clashes in the area of the displayed atom
Blue atoms indicate that there are less significant but still present clashes in the area of the displayed atom.
Overall Blue indicates a minor issue, while Red indicates a major discrepancy between the measured electron density and the location in the model.
The size of the clash is also indicated with BIG atoms indicating a larger clash than small atoms.
3Q8W
1NU6
1NU6 protein along with the ligand and catalytic triad displayed. The data was captured with a 2.10 Å resolution. The ligand NDG is not found in the binding site, rather it is bound to the outside of the binding pocket. This indicates that the ligand may be binding to an allosteric site and modulating the activity at the binding site. The ligands present in this model are two sugars (NAD and NDG), a Mercury (II) ion, and water. Of these, the mercury ion is closest to the triad, but is not close enough to represent a binding interaction. NDG however is found near the opening of the binding pocket, and thus may be an allosteric site for the protein.
The catalytic triad of the protein is shown here. Important to note that there are no clashes surrounding the site, and thus the model may provide an accurate representation of the binding capabilities of this binding pocket.
1PFQ
5T4B
5T4B has a resolution of 1.76 Å and can be seen here with the 75N ligand within the binding pocket. There are more RSRZ outliers near the entrance to the binding cavity, but few clashes near the actual binding site. This indicates that the binding pocket itself has validity, but the mechanism for the ligand entering the cavity may be in question.
Shown in Figure 1c is a view of a the 75N ligand inside the binding pocket of DPP-4.
The 5T4B catalytic triad shown with electron density around the SER630, HIS740 and ASP706 residuals. There are no clashes at the triad.
To see the binding pocket of the 75N ligand at the catalytic triad, click on Figure 1d. There is electron density from the catalytic triad that extends into the binding pocket, and surrounding the functional binding groups on the ligand. No RSRZ outliers are found within the binding pocket, and this conformation of the molecule is supported by the electron density surrounding the catalytic triad.
6B1E
4N8D
4A5S
Structural highlights
This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
Authors
Lana Jevtic, Kaeli Jacobson, Tayler Aarness, Eric Ruterbories.
St. Olaf College.
Medicinal Chemistry, Interim 2018.
Professor Robert Hanson.
![[1]](http://proteopedia.org//wiki/images/d/df/RSRZ_validation.png){kind=link}