Fig. 4: Illustration of one representative prediction of SMARCA2BD:PROTAC 2:VHL produced by WE-HDX simulations and its comparison to the crystal structure (PDB ID: 6HAX). | Nature Communications

Fig. 4: Illustration of one representative prediction of SMARCA2BD:PROTAC 2:VHL produced by WE-HDX simulations and its comparison to the crystal structure (PDB ID: 6HAX).

From: Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Fig. 4: Illustration of one representative prediction of SMARCA2BD:PROTAC 2:VHL produced by WE-HDX simulations and its comparison to the crystal structure (PDB ID: 6HAX).The alternative text for this image may have been generated using AI.

a A simulated ternary structure with minimum I-RMSD = 1.1 Å. SMARCA2BD (purple) and VHL (orange) are shown in cartoon and transparent surface representations and PROTAC 2 is shown in stick representation. b Structural details of the binding interface. Annotated residues are among those that make the highest number of contacts (see panel c). c A contact map of the interfaces from the crystal (salmon) and the simulated structure (purple). d Structural alignment of the simulated (purple) with the crystal structure (salmon) with a detailed PROTAC 2 comparison.

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