Computational protocol: Synergistic activation of human pregnane X receptor by binary cocktails of pharmaceutical and environmental compounds

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Protocol publication

[…] For all complexes, native data were collected from one crystal cryoprotected with 20% (v/v) MPD on the ID23-2 beamline at the European Synchrotron Radiation Facilities (λ=0.8726 Å, 100 K), Grenoble, France. Data were processed and scaled with XDS and XSCALE. Crystals belong to space group P 43212. The X-ray structures were solved and refined using Phenix (phenix.refine) and COOT. The percentages of residues located in the favoured Ramachandran plot region are 98.1, 98.2 and 97.9% for the PXR−EE2, PXR−TNC and PXR−EE2−TNC complex structures respectively (calculated with MolProbity). Data collection and refinement statistics are summarized in . Figures were prepared with PyMOL (http://pymol.org/). […]

Pipeline specifications

Software tools XDS, PHENIX, Coot, MolProbity, PyMOL
Applications Small-angle scattering, Protein structure analysis
Organisms Homo sapiens