A two-in-one expression construct for biophysical and structural studies of the human pregnane X receptor ligand-binding domain, a pharmaceutical and environmental target

Carivenc, C.; Laconde, G.; Blanc, P.; Amblard, M.; Bourguet, W.; Delfosse, V.

doi:10.1107/S2053230X2500069X

Figure 3
The novel cleavable linker does not affect the structural configuration of the PXR_LBD. (a) Superimposition of a known structure (PDB entry 3hvl; gray) and the new structure (PDB entry 9fzi; blue) of PXR_LBD-SRC-1 in complex with SR12813 (r.m.s.d. of 0.9 Å over 275 C^α atoms). The SRC-1 peptide moiety is represented in green. (b) A close-up view of the ligand-binding pockets in the PXR_LBD-SRC-1 structures. The F_o − F_c simulated-annealing omit map is presented at an r.m.s.d. of 2 for PDB entry 9fzi (2.7 Å resolution). (c) Superimposition of the known structure (PDB entry 1ilh; gray) and new structure (PDB entry 9fzj; purple) of PXR_LBD in complex with SR12813 (r.m.s.d. of 1.2 Å over 241 C^α atoms). In PDB entry 1ilh, SR12813 was modeled in three different orientations, unlike PDB entry 9fzj, where it present in one. (d) A close-up view of the ligand-binding pockets in the PXR_LBD structures. The ligand of PDB entry 1ilh is not shown for clarity. The F_o − F_c simulated-annealing omit map is presented at an r.m.s.d. of 2 for PDB entry 9fzj (1.6 Å resolution). Oxygen, red; nitrogen, blue; phosphorus, orange. Black dashed lines show hydrogen bonds. Gray dashed lines represent flexible regions that are not visible in the crystal structures.

STRUCTURAL BIOLOGY
COMMUNICATIONS

ISSN: 2053-230X

Volume 81| Part 3| March 2025|

https://doi.org/10.1107/S2053230X2500069X

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