Table 2.

Volumes of ligand-binding pockets of bHLH-PAS proteins.

DOI: http://dx.doi.org/10.7554/eLife.18790.012

Location	NPAS1	NPAS3	HIF-1α	HIF-2α	HIF-3α	ARNT	CLOCK	BMAL1	NPAS2	SIM1	SIM2
PAS-A	190	100	100	150	170	110	120	200	230	210	210
PAS-B	180	230	160	370	590	210	140	220	170	370	310

Pocket volumes (ų) were calculated using CASTp program (Dundas et al., 2006) using the default probe sphere radius of 1.4 Å. The PDB coordinate files used for NPAS1 and NPAS3 proteins were from the NPAS1-ARNT and NPAS3-ARNT-DNA complexes, the coordinates for ARNT and HIF-2α were from the apo HIF-2α-ARNT complex (PDB: 4ZP4), and the coordinates for CLOCK and BMAL1 were from the CLOCK-BMAL1 complex (PDB: 4F3L). The values of PAS-B domains of HIF-1α and HIF-3α (fatty acid bound) were from high-resolution single domain structures (PDBs: 4H6J and 4WN5), respectively. The PAS-A domain of HIF-3α, and both PAS domains of NPAS2, SIM1 and SIM2 were modeled using the SWISS-MODEL server (Biasini et al., 2014).