This domain encompasses the CaM binding site formed by helices A and B, followed by helix C, which is linked to the helix D coiled-coil.
The conformational binding interface of BV is composed of two major areas, a β-Gal binding site and a Le epitope binding site, formed by ten amino acids from 3 (P-, T-, and S-) loop regions (Fig. 5).
To be brief, in the Fp subunit succinate is dehydrogenated to fumarate, with two electrons being extracted by FAD and transferred through three Fe-S clusters to the UQ binding site formed by IP, CybL and CybS (Sun et al., 2005).
In order to speed up the docking procedure, the multi-mer was simplified by removing the redundant chains A and B. The receptor preparation was completed by the manual removal of all waters, the ligand molecule and the ADPs of the other binding site formed by chain C and D. The selected drug candidates were prepared using Ligprep 2.5.
This site interacts with the Le epitope through five H bonds, including three water bridged H bonds. Thus, unlike GI.1 NV that lacks a Le epitope binding site and GI.2 FUV/GI.7 TCH that has a Le epitope binding site formed by one (FUV) or two (TCH) residues (Bu et al., 2008; Choi et al., 2008; Kubota et al., 2012; Shanker et al., 2014).
S. pneumoniae ParC55 folds into a similar closed conformation to that of E. coli GyrA (Figure 3B) However, interestingly, the DNA binding site formed by the pneumococcal ParC55 dimer differs markedly in its electrostatic charge distribution from both the E. coli ParC and GyrA dimers (Figure 4).
The proximal Ub binds with an interface of 880 Å to an S1' Ub-binding site formed by helices α1 and α2 of OTULINcat via an unusual binding surface on Ub involving the Ub helix and the Phe4 patch.
The HBGA binding interface of BV is composed of a conserved central binding pocket (CBP) that interacts with the β-galactose of the precursor, and a well-developed Le epitope-binding site formed by five amino acids, including three consecutive residues from the long P-loop and one from the S-loop of the P1 subdomain, a feature that was not seen in the other GI NoVs.
Initial antigenic characterization of IV HA protein for basic understanding of serological assays has revealed the importance of epitope conformation at the receptor-binding site formed by HA monomer folding and trimerisation [10].
Each subunit contains one zinc-binding site formed by four cysteines, which are unusually spaced in the primary sequence.
Integrins comprise two transmembrane chains, termed α and β, with a ligand-binding site formed by the head domain of the two chains [ 2].
