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Docking of small ligands (GABA, Guvacine and R-/S Nipecotic Acid) into the occluded state model nicely indicated their preference to bind in an extended conformation (also demonstrated by long-term MD with GABA).
We show precisely where 5-substituted hydantoin substrates bind in an extended configuration at the interface of the bundle and hash domains.
Although soaking studies with model OGT substrate peptides were unsuccessful, the elongated nature of the groove on the catalytic domain (approximately 35 Å) suggests peptides may bind in an extended conformation.
In both AI-BP and Tm0922, NAD-related ligands bind in an extended conformation with their ADP moieties accommodated in the trench and nicotinamide moieties approaching an invariant aspartate residue positioned at the top of the pocket.
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However, in conventional serine proteases, the scissile bond of the substrate peptide is almost uniformly bound in the middle of an extended β-sheet.
The backbone of the resultant UNC-45 filament is thus composed by the tethered superhelices ARM1-8 and TPR1-3∗, whereas the UCS domain, which is proposed to bind myosin, extends in a characteristic manner away from the filament axis and does not participate in filament assembly.
As we discuss in Corollary 1, this bound can be extended to any m-dimensional symmetric normed linear space ((mgeq 2)).
Adherens junctions, which play a central role in intercellular adhesion, comprise clusters of type I classical cadherins that bind via extracellular domains extended from opposing cell surfaces.
In a context of 315,000 heroin addicts, the tolerance limits for experiments seeking "fundamental answers to the mysteries of drug effects" are bound to be extended.
The inhibitors bind in the S1′ pocket and extend into an additional S1′ side pocket, which is unique to MMP-13.
If this logic is extended to IQGAP2 and IQGAP3, then Mlc1sa is bound in a compact formation to 3IQ1 and CaM binds in a compact formation, except to 2IQ3 and 3IQ3.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com