What the wiki helped me understand is that the presentation of the molecule to its environment is dynamic. It wriggles incessantly so that the relevant moiety appears and disappears depending on the instantaneous conformation. Your graphics are excellent aids to understanding but it's very hard to depict this dynamism in a necessarily static image.
All I am saying is that giving something a name can beguile us--the name remains constant but that doesn't mean the thing named does. Antithrombin is a "substance", but we have to take that with a grain of salt: it's not a statue like sugar or salt but a dancer.
I'm sure the science guys are laughing but this "now you see it/now you don't" aspect gave me a lot of trouble. It's one thing to understand that a vial of stuff is a mixture of different similar entities, but that a single molecule has like nature--that its proclivities and behavior are also a blend--that's a bit trickier.
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