Word for "something that looks man-made/ fabricated/ artificial"

Solution 1:

Synthetic or manufactured is now often recommended in the academic/technical literature as a replacement for the gendered manmade.

If you're certain that the protein was designed rather than evolved, you could use "The synthetic structure..." However, it sounds like you aren't certain. In this case, you could use

"The synthetic-appearing structure..." or

"The synthetic aspects [or nature or appearance or configuration or arrangement] of the structure..." or

"The protein characteristics, which evoke synthetic structures..." or

"The protein structure, which appears similar to those of manufactured proteins, ..." and so on.