The pdb files are modified from actual structures from domesticated animal species.
Each numbered file can be paired with a board/tray combo using the hinted species name above each one; the example file goes with the combo labeled as such.
These pairings can be found/verified by doing a BLAST search of the protein sequence.
Viewing the file in a molecular structure viewer and coloring by B-factor (or temperature factor, or Debye-Waller factor, as hinted in the flavor text) shows one or two special highlighted areas on the the beta sheets, areas where the protein has been mutated from the original sequence.
In particular, the highlighted areas can be mapped as a grid to the "meats" on the cutting boards, one residue per grid square.
The colors in the recommended viewers more-or-less match the colors in the example: dark red = 100, pink = 75, white = 50, light blue = 25.
Additionally, a B-factor of 0 (dark blue) is used for unmutated residues.
Note that the polypeptide chains always lie horizontally on the board.
Interpreting residues as letters using the one-letter amino acid code (including the extended alphabet where ASX = B, SEC = U, and PYL = O) and coloring them as in the protein yields Bonza pieces.
The theme of each Bonza is synonyms of the animals names/meats made from that animal (the length of which is enumerated).
Extracting letters in highlighted squares yields THREE WORD PASTRY WITH SPECIES FOUR.
This is a clue phrase for the answer; as 4.pdb is a chicken protein (and also is used in the 4th non-example board), the answer is CHICKEN POT PIE.
The extracted protein grids and temperature colors, along with the solved grids with extracted letters bolded, are as follows:
Example
Ovis aries = lamb (i.e., ingénue, new person)
| | | | | | |
| I | N | V | I | | |
| G | E | B | E | | |
| R | L | E | N | | |
| | T | R | N | H | |
| | I | N | O | O | |
| | | | | | |
| E | B | C | N | | |
| N | R | G | G | | |
| | | N | O | I | |
| | | | A | C | |
| | | | | | |
| | | | | | | | | | | | |
| | | | | | | | | G | | | |
| | | | | | | | | R | | | |
| | | | I | N | N | O | C | E | N | T | |
| | | | | | | | | E | | | |
| | | | | | | | | N | | | |
| | | | | | | | | H | | | |
| | | | N | | | | | O | | | |
| | | | O | | | | | R | | | |
| | | | V | I | R | G | I | N | | | |
| | | | I | | | | | | | | |
| | | | C | | | | | | | | |
| B | A | B | E | | | | | | | | |
| | N | | | | | | | | | | |
| | G | | | | | | | | | | |
| | E | | | | | | | | | | |
| | L | | | | | | | | | | |
| | | | | | | | | | | | |
Anas platyrhynchos = duck (i.e., bend down, escape)
| | | | | | | | |
| E | L | U | O | D | B | O | |
| C | H | E | P | W | O | U | |
| | | D | E | N | G | E | |
| | | C | R | D | A | S | |
| | | | | | | | |
| | | | | | | | | | | |
| B | O | W | | | | | | | | |
| E | | | | | | | | | | |
| N | | | | | | | | | | |
| D | O | D | G | E | | | | | | |
| | | | | S | | | | | | |
| | | | | C | R | O | U | C | H | |
| | | | | A | | | | | | |
| | | | | P | | | | | | |
| E | L | U | D | E | | | | | | |
| | | | | | | | | | | |
Meleagris gallopavo = turkey (i.e., dumb or silly person)
| | | | | | | | | |
| | D | R | E | E | | | | |
| B | U | M | A | N | N | S | W | |
| O | P | B | D | C | N | K | T | |
| | | | | | | | | |
| D | U | | | | | | | |
| O | L | I | T | T | I | Y | | |
| | L | N | H | N | N | I | | |
| | | I | E | U | E | C | | |
| | | | | | | | | |
| | | | | | | | | |
| | | B | | | | | | |
| | D | O | P | E | | | | |
| | | N | | | | | | |
| | | E | | | | | | |
| | | H | | | | | | |
| | | E | | N | | | | |
| | | A | | U | | | | |
| | | D | I | M | W | I | T | |
| | | | | B | | | | |
| | | | | S | | | | |
| | | | | K | | | | |
| | | | | U | | | | |
| | | D | O | L | T | | | |
| | | U | | L | | | | |
| | | N | | | | | | |
| | | C | | | | | | |
| C | R | E | T | I | N | | | |
| | | | | | I | | | |
| | | | | | N | | | |
| | | | | | N | | | |
| | | | | | Y | | | |
| | | | | | | | | |
Gallus gallus = chicken (i.e., scared)
| | | | | | | | |
| P | R | V | E | H | | | |
| I | D | I | M | T | L | E | |
| A | P | G | E | H | Y | N | |
| | | | | | | | |
| D | C | F | S | I | W | | |
| | O | R | T | R | A | | |
| | | | E | N | | | |
| | | | | | | | |
| | | | | | | | | | | | | |
| | | | | | | | C | | | | | |
| | | | | | | | O | | | | | |
| | | | | | | | W | | | | | |
| | | | | F | | | A | | | | | |
| | | | | R | | | R | | | | | |
| | | | T | I | M | I | D | | | | | |
| | | | | G | | | L | | | | | |
| | | | | H | | | Y | | | | | |
| | | | | T | | | | | | | | |
| | | | | E | | | | | | | | |
| | | | | N | | | | | | | | |
| A | P | P | R | E | H | E | N | S | I | V | E | |
| | | | | D | | | | | | | | |
| | | | | | | | | | | | | |
Bos taurus = beef (i.e., fight, argument)
| | | | | | | | | | | |
| A | B | P | E | E | S | R | I | | | |
| P | U | S | T | G | M | B | S | | | |
| | R | C | T | R | I | C | A | O | N | |
| | | R | D | E | T | I | S | T | E | |
| | | | | | | | | | | |
| | | | L | E | C | | | | | |
| | | | Q | U | I | F | | | | |
| | | | U | F | L | I | | | | |
| | | | | | | | | | | |
| | | | | | | | | | | | | |
| | | | S | Q | U | A | B | B | L | E | | |
| | | | | U | | | | | | | | |
| | | | | A | | | | | | | | |
| | | | G | R | I | P | E | | | | | |
| | | | | R | | | | | | | | |
| | | | | E | | | | | | | | |
| C | O | N | F | L | I | C | T | | | | | |
| | | | | | | R | | | | | | |
| | | | | | | I | | | | | | |
| | | | | | | T | | | | | | |
| | | | S | T | R | I | F | E | | | | |
| | | | | | | C | | | | | | |
| | | | | | D | I | S | P | U | T | E | |
| | | | | | | S | | | | | | |
| | | | | | | M | | | | | | |
| | | | | | | | | | | | | |
Bison bison = buffalo (i.e., to bully)
| | | | | | | | | |
| | B | U | C | E | W | E | | |
| A | W | R | O | A | B | L | L | |
| | O | O | R | T | Y | | | |
| | | | | | | | | |
| | | | | O | R | | | |
| | | E | M | V | E | | | |
| | | | P | F | | | | |
| | | | | | | | | |
| | | | | | | | |
| | F | O | R | C | E | | |
| | | | | O | | | |
| | | | | M | | | |
| | | | | P | | | |
| | | | | E | | | |
| | | B | U | L | L | Y | |
| | | R | | | | | |
| | | O | | | | | |
| | | W | | | | | |
| | | B | | | | | |
| O | V | E | R | A | W | E | |
| | | A | | | | | |
| | | T | | | | | |
| | | | | | | | |
Author's Notes
I must note two inspirations for this one:
- The program CONSURF (https://consurf.tau.ac.il/), which similarly uses B-factors to indicate something other than actual B-factors (i.e., evolutionary rates by residue).
- Introduction to Protein Structure, 2nd ed., by Branden and Tooze, for laying out how beta sheets can be regarded as grids.