RuBisCO

PDB file 1AA1

This file depicts activated spinach RuBisCO (RuBP Carboxylase - Oxygenase) with the product 3-phosphoglycerate (3PG, 2 copies) bound at the active site. The display shows only 4 large protein chains and 4 small protein chains (L₄S₄), although the biological unit is L₈S₈. This structure was solved by T. C. Taylor and I. Andersson in 1997.

Suggested display options:

To distinguish the different polypeptides right click the image, select color chain and display as cartoon.
Each small subunit has a color similar to but slightly different than its paired large subunit.

To visualize the lysine-carbamate and the 3PG product select hetero-ligand, color CPK, and display as ball & stick. (The lysine-carbamate is also selectable as KCX, and the product 3-phosphoglycerate as 3PG.) 
Zoom in on one of the active sites for a closer look.
Identify the carbamate group.

To get a clearer view, select protein and then select hide.
Select atom MG and display as spacefill with color CPK.
Where is magnesium located relative to the carbamate and 3PG?
Note that the carboxyl end of one 3PG has swiveled out from the active site.
Now select protein-polar and display as wireframe with color CPK,
and select hetero-ligand and display as spacefill.
Question: What are some of the polar active site residues that interact with 3PG?

To visualize only a single LS pair, first select protein-protein, and select hide.
Then select chain L (one of the large subunits), display as cartoon with color structure.
Similarly select and display chain S, display as cartoon with color chain (or specify a color).
Select hetero-ligand, display as spacefill and color CPK. 
Questions:
On which subunit is the active site?
Where is the active site relative to the a,b-barrel?
Is this on the same side of the barrel as the active site of TIM?

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