Sandbox Reserved 804

From Proteopedia

INTRO: Triose phosphate isomerase (TIM) is an enzyme that catalyzes the reaction of D-glyceraldehyde 3-phosphate to glycerone phosphate. It binds with the ligand 2-Phosphoglycolic acid (PGA).This is the of TIM.

SECONDARY STRUCTURE: This is in TIM. This is the of chain A. The indigo represents the alpha helices and the violet represents the beta sheets. The structure is an alpha-beta-alpha conformation. The beta barrel is parallel and is surrounded by alpha helices.

IMF: This is the secondary structure of TIM with interactions between the backbone. H Bonds are depicted in orange. Disulfide bonds should be represented in black but they are not seen. Most of the hydrogen bonds are present within the secondary structures of the alpha helices and beta barrels. The hydrogen bonds within the beta sheet are strained at an angle, meaning This image depicts the within TIM in grey. The are displayed in blue. Ignore the hydrophilic residues shown floating above the structure because they represent the hydrophilic residues in chain B, not A. The hydrophobic interactions are within the protein while the hydrophilic interactions are on the outside/surface of the protein.

SOLVENT AND LIGAND: The is labeled in purple and forms a cage around the exterior of the protein. PGA is the ligand that binds TIM. is displayed in yellow. Its binding catalyzes the reaction of D-glyceraldehyde 3-phosphate to glycerone phosphate. The are displayed in red, white, and blue. Red represent anionic side chains, the blue represent cationic side chains, and the white resemble nonpolar side chains. The ligand contacts make sense as both anionic and cationic residues are present to interact with the ligand.

CATALYTIC RESIDUES: The are shown in green . These residues are N10, K12, H95, E165, G171 and were selected within a distance of 4 angstroms. The N, K, H, and E most likely interact with the oxygen portion as G interacts with the phosphate portion of PGA.