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Crystal structures of InhA reveal a <scene name='69/694241/Homotetramer_subunits_labeled/1'>homotetramer</scene> (each subunit featured with a different color) in aqueous solution with separate ligand binding sites in each subunit. Each <scene name='69/694241/Monomer_subunit_no_ligands/1'>monomer</scene> subunit is composed of 289 residues and features a typical [http://en.wikipedia.org/wiki/Rossmann_fold Rossmann fold] containing a single NADH binding site. The <scene name='69/694241/Secondary_structure_black/1'>secondary structure</scene> of InhA is made up of several alpha helices (pink), beta sheets (gold), and beta turns (white). This enzyme also features a fatty acyl binding crevice that accommodates the long-chain fatty acyl substrate (2TK) needed to synthesize mycolic acid precursors. The <scene name='69/694241/Helix6_helix7_updated/1'>alpha-6 and alpha-7 helices</scene> of the InhA form one side of the fatty acyl binding crevice, referred to as the <scene name='69/694241/Monomer_subunit_196_219/1'> substrate binding loop</scene> (residues 196-219). [[Image:Fatty Acyl Binding Crevice.jpg|thumb|200px|left|Fatty Acyl Binding Crevice (substrate binding loop in purple; substrates pictured inside the crevice)]] One side of this crevice is open and exposed to solvent, which allows the substrates to access the binding pocket of this enzyme. The size of the substrate binding loop is a primary determinant of the ability of InhA to select for fatty acyl chains longer than 16 carbons to successfully produce mycolic acid precursors.

Within the fatty acyl binding crevice, the NADH substrate sits on the top shelf of the Rossmann fold, and the fatty acyl substrate sits on top of the NADH substrate. Both of these substrates are held in place through interactions with the <scene name='69/694241/Sbl_hydrophobic/1'>hydrophobic</scene> (purple) residues in the substrate binding loop. [[Image:Binding Pocket - Mesh.jpg|thumb|250px|right|Substrate Binding Pocket (NADH in green; fatty acyl substrate in red)]] Studies have found that the fatty acyl substrate adopts a <scene name='69/694241/2tk_labeled/1'>u-shaped</scene> conformation to facilitate binding.