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Figure 3 | BMC Genomics

Figure 3

From: antibacTR: dynamic antibacterial-drug-target ranking integrating comparative genomics, structural analysis and experimental annotation

Figure 3

Automatic structural modeling and pocket analysis of 3-oxoacyl-[acyl-carrier-protein] synthase 3. The spheres displayed on Escherichia coli’s 3-oxoacyl-[acyl-carrier-protein] synthase 3 [Swiss-Prot:P0A6R0] homology model (based on template [PDB:1UB7]) represent putative ligand-binding sites as predicted by the automatic pocket analysis. The orange sphere marks the only cavity predicted to significantly affect overall protein flexibility. This predicted position occupies the same cavity and is very close (4.1 Å) to the known inhibitor molecule (in ‘sticks’ representation) after superimposing the homology model to the known structure of the inhibitor-bound protein [PDB:1MZS] (RMSD 1.1 Å). This shows how automatic homology modeling and pocket analysis are combined to correctly identify a regulatory cavity.

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