Skip to main content
Figure 3 | BMC Bioinformatics

Figure 3

From: Genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles

Figure 3

Identification of Specificity Determining Residues (SDRs). (a)The crystal structure of adenylation domain of gramicidin synthetase (PDB code: 1AMU). The C terminal domain is colored in ochre. The A and B subdomains of the N-terminal domain are shown in green and pink respectively. The cofactor AMP (orange) and substrate phenylalanine (red) are depicted as CPK models. The 15 SDRs lining the substrate binding pocket are shown in cyan. (b) Zoomed in version of the active site. The substrate phenylalanine and AMP are shown as stick in red and orange respectively and the 15 SDRs as ball and stick. (c) The extraction of SDRs from a protein sequence. The query sequence is aligned with the structural template and the amino acids of the query corresponding to the SDRs of the template are extracted. The residues highlighted in red represent the SDRs.

Back to article page