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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner

Fig. 2

Example of a rigid body shift caused by the rearrangement of two structural domains upon ligand binding. Structure superposition generated with MOMA of the Calmodulin-target peptide complex (the query; PDB code 2BBM, chain A) and the calcium-free Calmodulin (the target; PDB code 1CFC, chain A). Top Panel: The conserved domains are shown in the alignment of SSEs and the respective sub-matrices surrounded by grey and red blocks. Bottom Panel: The two structures and the superposition of their aligned domain pairs are shown respectively in rainbow color representation (Left) and with the SSE pairs structurally aligned in red and orange colours (Right). Non-aligned residues are shown in grey. The alignment of SSE elements is also represented with aligned blocks highlighted (Bottom Right). The structural superposition of these two domain pairs required different rotation matrices and translation vectors. In this example MOMA was executed with the following parameters: g1ā€‰=ā€‰āˆ’4, g2ā€‰=ā€‰āˆ’4 and Cā€‰=ā€‰90

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