Skip to main content
Figure 2 | BMC Structural Biology

Figure 2

From: Prediction of calcium-binding sites by combining loop-modeling with machine learning

Figure 2

FEATURE predictions confirmed by experimentally solved structures. The structure of obelin from obelia longissima in its apo form (PDB ID: 1SL9) is shown in blue. In the original structure, loop 122-128 (residues 122-128, sequence: FDKDGSG) is unstructured. The structure of this region was built using modeling methods. FEATURE predicts a calcium-binding site in 1SL9 in the presence of the structure rebuilt for loop 122-128. The predicted site adopts an EF-hand motif. Searching for homologs, we found that the calcium-binding form obelin has been resolved experimentally (PDB ID: 1SL7). The predicted binding site in 1SL9 is similar with one of the three calcium-binding sites observed in 1SL7. Both sites are in close association with oxygen atoms (red in close-up view) from residues 125D, 129T and 134E. The RMSD between 1SL9 and 1SL7 is 3.01 Ã… and that between the rebuilt loop in 1SL9 and the counterpart in 1SL7 (pink) is 2.27 Ã….

Back to article page