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Table 3 Results of NMR ensembles scanned with FEATURE Ca2+ binding site model

From: The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications

Protein Name PDB ID Number of Models Number of Models Characterized as Calcium Binding
Lipoprotein receptor-related protein repeat 8 1CR8 20 20
Lipoprotein receptor-related protein repeat 3 1D2L 20 20
RALBP1-intercating protein 1IQ3 18 18
Rous Sarcoma virus receptor 1JRF 20 20
Tyrosine-protein kinase SRC 1KSW 20 20
Calerythrin 1NYA 20 20
Human Notch1 1PB5 16 16
Porcine pancreas phospholipase A2 1SFW 18 1
Rational design of a calcium-binding adhesion protein 1T6W 20 3
Human beta parvalbumin 1TTX 20 20
Cytochrome c peroxidase * 2B10 10 4
Matrilysin 2DDY 25 24
Calcium-binding protein p22 2E+30 20 17
Sodium/calcium exchanger 1 domain 1 2FWS 20 18
Sodium/calcium exchanger 1 domain 2 2FWU 20 18
Rat megalin 2I1P 20 19
Relaxin receptor 1 2JM4 24 22
Yeast frequenin 2JU0 15 15
  1. Scanning of the 18 NMR ensembles with the Ca2+ binding model revealed structural heterogeneity among the structures in the ensembles. In several, most of the models exhibited Ca2+ binding conformations, while in others, only a few. The first and the second columns contain names and PDB IDs of the examined proteins, respectively. The third and fourth columns show the total number of models and how many of those were identified by FEATURE as Ca2+ binding in the NMR ensemble, respectively. * – Results of this scan are shown in Figure 4.