Skip to main content

Table 3 Details of the intersection between binding sites and destabilizing regionsa.

From: Relating destabilizing regions to known functional sites in proteins

Pdb idb N sitec N des.d N IRe Sens.f PPVg Exp N IRh P-value
Small        
1e1a 13 38 7 53.8 18.4 1.6 0.00023
1e3f 32 18 8 25.0 44.4 1.2 5.9e-06
1gu7 62 53 10 16.1 18.9 4.5 0.00999
1gud 24 36 14 58.3 38.9 3.0 1.5e-08
1gus 24 73 0 0.0 0.0 4.4 1.0
1gusi 84 73 41 48.8 56.2 15.2 6.2e-14
1gxy 24 18 7 29.2 38.9 1.9 0.00100
1hf8 8 46 0 0.0 0.0 0.7 1.0
1hhq 102 126 30 29.4 23.8 14.3 1.2e-05
1is5 88 16 16 18.2 100.0 2.6 8.2e-14
1jcf 34 46 12 35.3 26.1 4.7 0.00061
1odl 150 190 60 40.0 31.6 20.3 3.3e-18
1ofn 30 46 13 43.3 28.3 3.4 2.9e-06
1tm2 19 26 6 31.6 23.1 1.6 0.00232
1usg 30 56 14 46.7 25.0 2.4 5.6e-09
1usl 36 28 15 41.7 53.6 3.2 5.5e-09
1w1h 10 7 6 60.0 85.7 0.5 9.6e-08
1w2i 16 24 0 0.0 0.0 2.1 1.0
1w37 48 101 16 33.3 15.8 4.1 6.5e-07
1y2t 108 66 0 0.0 0.0 12.6 1.0
Polysaccharide        
1nof 12 43 7 58.3 16.3 1.4 7.3e-05
1o88 15 34 12 80.0 35.3 1.4 3.2e-11
1ob0 41 24 8 19.5 33.3 2.0 0.00037
1ogb 32 53 4 12.5 7.5 1.7 0.08496
1qhz 14 29 10 71.4 34.5 1.3 1e-08
1qjv 10 45 4 40.0 8.9 1.3 0.03039
1uuq 16 35 10 62.5 28.6 1.4 3.1e-08
1w0n 8 10 0 0.0 0.0 0.7 1.0
1w6z 20 14 6 30.0 42.9 2.2 0.00887
Peptide        
1c7k 9 7 0 0.0 0.0 0.5 1.0
1e5t 18 33 4 22.2 12.1 0.8 0.00748
1ea7 7 41 0 0.0 0.0 0.9 1.0
1gt9 21 28 4 19.0 14.3 1.6 0.07134
1kl4 68 22 12 17.6 54.5 3.1 5.6e-06
1oes 16 27 5 31.2 18.5 1.5 0.01154
Protein        
1e3f 60 18 0 0.0 0.0 2.3 1.0
1e6l 10 6 3 30.0 50.0 0.5 0.00632
1e6l 15 6 0 0.0 0.0 0.7 1.0
1f2x 24 4 0 0.0 0.0 0.4 1.0
1gcp 21 10 2 9.5 20.0 3.1 0.89027
1gqv 36 8 6 16.7 75.0 2.1 0.00465
1obq 44 19 11 25.0 57.9 2.3 9.6e-07
1uns 19 4 0 0.0 0.0 0.9 1.0
1uns 20 4 4 20.0 100.0 0.9 0.00852
1uol 18 7 2 11.1 28.6 0.7 0.12811
1uq4 42 5 4 9.5 80.0 0.8 0.00254
Nucleic acid        
1o7i 5 4 0 0.0 0.0 0.2 1.0
1okb 30 24 12 40.0 50.0 3.2 3.7e-06
1uol 19 7 0 0.0 0.0 0.7 1.0
1gqv 9 8 0 0.0 0.0 0.5 1.0
1uq4 17 5 0 0.0 0.0 0.3 1.0
Lipid        
1obq 42 19 7 16.7 36.8 2.2 0.00305
1qmd 14 37 4 28.6 10.8 1.4 0.04088
Metal        
1e6l 7 6 0 0.0 0.0 0.3 1.0
1qmd 6 37 1 16.7 2.7 0.6 0.47097
Peptide-Protein        
1mix 26 21 6 23.1 28.6 2.6 0.03234
Small-Metal        
1h1y 38 33 17 44.7 51.5 2.9 8.6e-12
2poo 16 25 10 62.5 40.0 1.1 2.8e-09
1oid 19 60 14 73.7 23.3 2.2 1.2e-10
Polysaccharide-Metal        
1gkb 76 88 48 63.2 54.5 7.0 1.4e-36
Lipid-Metal        
1umv 34 19 0 0.0 0.0 2.6 1.0
Protein-Metal        
1o6v 49 40 12 24.5 30.0 4.2 0.00032
Small     34.4 (21.4) j 32.3 (25.5) k   
Polysaccharide     43.7 (27.3) 26.2 (17.4)   
Peptide     18.3 (14.0) 16.6 (16.7)   
Protein     13.0 (10.9) 36.2 (33.9)   
Nucleic acid     8.0 (17.9) 10.0 (22.4)   
Lipid     15.1 (14.4) 15.9 (18.9)   
Metal     35.7 (29.4) 25.3 (22.6)   
  1. aNo destabilizing regions were detected in 11 entries of the dataset (1utx, 1gv2, 1eao, 1e7l, 1vyi, 1w9s, 1upq, 1w53, 1tgr, 1r29, 1sif) and these entries are not listed in this table.
  2. bPdb identifier of structure used for energy calculations.
  3. cNumber of residues in binding site.
  4. dNumber of residues in destabilising region.
  5. eNumber of residues in intersection region.
  6. fSensitivity (in %).
  7. gPositive predictive value (in %).
  8. hExpected number of residues in intersection region (see text).
  9. i1gus appears twice here because it has 2 distinct binding sites for small ligands. The same observation applies to 1e6l and 1uns that have 2 distinct binding sites for different proteins.
  10. jAverage sensitivity (and standard deviation) for the given ligand type.
  11. kAverage PPV (and standard deviation) for the given ligand type.