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Table 2 Ensemble analysis of pockets at protein-protein interfaces

From: Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets

Complex Protein-protein interface size (atoms) Method Percentage of interface identified as pocket
    apo structure Provar Score > 0.75 Provar score > 0.25
Bcl-X L   PASS 28 16 42
+ 74 LIGSITE 66 39 83
Bak   fpocket 41 20 50
MDM2   PASS 27 11 45
+ 193 LIGSITE 41 30 74
p53   fpocket 31 8 46
XiapBir3   PASS 30 9 55
+ 128 LIGSITE 42 35 83
Caspase 9   fpocket 19 13 59
XiapBir3   PASS 17 0 43
+ 42 LIGSITE 21 17 81
SMAD   fpocket 21 0 65
ZipA   PASS 54 13 65
+ 63 LIGSITE 44 19 57
FtsZ   fpocket 10 2 19
HPVE2   PASS 42 22 51
+ 109 LIGSITE 44 22 58
HPVE1   fpocket 17 3 32
IL2   PASS 30 5 55
+ 103 LIGSITE 20 17 57
IL2-R   fpocket 4 1 19
Integrase   PASS 42 42 64
+ 33 LIGSITE 45 18 48
LEDGF   fpocket 52 3 51
TNFa   PASS 23 9 44
trimer 189 LIGSITE 34 18 63
interface   fpocket 15 3 31
TNFR1a   PASS 24 5 34
+ 41 LIGSITE 46 10 71
TNFb   fpocket 0 0 34
MDM4   PASS 55 24 48
+ 71 LIGSITE 38 32 52
p53   fpocket 44 0 47
   PASS 34 14 49.5
Mean Values 95 LIGSITE 40.5 23.5 66
   fpocket 23 5 41
  1. Provar analysis of a tCONCOORD generated ensemble of 250 structures of the apo form of each of the 11 first-named proteins in the complex. The proportion of protein interface atoms found to be persistently or variably lining pockets is, on average, significantly greater than for the protein as a whole. However, this enhanced variability is small and only found to be significant for 14/33 individual analyses. (Italic number in final column indicates the cases in which the proportion is notsignificantly greater at the p < 0.05 level).