Chemistry Reference
In-Depth Information
Table 9.2
Structural files of proteins presenting similar surfaces to bovine recoverin
PDB ID
RMSD (Å
2
)
Euclidian distance
CATH
1omv-A
1.761
1.10.238.10
0.28
3fxv-A
2.857
Unassigned
3.26
1q90-C
3.046
2.102.10.10
5.28
1pd5-J
3.107
3.30.559.10
4.28
2irv-A
3.108
Unassigned
3.99
1omr-A
3.125
1.10.238.10
0.33
1av4-A
3.178
2.70.98.20
4.24
1xnx-A
3.186
1.10.565.10
7.33
1q23-L
3.188
3.30.559.10
4.43
1p6v-C
3.199
2.40.280.10
5.47
3i1q-H
3.212
Unassigned
4.24
3esg-A
3.23
Unassigned
5.44
3d2s-C
3.231
Unassigned
5.54
1hj1-A
3.242
1.10.565.10
4.90
1w6 g-A
3.256
2.70.98.20
4.25
2qjf-A
3.257
Unassigned
4.86
3d2s-A
3.275
Unassigned
5.56
3kkk-A
3.306
Unassigned
4.91
1um1-A
3.311
2.30.42.10
4.91
3f56-B
3.318
Unassigned
6.68
1nlg-A
3.321
Unassigned
7.43
1wmp-A
3.322
2.70.98.20
4.32
1q23-C
3.33
3.30.559.10
4.29
3kk6-A
3.353
Unassigned
5.27
ILE52, LYS55, PHE56, TYR86, LEU90. Comparison of this result to residues iden-
tified by 3D-SURFER as forming the largest cavity of bovine recoverin (Fig.
9.5
)
emphasizes some common residues and also the areas and volumes of identified cav-
ities by the two tools are strongly different. It illustrates that the two computational
tools use distinct detection algorithms for identification of cavities.
Another online available resource for locating and characterization of pro-
tein potent binding sites is Fpocket (Le Guilloux et al.
2009
). Fpocket is a
fast open source protein pocket detection algorithm that can be used on-line
(http://fpocket.sourceforge.net/) or downloaded from the web page. The input of
Fpocket is a PDB file containing the receptor and cofactors and not the ligands, if
