3dSS: 3D structural superposition

Abstract

3dSS is a web-based interactive computing server, primarily designed to aid researchers, to superpose two or several 3D protein structures. In addition, the server can be effectively used to find the invariant and common water molecules present in the superposed homologous protein structures. The molecular visualization tool RASMOL is interfaced with the server to visualize the superposed 3D structures with the water molecules (invariant or common) in the client machine. Furthermore, an option is provided to save the superposed 3D atomic coordinates in the client machine. To perform the above, users need to enter Protein Data Bank (PDB)-id(s) or upload the atomic coordinates in PDB format. This server uses a locally maintained PDB anonymous FTP server that is being updated weekly. This program can be accessed through our Bioinformatics web server at the URL http://cluster.physics.iisc.ernet.in/3dss/ or http://10.188.1.15/3dss/.

Figure 1

The screen snapshot shows the superposition of 12 structures of recombinant phospholipase A₂. The top panel shows the status of superposition and the right RASMOL graphics panel displays the superposition in different colors (see the last column of the top panel for coloring scheme). The bottom left panel shows the graphical display of the r.m.s.d. values of the 12 structures and is generated using the data display engine, Ploticus. It is clear from the plot that the region 60–70 is having large deviations compared with the remaining portion of the molecule.

Figure 2

The screen shot displays the superposition of six OppA along with 209 invariant water molecules. This is carried out using the option (b), ‘Superpose several structures’ and ‘Superpose and identify invariant water molecules’.

Figure 3

The output panel depicts the superposition of eight different chains along with 36 invariant water molecules in PDB-id: 1JAC. The chains A, B, C, D (fixed) are colored green and the color red is used for the chains E, F, G, H (mobile). The invariant water molecules are having the same color as the corresponding subunits.

Figure 4

The output shows the common water molecules between the subunits A and B. The RASMOL panel shows eight common water molecules (blue color). This is carried out using the option (c) ‘Superpose subunits within a structure and ‘identify common water molecules’.