[Chimera-users] Substrate channel identification for homotrimer protein

Chakraborty, Joydeep jc323 at njit.edu
Thu Apr 4 19:04:05 PDT 2019


 I was trying to generate the substrate channel including the substrate
binding pocket for my enzyme using the 3V channel finder server. On setting
the outer probe radius to 9 Å and inner probe almost the same as that of a
water molecule, 1.5 Å, the software was able to generate very accurately
the solvent accessible substrate channel, that matches the crystallography
reference. The mrc file can be opened together with the pdb file in chimera
to generate a similar image that I have attached for reference.

 However, my protein happens to be a homotrimer and theoretically it should
have 3 substrate channels. Having said this, I have a general question for
the community. Can anyone shed some light on the fact why 3V server does
generate just one channel for the trimer instead of three?

 Since, very simply the server uses a rolling sphere (1.5 Å radii) to
detect the cavity, I am curious as to why only one channel is shown. Also,
the same thing happens with CastP that generates one substrate pocket for
an entire protein irrespective of a trimer or a dimer. Since, my
computational knowledge is quite limited being from a wet lab background,
any feedback on this would be much appreciated.


With regards,
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