[ccp4bb] Protein cavity volume calculation

[Seema H Irani]

I was wondering if anyone could recommend a good program or links to
calculate the cavity volume of the protein active site.



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[ccp4bb] Substrate density visible in relatively active mutant

[Seema H Irani]

I crystallized a PLP dependent enzyme and wanted to capture the enzyme
substrate complex, however due high activity of the enzyme I could see no
density at the active site upon soaking with the substrate. I hence made a
bunch of mutants of the active site residues and one of them showed density
consistent with the substrate in some of the molecules in the asymmetric
unit. Surprisingly however when I measured the activity of this mutant it
had 30% of the wildtype activity I am wondering why is it still possible
for me to see substrate density for this mutant?