search

rcsb / symmetry-benchmark

Benchmarks for testing the symmetry package
3 stars 8 forks source link

d1q3gl_ #30

Closed lafita closed 8 years ago

lafita commented 8 years ago

This entry is clearly D3, and the current tag C3 makes no sense (if it is not D3, the most obvious symmetry is C2).

sbliven commented 8 years ago

The problem is the circular permutation/strand-swapping. From a sequence-independent perspective this is a strong D3, with great superposition. However, D3 requires dropping (or flexibly aligning) that first strand, while C2 would allow the full length to be aligned. What should we do here?

lafita commented 8 years ago

I had a typo in the description. The entry was originally annotated as C3 in the benchmark instead of C2.

lafita commented 8 years ago

We decided to annotate the domain as D3 because SCOP annotates it as six repeats of the same fold:

Fold d.68: IF3-like beta-alpha-beta-alpha-beta(2); 2 layers; mixed sheet 1243, strand 4 is antiparallel to the rest

Furthermore, in the superfamily, two families exist: one with three repeats and no strand swapping and the one described here with 6 repeats and strand swapping. This adds support to our hypothesis that the six repeats are equivalent. Their symmetry is D3, then. http://scop.berkeley.edu/sunid=55205&ver=2.05