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rcsb / symmetry-benchmark

Benchmarks for testing the symmetry package
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d1xfha_: C2 core with extensive asymmetric n-terminal #69

Closed sbliven closed 6 years ago

sbliven commented 6 years ago

1XFH is a GltPh homolog. It consists of 6 n-term helices used for oligomerization that wrap around a c-terminal core transporter domain. The core domain has a 2-fold symmetry in the membrane plane, with the ligand passing through the axis during transport.

The core domain covers ~40% of the protein. Although it is functionally significant, this seems too low given our goal of high coverage by repeats.

CE-Symm can find the alignment if the domain is manually decomposed into the symmetric parts (e.g. running on 1xfh.A:255-416).

screen shot 2018-10-25 at 04 39 43

Figure: 1xfh projected along the C2 axis, which lies parallel to the membrane. Yellow and red form the core domain with clear symmetry. The helices in blue and green are responsible for oligomerization, and also form a very rough C2 symmetry but are offset from the membrane axis.

sbliven commented 6 years ago

We decided to keep the current C1 annotation.