Figure 3. Target T1121, a DNA-cleavage protein JetD (PDB: 7TIL).(A) a homodimer with two chains colored as cyan and green;(B) superposition of its two chains showing flexibility of the
C-term domain (Pfam DUF2220, right) with respect to the N-term arm-like
domain (DUF3322, left); (C) a Grishin plot showing the need for
splitting. The plot was built on the GDT_TS results for all groups on
the constituent domains D1: 2-204 and D2: 205-381 and the whole target
in the chain A configuration.
The last example in this category is target T1170, a Holliday junction
hexamer where some chains deform to accommodate DNA25 in such a way that
the overall structures of domains remain largely unchanged, yet their
relative position varies (Figure 4AB). Non-crystallographic symmetry of
the structure requires separate treatment of parts that have different
relative orientation. The target was originally split into three domains
(1: 4-164; 2: 165-243; 3: 244-315) and analyzed if any of those need to
be merged for the final evaluation. The Grishin plots (Fig 4C) advised
that domains 1 and 2 should be merged, while 3 should remain a separate
evaluation entity. Thus, for the final evaluation, this target was
represented by two EUs: D1: 4-243 and D2: 244-315 (encircled).