The molecular includes 2 identical Nkx2.5 HDs and a double-strand DNA with 20 base pairs, while the blue part is specific for the molecular. Each HD contains 3 alpha helices, two loops, N-terminous and C-terminous structures (ref 1).
References 1.Pradham, L., Genis, C, Scone, P., Weinberg, O.E., Kasahara, H., and Nam, H. (2012) Crystal Structure of the Human NKX2.5 Homeodomain in Complex with DNA Target. Biochemistry 51 (32), 6312-6319 DOI: 10.1021/bi300849c 2.Fodor, E., Mack, J. W., Maeng, J. S., Ju, J. H., Lee, H. S., Gruschus, J. M., Ferretti, J. A., and Ginsburg, A. (2005) Cardiacspecific Nkx2.5 homeodomain: conformational stability and specific DNA binding of Nkx2.5(C56S). Biochemistry 44, 12480−12490 3.Fraenkel,E., and Pabo, C.O. (1998) Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex. Nat. Struct. Biol.5,692−697
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