Figure 6
Predicted structural conformations of yeast Tdp1 N-terminal domain. The structure of the yeast Tdp1 NTD was predicted using homology modeling (Phyre2-server [http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index] followed by molecular modeling using MOE and AMBER99), AlphaFold (https://alphafold.ebi.ac.uk/) and I-Tasser (https://zhanggroup.org/I-TASSER/). Shown prediction models are overlayed on the yellow-colored yeast wild-type crystal structure of the catalytic core domain (missing NTD amino acid 1–79) PDB-1Q328. All shown prediction models passed quality control of UCLA SAVESv6.0 server based on ERRAT-overall quality factor (statistics of non-bonded interactions) and a verify_3D score (compatibility of atomic model with its own aa sequence). All structure cartoons were generated using PyMol 2.5.2 (Molecular Graphics System, Schrödinger, LLC).
