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. 2017 Mar 13;114(13):E2662–E2671. doi: 10.1073/pnas.1615068114

Fig. 6.

Fig. 6.

Prediction of homodimeric structures. The predicted interdomain contacts (compare Fig. 5) allow reliable predictions of homodimeric structures with up to crystal structure accuracy for the different RRs OmpR (PDB ID code 1nxs; A and D), LytTR (PDB ID code 4cbv; B and E), and GerE (PDB ID code 4e7p; C and F). (A–C) Displayed are the predicted homodimers (blue) overlaid with their known crystal structures; monomers are highlighted in green and purple. The backbone rmsds between the prediction and the crystal structures are 1.1 Å (OmpR), 1.1 Å (GerE), and 1.2 Å (LyTR). Interestingly, for LyTR, we predict the biological assembly 2. In the predictions, only part of the predicted interdomain contacts are realized (dinter < 8 Å; highlighted in green in D–F), whereas many predicted contacts are not formed (highlighted in orange in D–F). All these contacts, however, are close to being realized in the monomer as intra contacts within a threshold of 12 Å (dinter > 8 Å, dintra < 12 Å). None of the predicted contacts are >12 Å both inter and intra.