In both complexes, SA results in major clusters with CA-RMSDs of 4.0 4.5 Å from the extended conformation (Figure 6), which corresponds to the β-turn conformation observed in the structure of pYVNV complexed with Grb2 SH2 or with the ThrEF1Trp mutant of Src SH2 (Figure 7).
For the purpose of our study we have used the conformation observed in the crystal structure.
The conformation of E96 observed in the apo structure is clearly distinct from the E96 conformation observed in the Mg2+- and Mn2+-bound structures.
The compact conformation observed for Lys diUb is distinct from the compact conformations observed for Lys and Lys diUb [ 8, 9, 12].
Furthermore, the plug is virtually unaltered from the conformation observed in the isolated structures.
However, the bound flavin adopts the "flapped" FADox conformation observed in KtzI FADox Br.
The only peptide conformations observed under the conditions investigated were α-helix and random coil.
This extended conformation of Lys chains differs from the fully extended conformations observed for Lys and Met diUb [ 13].
The open conformations observed for the human IKK2 models suggest that the SDD mediates flexibility.
The β-strand slippage that gives rise to a reported minor conformation species 10 was not observed, thus indicating that our structure also represents the major conformation, despite having a different crystal form.
