Figure 3

PONDR-based analysis of hirudin and thrombin. The correspondence of PONDR^® VL-XT predictions and regions of known structure are shown. Two PDB structures are presented – 5HIR (left) and 1NO9 (right) – where each chain is color coded – folded N-terminal domain of hirudin (yellow, disulphide bridges are shown by maroon lines), acidic C-terminal domain of hirudin (red) bound to a heavy chain of thrombin (blue), and light chain of thrombin (green). These color codes are also used for bars in two PONDR^® VL-XT plots – (top) hirudin and (bottom) thrombin – to indicate the positions of the regions of known structure in the context of the PONDR^® VL-XT predictions. Drawn over these bars, hash marks show the residues in contact with other chains, where the color of the hash mark corresponds to the color code of the chain in contact. Black hash mark in the PONDR^® VL-XT plot for thrombin corresponds to the factor Xa cleavage site. A predicted α-MoRF region of hirudin is shown in corresponding PONDR^® VL-XT plot as a pink bar.