Figure 1.
FIG. 1. Ribbon and surface electrostatic representations of
thrombin bound to heparin. A, the asymmetric unit consists of
four thrombin monomers organized into two nearly equivalent
dimers. Because -thrombin is a
two-chain molecule, each monomer is denoted by two letters
according to the chain ID of the light and heavy chains, with
blue corresponding to monomer AB, red to monomer CD, orange to
monomer EF, and cyan to monomer GH. Each monomer is inhibited by
PPACK, shown in green space-filling. Two heparin chains were
independently built (ball-and-stick) between the dimer partners
in opposite orientations. B, the most intimate contact with
heparin (ball-and-stick) was found for monomer AB (surface
representation colored according to electrostatic potential,
with blue for positive and red for negative). Thrombin is
oriented so that exosite II is facing, and some of the
contacting residues are labeled (Lys236 was not fully modeled in
electron density and was rebuilt here for the purpose of
illustrating its contribution to the surface electrostatics).
The confidence in the positioning of the heparin fragment is
demonstrated by the 2F[o] - F[c] electron density map (green)
shown surrounding the modeled hexasaccharide fragment.
-thrombin is a
two-chain molecule, each monomer is denoted by two letters
according to the chain ID of the light and heavy chains, with
blue corresponding to monomer AB, red to monomer CD, orange to
monomer EF, and cyan to monomer GH. Each monomer is inhibited by
PPACK, shown in green space-filling. Two heparin chains were
independently built (ball-and-stick) between the dimer partners
in opposite orientations. B, the most intimate contact with
heparin (ball-and-stick) was found for monomer AB (surface
representation colored according to electrostatic potential,
with blue for positive and red for negative). Thrombin is
oriented so that exosite II is facing, and some of the
contacting residues are labeled (Lys236 was not fully modeled in
electron density and was rebuilt here for the purpose of
illustrating its contribution to the surface electrostatics).
The confidence in the positioning of the heparin fragment is
demonstrated by the 2F[o] - F[c] electron density map (green)
shown surrounding the modeled hexasaccharide fragment.