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Figure 8
Detailed view of the hydrophobic binding cleft in the dehydrated crystal structure of afamin. A cross-section of the deep hydrophobic binding pocket (left side) is shown over transparent property-coloured residue surfaces (white, lipophilic; green, aromatic lipophilic; red, hydrogen-bonding acceptor potential; blue, hydrogen-bond donor potential). The palmitoleic acid as modelled into the cavity of PDB entry 5okl chain B (MB) is overlaid as a green ball-and-stick model. The PEG fragments modelled into the density of the dehydrated structure PDB entry 6fak (OA) are shown in a yellow ball-and-stick representation. A narrow second channel (top middle of the figure) is visible harbouring a long PEG fragment in PDB entry 6fak. Environment and electron density for the PEG fragments can be readily inspected via the PDB tools, for example This figure was produced with ICM-Pro from Molsoft (Abagyan et al., 2006BB1).

Journal logoSTRUCTURAL
ISSN: 2059-7983
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