Figure 2.
Figure 2. Structures of LF in complex with peptides and
inhibitors. Molecular surface of LF is colored by charge
(red, negative; blue, positive), with Zn2+ as a solid sphere
(cyan) and the model of the peptide or inhibitor in
ball-and-stick representation. The individual electron density
surrounding each molecule is a 2F[o] - F[c] difference map
calculated at the respective final resolution and contoured at
1.0 .
(a) LF20 (yellow) in the absence of Zn2+, resolution limit 2.85
Å. The model of bound LF20 shows the sequence VYPYPMEPT
(residues 8 -16 of the 20-residue-long LF20). This is the
ordered region, and the electron density is clearly visible in
difference maps (2F[o] - F[c] and F[o] - F[c]) calculated from
crystal X-ray diffraction data. (b,c) SHAc-YPM (white, labeled
YPM), resolution limit 3.50 Å, and GM6001 (green), resolution
limit 2.70 Å, respectively. Continuous electron density extends
from the zinc atom to the metal-chelating moieties of the
inhibitors (hydroxamate and thioacetyl, respectively). (d) The
superposed individual complex structures of all three target
molecules from a -c in the substrate-binding groove of LF, using
the surface calculated for LF -LF20. The targets are all bound
in the same N-to-C peptide orientation. (e) An overview of LF
bound to the targets LF20, GM6001 and SHAc-YPM, superposed and
colored as in d. The molecular surface was calculated from the
LF -LF20 complex. The domains in LF are labeled I -IV. The
catalytic site is in domain IV, where the zinc atom (not shown
in this figure) is bound. These figures were prepared using
SPOCK (http://mackerel.tamu.edu/spock/).
The above figure is reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2004,
11,
60-66)
copyright 2004.
.
(a) LF20 (yellow) in the absence of Zn2+, resolution limit 2.85
Å. The model of bound LF20 shows the sequence VYPYPMEPT
(residues 8 -16 of the 20-residue-long LF20). This is the
ordered region, and the electron density is clearly visible in
difference maps (2F[o] - F[c] and F[o] - F[c]) calculated from
crystal X-ray diffraction data. (b,c) SHAc-YPM (white, labeled
YPM), resolution limit 3.50 Å, and GM6001 (green), resolution
limit 2.70 Å, respectively. Continuous electron density extends
from the zinc atom to the metal-chelating moieties of the
inhibitors (hydroxamate and thioacetyl, respectively). (d) The
superposed individual complex structures of all three target
molecules from a -c in the substrate-binding groove of LF, using
the surface calculated for LF -LF20. The targets are all bound
in the same N-to-C peptide orientation. (e) An overview of LF
bound to the targets LF20, GM6001 and SHAc-YPM, superposed and
colored as in d. The molecular surface was calculated from the
LF -LF20 complex. The domains in LF are labeled I -IV. The
catalytic site is in domain IV, where the zinc atom (not shown
in this figure) is bound. These figures were prepared using
SPOCK (http://mackerel.tamu.edu/spock/).