Figure 1.
Figure 1. (A) Overall structure of CypD in complex with CsA.
CypD and CsA are shown as ribbon- and stick-models,
respectively. Panels A, B, and D were drawn with PyMOL
(http://www.pymol.org). (B) Close-up view of CsA superimposed on
its Fo-Fc omit electron density map (blue mesh) contoured at 6.0
.
(C) Binding geometry of CsA on CypD. Green circles mark the CsA
atoms involved in the hydrophobic contact with CypD. The CypD
residues in green ellipsoids are involved in the hydrophobic
interactions with CsA. The red dotted lines represent hydrogen
bonding. This panel was prepared based on a scheme drawn with
LIGPLOT.[21] Abbreviations of CsA residues: Bmt,
(4R)-4[(E)-2-butenyl]-4,N-dimethyl-L-threonine; Aba: L- -aminobutyric
acid, Sar: sarcosine, Mle, N-methyl leucine; Dal, D-alanine;
Mva, N-methyl valine. (D) Distribution of the conserved residues
among human cyclophilins represented on the surface of the
present CypD-CsA structure. Residues conserved in all five known
human cyclophilins (CypA, CypB, CypC, CypD, and CypE) are shown
in red. CypD residues conserved in 3 of 4, 2 of 4, and 1 of 4
other cyclophilins are shown in orange, yellow, and green,
respectively, and the unconserved CypD residues in the other
four cyclophilins are shown in blue. CsA is shown as a stick
model.
The above figure is reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2008,
70,
1635-1639)
copyright 2008.
.
(C) Binding geometry of CsA on CypD. Green circles mark the CsA
atoms involved in the hydrophobic contact with CypD. The CypD
residues in green ellipsoids are involved in the hydrophobic
interactions with CsA. The red dotted lines represent hydrogen
bonding. This panel was prepared based on a scheme drawn with
LIGPLOT.[21] Abbreviations of CsA residues: Bmt,
(4R)-4[(E)-2-butenyl]-4,N-dimethyl-L-threonine; Aba: L- 
-aminobutyric
acid, Sar: sarcosine, Mle, N-methyl leucine; Dal, D-alanine;
Mva, N-methyl valine. (D) Distribution of the conserved residues
among human cyclophilins represented on the surface of the
present CypD-CsA structure. Residues conserved in all five known
human cyclophilins (CypA, CypB, CypC, CypD, and CypE) are shown
in red. CypD residues conserved in 3 of 4, 2 of 4, and 1 of 4
other cyclophilins are shown in orange, yellow, and green,
respectively, and the unconserved CypD residues in the other
four cyclophilins are shown in blue. CsA is shown as a stick
model.