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PDBsum entry 1cwo

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Isomerase/immunosuppressant PDB id
1cwo
Jmol
Contents
Protein chains
165 a.a. *
11 a.a. *
Waters ×648
* Residue conservation analysis

References listed in PDB file
Key reference
Title Conformational differences of an immunosuppressant peptolide in a single crystal and in a crystal complex with human cyclophilin a.
Authors V.Mikol, P.Taylor, J.Kallen, M.D.Walkinshaw.
Ref. J Mol Biol, 1998, 283, 451-461. [DOI no: 10.1006/jmbi.1998.2109]
PubMed id 9769217
Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a perfect match.
Abstract
The crystal structure of (Thr2, Leu5, d-Hiv8, Leu10)-cyclosporin (cyclic peptolide SDZ 214-103) has been determined as the unbound crystal form and as a complex with human cyclophilin A. This pair of structures provides an example of a significant difference in conformation between free and bound ligand in crystals. The conformation of the unbound form is unlike that of both free and bound conformations of cyclosporin A (with the amide bond between residues 3 and 4 in the cis conformation), while the bound conformation is similar to that of CsA bound to cyclophilin. The cyclophilin-bound conformations of both ligands are similar, though this involves a significantly different waterellipsisligand hydrogen-bonding structure, which compensates for the chemical differences between the two ligands.
Figure 6.
Figure 6. Overlay of X-ray struc- tures of CypA/peptolide-214103 (red) and CypA/CsA (yellow). Residue numbers for the peptolide and CsA ligands are shown. Only C atoms for CypA are shown. All non-hydrogen atoms are shown for the two ligands.
Figure 8.
Figure 8. A comparison of the binding of Thr2 side- chain of peptolide-214103 and the Abu side-chain of CsA. The cyclophilin/peptolide- 214103 is drawn with white bonds and type-coloured atoms. The least-squares fit- ted cyclophilin/CsA struc- ture (Kallen et al., 1998) is coloured yellow. The CG atom of the Thr2 side-chain takes up a very similar pos- ition to that of the CG atom of the Abu side-chain of CsA. The hydroxy group can then form three possible hydrogen bonds (Table 3) drawn in green. The van der Waals sur- face for the Abu-pocket is represented as a blue chicken- wire and provides a picture of the available space for the ligand. Ligand atoms pene- trating this surface would be energetically disfavoured. The red contours indicate regions where hydrogen- bonding donor or acceptor atoms can form favourable hydrogen-bonding interactions with the protein. Water mol- ecules, drawn as red spheres are found in these regions.
The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 283, 451-461) copyright 1998.
PROCHECK
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