PDBsum entry 2z6w

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Isomerase/immunosuppressant PDB id
Protein chains
164 a.a. *
11 a.a. *
Waters ×524
* Residue conservation analysis
PDB id:
Name: Isomerase/immunosuppressant
Title: Crystal structure of human cyclophilin d in complex with cyc
Structure: Peptidyl-prolyl cis-trans isomerase. Chain: a, b. Fragment: residues 2-165. Synonym: ppiase, rotamase, cyclophilin d. Engineered: yes. Mutation: yes. Cyclosporin a. Chain: m, n. Synonym: ciclosporin, ciclosporine.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ppif, cyp3. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Tolypocladium inflatum. Organism_taxid: 29910
0.96Å     R-factor:   0.130     R-free:   0.153
Authors: K.Kajitani,M.Fujihashi,Y.Kobayashi,S.Shimizu,Y.Tsujimoto,K.M
Key ref:
K.Kajitani et al. (2008). Crystal structure of human cyclophilin D in complex with its inhibitor, cyclosporin A at 0.96-A resolution. Proteins, 70, 1635-1639. PubMed id: 18076075 DOI: 10.1002/prot.21855
09-Aug-07     Release date:   29-Apr-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P30405  (PPIF_HUMAN) -  Peptidyl-prolyl cis-trans isomerase F, mitochondrial
207 a.a.
164 a.a.*
Protein chains
No UniProt id for this chain
Struc: 11 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
= peptidylproline (omega=0)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein folding   2 terms 
  Biochemical function     peptidyl-prolyl cis-trans isomerase activity     1 term  


    Added reference    
DOI no: 10.1002/prot.21855 Proteins 70:1635-1639 (2008)
PubMed id: 18076075  
Crystal structure of human cyclophilin D in complex with its inhibitor, cyclosporin A at 0.96-A resolution.
K.Kajitani, M.Fujihashi, Y.Kobayashi, S.Shimizu, Y.Tsujimoto, K.Miki.
No abstract given.

  Selected figure(s)  
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 ( (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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20175748 K.E.Muirhead, E.Borger, L.Aitken, S.J.Conway, and F.J.Gunn-Moore (2010).
The consequences of mitochondrial amyloid beta-peptide in Alzheimer's disease.
  Biochem J, 426, 255-270.  
19832699 S.Malouitre, H.Dube, D.Selwood, and M.Crompton (2010).
Mitochondrial targeting of cyclosporin A enables selective inhibition of cyclophilin-D and enhanced cytoprotection after glucose and oxygen deprivation.
  Biochem J, 425, 137-148.  
20676357 T.L.Davis, J.R.Walker, V.Campagna-Slater, P.J.Finerty, R.Paramanathan, G.Bernstein, F.MacKenzie, W.Tempel, H.Ouyang, W.H.Lee, E.Z.Eisenmesser, and S.Dhe-Paganon (2010).
Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases.
  PLoS Biol, 8, e1000439.  
19005620 A.Czogalla (2009).
Oral cyclosporine A--the current picture of its liposomal and other delivery systems.
  Cell Mol Biol Lett, 14, 139-152.  
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