spacer
spacer

PDBsum entry 1cwk

Go to PDB code: 
protein Protein-protein interface(s) links
Isomerase/immunosuppressant PDB id
1cwk
Jmol
Contents
Protein chains
165 a.a. *
11 a.a. *
Waters ×149
* Residue conservation analysis
PDB id:
1cwk
Name: Isomerase/immunosuppressant
Title: Human cyclophilin a complexed with 1-(6,7-dihydro)mebmt 2-va s-methyl)sarcosine cyclosporin
Structure: Peptidyl-prolyl cis-trans isomerase a. Chain: a. Synonym: ppiase, rotamase, cyclophilin a. Engineered: yes. Cyclosporin d. Chain: c. Synonym: cyclosporine, ciclosporin, ciclosporine. Engineered: yes. Mutation: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: cyclophilin. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Tolypocladium inflatum. Organism_taxid: 29910
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.165    
Authors: V.Mikol,J.Kallen,P.Taylor,M.D.Walkinshaw
Key ref:
J.Kallen et al. (1998). X-ray structures and analysis of 11 cyclosporin derivatives complexed with cyclophilin A. J Mol Biol, 283, 435-449. PubMed id: 9769216 DOI: 10.1006/jmbi.1998.2108
Date:
26-May-98     Release date:   15-Jul-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62937  (PPIA_HUMAN) -  Peptidyl-prolyl cis-trans isomerase A
Seq:
Struc:
165 a.a.
165 a.a.
Protein chain
No UniProt id for this chain
Struc: 11 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain A: E.C.5.2.1.8  - 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!
  Cellular component     extracellular region   8 terms 
  Biological process     viral reproduction   18 terms 
  Biochemical function     protein binding     7 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1998.2108 J Mol Biol 283:435-449 (1998)
PubMed id: 9769216  
 
 
X-ray structures and analysis of 11 cyclosporin derivatives complexed with cyclophilin A.
J.Kallen, V.Mikol, P.Taylor, M.D.Walkinshaw.
 
  ABSTRACT  
 
Eight new X-ray structures of different cyclophilin A/cyclosporin-derivative complexes are presented. These structures, combined with the existing three published cyclosporin complexes, provide a useful structural database for the analysis of protein-ligand interactions. The effect of small chemical differences on protein-ligand hydrogen-bonding, van der Waals interactions and water structure is presented.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Residue labelling scheme for CsA-analogues (see also Table 1). Atom labelling is according to the IUPAC convention. CN is the methyl carbon atom of the N-methylated amino acids. MLE for MeLeu; MVA for MeVal; BMT for MeBmt; ABU for Abu; SAR for Sar; VAL for Val; ALA for Ala; DAL for D-Ala. All amino acid residues with the exception of D-Ala8 (and Sar3) are in the L-configuration.
Figure 5.
Figure 5. Stereo picture of CsA/CypA with the most conserved water molecules. CsA is coloured magenta, CypA is coloured cyan and the 11 water molecules which occur in 10 or 11 of the 11 structures discussed in this paper are shown as labelled yellow spheres. The label corresponds to the number in Table 5 and also to the label of the water molecule in the deposited PDB file. The position of the sphere is the average position of the water molecules from the different structures which all refine to within 0.2 Å of each other.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 283, 435-449) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21245533 A.Kuglstatter, F.Mueller, E.Kusznir, B.Gsell, M.Stihle, R.Thoma, J.Benz, L.Aspeslet, D.Freitag, and M.Hennig (2011).
Structural basis for the cyclophilin A binding affinity and immunosuppressive potency of E-ISA247 (voclosporin).
  Acta Crystallogr D Biol Crystallogr, 67, 119-123.
PDB codes: 3odi 3odl
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.  
19180449 K.S.Keating, S.C.Flores, M.B.Gerstein, and L.A.Kuhn (2009).
StoneHinge: hinge prediction by network analysis of individual protein structures.
  Protein Sci, 18, 359-371.  
19923714 V.Venugopal, A.K.Datta, D.Bhattacharyya, D.Dasgupta, and R.Banerjee (2009).
Structure of cyclophilin from Leishmania donovani bound to cyclosporin at 2.6 A resolution: correlation between structure and thermodynamic data.
  Acta Crystallogr D Biol Crystallogr, 65, 1187-1195.
PDB code: 3eov
17225137 P.Mark, and L.Nilsson (2007).
A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide.
  Eur Biophys J, 36, 213-224.  
  17277440 V.Venugopal, B.Sen, A.K.Datta, and R.Banerjee (2007).
Structure of cyclophilin from Leishmania donovani at 1.97 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 60-64.
PDB code: 2haq
16782708 O.Yasuda, K.Fukuo, X.Sun, M.Nishitani, T.Yotsui, M.Higuchi, T.Suzuki, H.Rakugi, O.Smithies, N.Maeda, and T.Ogihara (2006).
Apop-1, a novel protein inducing cyclophilin D-dependent but Bax/Bak-related channel-independent apoptosis.
  J Biol Chem, 281, 23899-23907.  
15858260 D.Schlatter, R.Thoma, E.Küng, M.Stihle, F.Müller, E.Borroni, A.Cesura, and M.Hennig (2005).
Crystal engineering yields crystals of cyclophilin D diffracting to 1.7 A resolution.
  Acta Crystallogr D Biol Crystallogr, 61, 513-519.
PDB codes: 2bit 2biu
15832403 K.Levitsky, M.D.Boersma, C.J.Ciolli, and P.J.Belshaw (2005).
Exo-mechanism proximity-accelerated alkylations: investigations of linkers, electrophiles and surface mutations in engineered cyclophilin-cyclosporin systems.
  Chembiochem, 6, 890-899.  
14993672 G.Kontopidis, P.Taylor, and M.D.Walkinshaw (2004).
Enzymatic and structural characterization of non-peptide ligand-cyclophilin complexes.
  Acta Crystallogr D Biol Crystallogr, 60, 479-485.
PDB codes: 1w8l 1w8m 1w8v
15340912 M.I.Zavodszky, M.Lei, M.F.Thorpe, A.R.Day, and L.A.Kuhn (2004).
Modeling correlated main-chain motions in proteins for flexible molecular recognition.
  Proteins, 57, 243-261.  
12351834 R.Banerjee, M.Dutta, M.Sen, and A.K.Datta (2002).
Crystallization and preliminary X-ray analysis of cyclophilin from Leishmania donovani.
  Acta Crystallogr D Biol Crystallogr, 58, 1846-1847.  
11377203 P.Taylor, J.Dornan, A.Carrello, R.F.Minchin, T.Ratajczak, and M.D.Walkinshaw (2001).
Two structures of cyclophilin 40: folding and fidelity in the TPR domains.
  Structure, 9, 431-438.
PDB codes: 1ihg 1iip
11180378 Wu Sy, J.Dornan, G.Kontopidis, P.Taylor, and M.D.Walkinshaw (2001).
The First Direct Determination of a Ligand Binding Constant in Protein Crystals.
  Angew Chem Int Ed Engl, 40, 582-586.
PDB code: 1e8k
10679456 C.Schiene, and G.Fischer (2000).
Enzymes that catalyse the restructuring of proteins.
  Curr Opin Struct Biol, 10, 40-45.  
11058892 M.T.Ivery (2000).
Immunophilins: switched on protein binding domains?
  Med Res Rev, 20, 452-484.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.