1CYN

CYCLOPHILIN B COMPLEXED WITH [D-(CHOLINYLESTER)SER8]-CYCLOSPORIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

X-Ray Structure of a Cyclophilin B/Cyclosporin Complex: Comparison with Cyclophilin a and Delineation of its Calcineurin-Binding Domain.

Mikol, V.Kallen, J.Walkinshaw, M.D.

(1994) Proc Natl Acad Sci U S A 91: 5183

  • DOI: 10.1073/pnas.91.11.5183
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of a complex between recombinant human cyclophilin B (CypB) and a cyclosporin A (CsA) analog has been determined and refined at 1.85-A resolution to a crystallographic R factor of 16.0%. The overall structures of CypB and of cyc ...

    The crystal structure of a complex between recombinant human cyclophilin B (CypB) and a cyclosporin A (CsA) analog has been determined and refined at 1.85-A resolution to a crystallographic R factor of 16.0%. The overall structures of CypB and of cyclophilin A (CypA) are similar; however, significant differences occur in two loops and at the N and C termini. The CsA-binding pocket in CypB has the same structure as in CypA and cyclosporin shows a similar bound conformation and network of interactions in both CypB and CypA complexes. The network of the water-mediated contacts is also essentially conserved. The higher potency of the CypB/CsA complex versus CypA/CsA in inhibiting the Ca(2+)- and calmodulin-dependent protein phosphatase calcineurin is discussed in terms of the structural differences between the two complexes. The three residues Arg90, Lys113, and Ala128 and the loop containing Arg158 on the surface of CypB are likely to modulate the differences in calcineurin inhibition between CypA and CypB.


    Related Citations: 
    • X-Ray Structure of a Monomeric Cyclophilin A- Cyclosporin a Crystal Complex at 2.1 A Resolution.
      Mikol, V., Kallen, J., Pflugl, G., Walkinshaw, M.D.
      (1993) J Mol Biol 234: 1119
    • A Novel Secreted Cyclophilin-Like Protein (Scylp)
      Spik, G., Haendler, B., Delemas, O., Mariller, C., Chamoux, M., Maes, P., Tartar, A., Montreuil, J., Stedman, K., Kocher, H.P., Keller, R., Hiestand, P.C., Movva, R.
      (1991) J Biol Chem 266: 10735

    Organizational Affiliation

    Preclinical Research, Sandoz AG, Basel, Switzerland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE B
A
178Homo sapiensMutation(s): 0 
Gene Names: CYCLOPHILINPPIBCYPB
EC: 5.2.1.8
Find proteins for P23284 (Homo sapiens)
Go to UniProtKB:  P23284
NIH Common Fund Data Resources
PHAROS  P23284
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYCLOSPORIN A
C
11Tolypocladium inflatumMutation(s): 1 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002324
Query on PRD_002324
C [D-(CHOLINYLESTER)SER8]-CYCLOSPORINCyclic peptide /  Immunosuppressant

--

Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
CL-PEPTIDE LINKINGC4 H9 N O2ALA
BMT
Query on BMT
CL-PEPTIDE LINKINGC10 H19 N O3THR
MLE
Query on MLE
CL-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA
CL-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
CPEPTIDE LINKINGC3 H7 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.46α = 90
b = 46.944β = 90
c = 115.442γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-01-29
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 1.5: 2018-09-12
    Changes: Data collection, Other, Structure summary