1IKF | pdb_00001ikf

A CONFORMATION OF CYCLOSPORIN A IN AQUEOUS ENVIRONMENT REVEALED BY THE X-RAY STRUCTURE OF A CYCLOSPORIN-FAB COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1IKF/pdb

• Classification: IMMUNE SYSTEM/IMMUNOSUPPRESSANT
• Organism(s): Homo sapiens, Tolypocladium inflatum
• Mutation(s): No 


• Deposited: 1993-12-09 Released: 1995-03-31 
• Deposition Author(s): Vix, O., Altschuh, D., Rees, B., Thierry, J.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

A Conformation of Cyclosporin a in Aqueous Environment Revealed by the X-Ray Structure of a Cyclosporin-Fab Complex.

Altschuh, D., Vix, O., Rees, B., Thierry, J.C.

(1992) Science 256: 92

• PubMed: 1566062 
• DOI: https://doi.org/10.1126/science.1566062
• Primary Citation Related Structures: 
  1IKF


• PubMed Abstract: 
  

  The conformation of the immunosuppressive drug cyclosporin A (CsA) in a complex with a Fab molecule has been established by crystallographic analysis to 2.65 angstrom resolution. This conformation of CsA is similar to that recently observed in the complex with the rotamase cyclophilin, its binding protein in vivo, and totally different from its conformation in an isolated form as determined from x-ray and nuclear magnetic resonance analysis. Because the surfaces of CsA interacting with cyclophilin or with the Fab are not identical, these results suggest that the conformation of CsA observed in the bound form preexists in aqueous solution and is not produced by interaction with the proteins.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.55 kDa 
• Atom Count: 3,651 
• Modeled Residue Count: 453 
• Deposited Residue Count: 453 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG1-KAPPA R45-45-11 FAB (LIGHT CHAIN)	A [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG1-KAPPA R45-45-11 FAB (HEAVY CHAIN)	B [auth H]	228	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOSPORIN A	C	11	Tolypocladium inflatum	Mutation(s): 0

Small Molecules

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	C	L-PEPTIDE LINKING	C4 H9 N O2		ALA
BMT	C	L-PEPTIDE LINKING	C10 H19 N O3		THR
DAL	C	D-PEPTIDE LINKING	C3 H7 N O2		--
MLE	C	L-PEPTIDE LINKING	C7 H15 N O2		LEU
MVA	C	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	C	PEPTIDE LINKING	C3 H7 N O2		GLY

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000142	C	Cyclosporin A	Cyclic peptide / Immunosuppressant

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.6	α = 90
b = 70.2	β = 90
c = 118.4	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-03-31 
Deposition Author(s): Vix, O., Altschuh, D., Rees, B., Thierry, J.-C.

Revision History  

• Version 1.0: 1995-03-31
  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: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other