1FKF

ATOMIC STRUCTURE OF FKBP-FK506, AN IMMUNOPHILIN-IMMUNOSUPPRESSANT COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1FKF/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1991-05-07 Released: 1991-07-15 
• Deposition Author(s): Vanduyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L., Clardy, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Work: 0.170 

Literature

Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex.

Van Duyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L., Clardy, J.

(1991) Science 252: 839-842

• PubMed: 1709302 
• DOI: https://doi.org/10.1126/science.1709302
• Primary Citation of Related Structures:  
  1FKF


• PubMed Abstract: 
  

  The structure of the human FK506 binding protein (FKBP), complexed with the immunosuppressant FK506, has been determined to 1.7 angstroms resolution by x-ray crystallography. The conformation of the protein changes little upon complexation, but the conformation of FK506 is markedly different in the bound and unbound forms. The drug's association with the protein involves five hydrogen bonds, a hydrophobic binding pocket lined with conserved aromatic residues, and an unusual carbonyl binding pocket. The nature of this complex has implications for the mechanism of rotamase catalysis and for the biological actions of FK506 and rapamycin.

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Organizational Affiliation: 

Department of Chemistry, Baker Laboratory, Cornell University, Ithaca, NY 14853-1301.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.64 kDa 
• Atom Count: 968 
• Modelled Residue Count: 107 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FK506 BINDING PROTEIN	A	107	Homo sapiens	Mutation(s): 0  EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens) Explore P62942  Go to UniProtKB:  P62942
PHAROS:  P62942 GTEx:  ENSG00000088832

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FK5	B [auth A]	8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN C44 H69 N O12 QJJXYPPXXYFBGM-LFZNUXCKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FK5	BindingDB:  1FKF	Ki: 0.4 (nM) from 1 assay(s)
		Kd: min: 0.2, max: 0.4 (nM) from 2 assay(s)
		IC50: min: 2.3, max: 1000 (nM) from 3 assay(s)
		EC50: 0.9 (nM) from 1 assay(s)
	PDBBind:  1FKF	Kd: 0.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Work: 0.170 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.07	α = 90
b = 58.07	β = 90
c = 55.65	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1991-07-15 
Deposition Author(s): Vanduyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L., Clardy, J.

Revision History  

• Version 1.0: 1991-07-15
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.5: 2024-02-07
  Changes: Data collection, Database references, Derived calculations