2PPN

Crystal structure of FKBP12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.209 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural coupling between FKBP12 and buried water.

Szep, S.Park, S.Boder, E.T.Van Duyne, G.D.Saven, J.G.

(2009) Proteins 74: 603-611

  • DOI: https://doi.org/10.1002/prot.22176
  • Primary Citation of Related Structures:  
    2PPN, 2PPO, 2PPP

  • PubMed Abstract: 

    Globular proteins often contain structurally well-resolved internal water molecules. Previously, we reported results from a molecular dynamics study that suggested that buried water (Wat3) may play a role in modulating the structure of the FK506 binding protein-12 (FKBP12) (Park and Saven, Proteins 2005; 60:450-463). In particular, simulations suggested that disrupting a hydrogen bond to Wat3 by mutating E60 to either A or Q would cause a structural perturbation involving the distant W59 side chain, which rotates to a new conformation in response to the mutation. This effectively remodels the ligand-binding pocket, as the side chain in the new conformation is likely to clash with bound FK506. To test whether the protein structure is in effect modulated by the binding of a buried water in the distance, we determined high-resolution (0.92-1.29 A) structures of wild-type FKBP12 and its two mutants (E60A, E60Q) by X-ray crystallography. The structures of mutant FKBP12 show that the ligand-binding pocket is indeed remodeled as predicted by the substitution at position 60, even though the water molecule does not directly interact with any of the amino acids of the binding pocket. Thus, these structures support the view that buried water molecules constitute an integral, noncovalent component of the protein structure. Additionally, this study provides an example in which predictions from molecular dynamics simulations are experimentally validated with atomic precision, thus showing that the structural features of protein-water interactions can be reliably modeled at a molecular level.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FK506-binding protein 1A107Homo sapiensMutation(s): 0 
Gene Names: FKBP1AFKBP1FKBP12
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62942
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.767α = 90
b = 62.7β = 113.66
c = 32.277γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description