1D6O

NATIVE FKBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

X-ray structures of small ligand-FKBP complexes provide an estimate for hydrophobic interaction energies.

Burkhard, P.Taylor, P.Walkinshaw, M.D.

(2000) J.Mol.Biol. 295: 953-962

  • DOI: 10.1006/jmbi.1999.3411
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A new crystal form of native FK506 binding protein (FKBP) has been obtained which has proved useful in ligand binding studies. Three different small molecule ligand complexes and the native enzyme have been determined at higher resolution than 2.0 A. ...

    A new crystal form of native FK506 binding protein (FKBP) has been obtained which has proved useful in ligand binding studies. Three different small molecule ligand complexes and the native enzyme have been determined at higher resolution than 2.0 A. Dissociation constants of the related small molecule ligands vary from 20 mM for dimethylsulphoxide to 200 microM for tetrahydrothiophene 1-oxide. Comparison of the four available crystal structures shows that the protein structures are identical to within experimental error, but there are differences in the water structure in the active site. Analysis of the calculated buried surface areas of these related ligands provides an estimated van der Waals contribution to the binding energy of -0.5 kJ/A(2) for non-polar interactions between ligand and protein.


    Related Citations: 
    • Atomic Structure of the Rapamycin Human Immunophilin Fkbp-12 Complex
      Van Duyne, G.D.,Standaert, R.F.,Schreiber, S.L.,Clardy, J.
      (1991) J.Am.Chem.Soc. 113: 7433


    Organizational Affiliation

    Department of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, Basel, CH, 4056, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (FK506-BINDING PROTEIN)
A, B
107Homo sapiensGene Names: FKBP1A (FKBP1, FKBP12)
EC: 5.2.1.8
Find proteins for P62942 (Homo sapiens)
Go to Gene View: FKBP1A
Go to UniProtKB:  P62942
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NH4
Query on NH4

Download SDF File 
Download CCD File 
A, B
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.800α = 90.00
b = 36.450β = 96.00
c = 56.000γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
MADNESSdata reduction
ROTAVATAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-21
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-10-04
    Type: Derived calculations, Refinement description