4Y0Z

Trypsin in complex with with BPTI mutant AMINOBUTYRIC ACID

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history. 

Literature

Fluorine teams up with water to restore inhibitor activity to mutant BPTI.

Ye, S., Loll, B., Berger, A.A., Mulow, U., Alings, C., Wahl, M.C., Koksch, B.

(2015) Chem Sci 6: 5246-5254

  • DOI: 10.1039/c4sc03227f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Introducing fluorine into molecules has a wide range of effects on their physicochemical properties, often desirable but in most cases unpredictable. The fluorine atom imparts the C-F bond with low polarizability and high polarity, and significantly ...

    Introducing fluorine into molecules has a wide range of effects on their physicochemical properties, often desirable but in most cases unpredictable. The fluorine atom imparts the C-F bond with low polarizability and high polarity, and significantly affects the behavior of neighboring functional groups, in a covalent or noncovalent manner. Here, we report that fluorine, present in the form of a single fluoroalkyl amino acid side chain in the P1 position of the well-characterized serine-protease inhibitor BPTI, can fully restore inhibitor activity to a mutant that contains the corresponding hydrocarbon side chain at the same site. High resolution crystal structures were obtained for four BPTI variants in complex with bovine β-trypsin, revealing changes in the stoichiometry and dynamics of water molecules in the S1 subsite. These results demonstrate that the introduction of fluorine into a protein environment can result in "chemical complementation" that has a significantly favorable impact on protein-protein interactions.

    Organizational Affiliation: 

    Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry , Takustr. 3 , Berlin, 14195 , Germany . Email: beate.koksch@fu-berlin.de ; ; Tel: +49-30-83855344.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cationic trypsin
E
223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pancreatic trypsin inhibitor
I
58Bos taurusMutation(s): 1 
Find proteins for P00974 (Bos taurus)
Go to UniProtKB:  P00974
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
E, I
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
I
L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.134 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 74.907α = 90.00
b = 82.299β = 90.00
c = 123.352γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyGraduate 25 School GRK 1582/1

Revision History 

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-08-26
    Type: Database references
  • Version 2.0: 2018-04-18
    Type: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations