1K1J

BOVINE TRYPSIN-INHIBITOR COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition.

Dullweber, F.Stubbs, M.T.Musil, D.Sturzebecher, J.Klebe, G.

(2001) J Mol Biol 313: 593-614

  • DOI: 10.1006/jmbi.2001.5062
  • Primary Citation of Related Structures:  
    1K1N, 1K1M, 1K1L, 1K1J, 1K1I, 1K22, 1K1P, 1K21, 1K1O

  • PubMed Abstract: 
  • The binding of a series of low molecular weight ligands towards trypsin and thrombin has been studied by isothermal titration calorimetry and protein crystallography. In a series of congeneric ligands, surprising changes of protonation states occur a ...

    The binding of a series of low molecular weight ligands towards trypsin and thrombin has been studied by isothermal titration calorimetry and protein crystallography. In a series of congeneric ligands, surprising changes of protonation states occur and are overlaid on the binding process. They result from induced pK(a) shifts depending on the local environment experienced by the ligand and protein functional groups in the complex (induced dielectric fit). They involve additional heat effects that must be corrected before any conclusion on the binding enthalpy (DeltaH) and entropy (DeltaS) can be drawn. After correction, trends in both contributions can be interpreted in structural terms with respect to the hydrogen bond inventory or residual ligand motions. For all inhibitors studied, a strong negative heat capacity change (DeltaC(p)) is detected, thus binding becomes more exothermic and entropically less favourable with increasing temperature. Due to a mutual compensation, Gibbs free energy remains virtually unchanged. The strong negative DeltaC(p) value cannot solely be explained by the removal of hydrophobic surface portions of the protein or ligand from water exposure. Additional contributions must be considered, presumably arising from modulations of the local water structure, changes in vibrational modes or other ordering parameters. For thrombin, smaller negative DeltaC(p) values are observed for ligand binding in the presence of sodium ions compared to the other alkali ions, probably due to stabilising effects on the protein or changes in the bound water structure.


    Related Citations: 
    • Structural and Functional Analyses of Benzamidine-Based Inhibitors in Complex with Trypsin: Implications for the Inhibition of Factor Xa, Tpa, and Urokinase
      Renatus, M., Bode, W., Huber, R., Stuerzebecher, J., Stubbs, M.T.
      (1998) J Med Chem 41: 5445
    • Crystal Structures of Factor Xa Specific Inhibitors in Complex with Trypsin: Structural Grounds for Inhibition of Factor Xa and Selectivity Against Thrombin
      Stubbs, M.T., Huber, R., Bode, W.
      (1995) FEBS Lett 375: 103
    • A Player of Many Parts: The Spotlight Falls on Thrombin'S Structure
      Stubbs, M.T., Bode, W.
      (1993) Thromb Res 69: 1

    Organizational Affiliation

    Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg (Lahn), Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRYPSINA223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FD2
Query on FD2

Download CCD File 
A
N-ALPHA-(2-NAPHTHYLSULFONYL)-N(3-AMIDINO-L-PHENYLALANINYL)ISOPIPECOLINIC ACID METHYL ESTER
C27 H30 N4 O5 S
JJLGQWCKMHPBEB-DEOSSOPVSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FD2Kd:  28   nM  Binding MOAD
FD2Ki:  36   nM  BindingDB
FD2Kd :  28   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.941α = 90
b = 68.913β = 90
c = 63.603γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2001-09-25 
  • Released Date: 2001-11-28 
  • Deposition Author(s): Stubbs, M.T.

Revision History 

  • Version 1.0: 2001-11-28
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance