Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Work: 0.173 

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Reconstructing the Binding Site of Factor Xa in Trypsin Reveals Ligand-induced Structural Plasticity

Reyda, S.Sohn, C.Klebe, G.Rall, K.Ullmann, D.Jakubke, H.D.Stubbs, M.T.

(2003) J Mol Biol 325: 963-977

  • DOI: 10.1016/s0022-2836(02)01337-2
  • Primary Citation of Related Structures:  
    1QL9, 1J17, 1J16, 1J15, 1J14

  • PubMed Abstract: 
  • In order to investigate issues of selectivity and specificity in protein-ligand interactions, we have undertaken the reconstruction of the binding pocket of human factor Xa in the structurally related rat trypsin by site-directed mutagenesis. Three s ...

    In order to investigate issues of selectivity and specificity in protein-ligand interactions, we have undertaken the reconstruction of the binding pocket of human factor Xa in the structurally related rat trypsin by site-directed mutagenesis. Three sequential regions (the "99"-, the "175"- and the "190"- loops) were selected as representing the major structural differences between the ligand binding sites of the two enzymes. Wild-type rat trypsin and variants X99rT and X(99/175/190)rT were expressed in yeast, and analysed for their interaction with factor Xa and trypsin inhibitors. For most of the inhibitors studied, progressive loop replacement at the trypsin surface resulted in inhibitory profiles akin to factor Xa. Crystals of the variants were obtained in the presence of benzamidine (3), and could be soaked with the highly specific factor Xa inhibitor (1). Binding of the latter to X99rT results in a series of structural adaptations to the ligand, including the establishment of an "aromatic box" characteristic of factor Xa. In X(99/175/190)rT, introduction of the 175-loop results in a surprising re-orientation of the "intermediate helix", otherwise common to trypsin and factor Xa. The re-orientation is accompanied by an isomerisation of the Cys168-Cys182 disulphide bond, and burial of the critical Phe174 side-chain. In the presence of (1), a major re-organisation of the binding site takes place to yield a geometry identical to that of factor Xa. In all, binding of (1) to trypsin and its variants results in significant structural rearrangements, inducing a binding surface strongly reminiscent of factor Xa, against which the inhibitor was optimised. The structural data reveal a plasticity of the intermediate helix, which has been implicated in the functional cofactor dependency of many trypsin-like serine proteinases. This approach of grafting loops onto scaffolds of known related structures may serve to bridge the gap between structural genomics and drug design.

    Related Citations: 
    • pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design
      Stubbs, M.T., Reyda, S., Dullweber, F., Moeller, M., Klebe, G., Dorsch, D., Mederski, W.W.K.R., Wurziger, H.
      (2002) Chembiochem 3: 246
    • Structural and functional analyses of benzamidine-based inhibitors in complex with trypsin: implications for the inhibition of factor Xa, tPA, and urokinas
      Renatus, M., Bode, W., Huber, R., Stuerzebecher, J., Stubbs, M.T.
      (1998) J Med Chem 41: 5445
    • Structural Aspects of Factor Xa Inhibition
      Stubbs, M.T.
      (1996) Curr Pharm Des 2: 543
    • 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

    Organizational Affiliation

    Institut für Pharmazeutische Chemie der Philipps-Universität Marburg, Marbacher Weg 6, D35032, Marburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Trypsin II, anionicA223Rattus norvegicusMutation(s): 7 
Gene Names: Prss2Try2
Find proteins for P00763 (Rattus norvegicus)
Explore P00763 
Go to UniProtKB:  P00763
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on BEN

Download CCD File 
C7 H8 N2
 Ligand Interaction
Query on SO4

Download CCD File 
O4 S
 Ligand Interaction
Query on CA

Download CCD File 
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BENKi :  143000   nM  PDBBind
BENKi:  143000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Work: 0.173 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.7α = 90
b = 124.7β = 90
c = 124.7γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Deposited Date: 2002-11-30 
  • Released Date: 2002-12-23 
  • Deposition Author(s): Stubbs, M.T.

Revision History 

  • Version 1.0: 2002-12-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance