Experimental Data Snapshot

  • Resolution: 2.6 Å
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history


The second Kunitz domain of human tissue factor pathway inhibitor: cloning, structure determination and interaction with factor Xa.

Burgering, M.J.Orbons, L.P.van der Doelen, A.Mulders, J.Theunissen, H.J.Grootenhuis, P.D.Bode, W.Huber, R.Stubbs, M.T.

(1997) J.Mol.Biol. 269: 395-407

  • DOI: 10.1006/jmbi.1997.1029
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tissue Factor Pathway Inhibitor (TFPI) is a 36 kDa glycoprotein that helps maintain haemostasis by inhibiting Factor Xa and the Factor VIIa/Tissue Factor (TF) complex. TFPI contains three tandemly linked Kunitz inhibitor domains, of which the second ...

    Tissue Factor Pathway Inhibitor (TFPI) is a 36 kDa glycoprotein that helps maintain haemostasis by inhibiting Factor Xa and the Factor VIIa/Tissue Factor (TF) complex. TFPI contains three tandemly linked Kunitz inhibitor domains, of which the second inhibits factor Xa. We have undertaken a multidisciplinary approach to study the structure and function of the second Kunitz domain of TFPI, with a view towards the rational design of factor Xa inhibitors. Amino acid residues 93 to 154 of the mature TFPI protein, corresponding to the second Kunitz domain (TFPI-kII), were expressed in Escherichia coli. The protein was purified to near homogeneity by ion exchange, hydrophobic interaction, and size exclusion chromatography, respectively. TFPI-kII is a potent factor Xa inhibitor with a Ki of 1.5 x 10(-10) M, a value that does not differ significantly from that of intact TFPI. The three-dimensional structure of TFPI-kII in aqueous solution was determined by 1H nuclear magnetic resonance spectroscopy (NMR). A set of 30 conformers was calculated with the program DIANA using 906 distance constraints derived from nuclear Overhauser effects and 23 dihedral angle constraints. This set, representing the solution structure of TFPI-kII, has an average root-mean-square deviation of 0.78 A for the backbone atoms and 1.38 A for all heavy atoms of residues 1 to 58. The structure of TFPI-kII has also been determined in complex with porcine trypsin using X-ray crystallographic techniques. The complex has been solved to a resolution of 2.6 A, with a final R-factor of 16.2%. Comparison of the NMR derived structure with that of TFPI-kII in complex with trypsin reveals little divergence of the two structures, with the exception of residue Tyr17. Superposition of the trypsin:TFPI-kII complex on factor Xa provides insights into macromolecular determinants for the inhibition of factor Xa. Complexation would require a degree of reorganisation of factor Xa residues, in particular of TyrF99, but also perhaps of the F148-loop. The interaction was further investigated using restrained molecular dynamics. Electrostatic interactions would appear to play a major role. The reorganisation of factor Xa is in contrast to the proposed factor Xa:TAP interaction, where TAP would bind to the "ground state" structure of factor Xa.

    Related Citations: 
    • The Three-Dimensional Structure of Recombinant Leech-Derived Tryptase Inhibitor in Complex with Trypsin. Implications for the Structure of Human Mast Cell Tryptase and its Inhibition
      Stubbs, M.T.,Morenweiser, R.,Sturzebecher, J.,Bauer, M.,Bode, W.,Huber, R.,Piechottka, G.P.,Matschiner, G.,Sommerhoff, C.P.,Fritz, H.,Auerswald, E.A.
      (1997) J.Biol.Chem. 272: 19931
    • 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
    • X-Ray Structure of Active Site-Inhibited Clotting Factor Xa. Implications for Drug Design and Substrate Recognition
      Brandstetter, H.,Kuhne, A.,Bode, W.,Huber, R.,Von Der Saal, W.,Wirthensohn, K.,Engh, R.A.
      (1996) J.Biol.Chem. 271: 29988
    • Structure of Human Des(1-45) Factor Xa at 2.2 A Resolution
      Padmanabhan, K.,Padmanabhan, K.P.,Tulinsky, A.,Park, C.H.,Bode, W.,Huber, R.,Blankenship, D.T.,Cardin, A.D.,Kisiel, W.
      (1993) J.Mol.Biol. 232: 947
    • Structural Aspects of Factor Xa Inhibition
      Stubbs II, M.T.
      (1996) Curr.Pharm.Des. 2: 543
    • The Ornithodorin-Thrombin Crystal Structure, a Key to the Tap Enigma?
      Van De Locht, A.,Stubbs, M.T.,Bode, W.,Friedrich, T.,Bollschweiler, C.,Hoffken, W.,Huber, R.
      (1996) Embo J. 15: 6011

    Organizational Affiliation

    Scientific Development Group, N.V. Organon, Oss, The Netherlands.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A, B
223Sus scrofaMutation(s): 0 
Find proteins for P00761 (Sus scrofa)
Go to UniProtKB:  P00761
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C, D
58Homo sapiensMutation(s): 0 
Gene Names: TFPI (LACI, TFPI1)
Find proteins for P10646 (Homo sapiens)
Go to Gene View: TFPI
Go to UniProtKB:  P10646
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download SDF File 
Download CCD File 
A, B
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 2.6 Å
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.900α = 90.00
b = 96.200β = 90.00
c = 137.700γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
XDSdata scaling
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance