1BTH

STRUCTURE OF THROMBIN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The thrombin E192Q-BPTI complex reveals gross structural rearrangements: implications for the interaction with antithrombin and thrombomodulin.

van de Locht, A.Bode, W.Huber, R.Le Bonniec, B.F.Stone, S.R.Esmon, C.T.Stubbs, M.T.

(1997) EMBO J. 16: 2977-2984

  • DOI: 10.1093/emboj/16.11.2977

  • PubMed Abstract: 
  • Previous crystal structures of thrombin indicate that the 60-insertion loop is a rigid moiety that partially occludes the active site, suggesting that this structural feature plays a decisive role in restricting thrombin's specificity. This restricte ...

    Previous crystal structures of thrombin indicate that the 60-insertion loop is a rigid moiety that partially occludes the active site, suggesting that this structural feature plays a decisive role in restricting thrombin's specificity. This restricted specificity is typified by the experimental observation that thrombin is not inhibited by micromolar concentrations of basic pancreatic trypsin inhibitor (BPTI). Surprisingly, a single atom mutation in thrombin (E192Q) results in a 10(-8) M affinity for BPTI. The crystal structure of human thrombin mutant E192Q has been solved in complex with BPTI at 2.3 A resolution. Binding of the Kunitz inhibitor is accompanied by gross structural rearrangements in thrombin. In particular, thrombin's 60-loop is found in a significantly different conformation. Concomitant reorganization of other surface loops that surround the active site, i.e. the 37-loop, the 148-loop and the 99-loop, is observed. Thrombin can therefore undergo major structural reorganization upon strong ligand binding. Implications for the interaction of thrombin with antithrombin and thrombomodulin are discussed.


    Related Citations: 
    • Two Heads are Better Than One: Crystal Structure of the Insect Derived Double Domain Kazal Inhibitor Rhodniin in Complex with Thrombin
      Van De Locht, A.,Lamba, D.,Bauer, M.,Huber, R.,Friedrich, T.,Kroger, B.,Hoffken, W.,Bode, W.
      (1995) Embo J. 14: 5149
    • 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
    • The Refined 1.9 A Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment
      Bode, W.,Mayr, I.,Baumann, U.,Huber, R.,Stone, S.R.,Hofsteenge, J.
      (1989) Embo J. 8: 3467


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THROMBIN
L, J
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
THROMBIN
H, K
259Homo sapiensMutation(s): 1 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
BOVINE PANCREATIC TRYPSIN INHIBITOR
P, Q
58Bos taurusMutation(s): 0 
Find proteins for P00974 (Bos taurus)
Go to UniProtKB:  P00974
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 71.200α = 90.00
b = 74.500β = 92.50
c = 83.400γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-12-24
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance