1TBR

CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR RHODNIIN IN COMPLEX WITH THROMBIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 5149-5157

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rhodniin is a highly specific inhibitor of thrombin isolated from the assassin bug Rhodnius prolixus. The 2.6 Angstrum crystal structure of the non-covalent complex between recombinant rhodniin and bovine alpha-thrombin reveals that the two Kazal-typ ...

    Rhodniin is a highly specific inhibitor of thrombin isolated from the assassin bug Rhodnius prolixus. The 2.6 Angstrum crystal structure of the non-covalent complex between recombinant rhodniin and bovine alpha-thrombin reveals that the two Kazal-type domains of rhodniin bind to different sites of thrombin. The amino-terminal domain binds in a substrate-like manner to the narrow active-site cleft of thrombin; the imidazole group of the P1 His residue extends into the S1 pocket to form favourable hydrogen/ionic bonds with Asp189 at its bottom, and additionally with Glu192 at its entrance. The carboxy-terminal domain, whose distorted reactive-site loop cannot adopt the canonical conformation, docks to the fibrinogen recognition exosite via extensive electrostatic interactions. The rather acidic polypeptide linking the two domains is displaced from the thrombin surface, with none of its residues involved in direct salt bridges with thrombin. The tight (Ki = 2 x 10(-13) M) binding of rhodniin to thrombin is the result of the sum of steric and charge complementarity of the amino-terminal domain towards the active-site cleft, and of the electrostatic interactions between the carboxy-terminal domain and the exosite.


    Related Citations: 
    • A Kazal-Type Inhibitor with Thrombin Specificity from Rhodnius Prolixus
      Friedrich, T.,Kroger, B.,Bialojan, S.,Lemaire, H.G.,Hoffken, H.W.,Reuschenbach, P.,Otte, M.,Dodt, J.
      (1993) J.Biol.Chem. 268: 16216
    • Crystal Structure of the Thrombin-Hirudin Complex: A Novel Mode of Serine Protease Inhibition
      Grutter, M.G.,Priestle, J.P.,Rahuel, J.,Grossenbacher, H.,Bode, W.,Hofsteenge, J.,Stone, S.R.
      (1990) Embo J. 9: 2361
    • 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
    • The Structure of a Complex of Recombinant Hirudin and Human Alpha-Thrombin
      Rydel, T.J.,Ravichandran, K.G.,Tulinsky, A.,Bode, W.,Huber, R.,Roitsch, C.,Fenton II, J.W.
      (1990) Science 249: 277
    • Refined Structure of the Hirudin-Thrombin Complex
      Rydel, T.J.,Tulinsky, A.,Bode, W.,Huber, R.
      (1991) J.Mol.Biol. 221: 583
    • The Refined 1.9-A X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships
      Bode, W.,Turk, D.,Karshikov, A.
      (1992) Protein Sci. 1: 426


    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
49Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00735 (Bos taurus)
Go to Gene View: F2
Go to UniProtKB:  P00735
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
THROMBIN
H, K
259Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00735 (Bos taurus)
Go to Gene View: F2
Go to UniProtKB:  P00735
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RHODNIIN
R, S
103Rhodnius prolixusMutation(s): 0 
Find proteins for Q06684 (Rhodnius prolixus)
Go to UniProtKB:  Q06684
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 114.735α = 90.00
b = 112.297β = 94.97
c = 92.069γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
MOSFLMdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance