1HRT

THE STRUCTURE OF A COMPLEX OF BOVINE ALPHA-THROMBIN AND RECOMBINANT HIRUDIN AT 2.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of a complex of bovine alpha-thrombin and recombinant hirudin at 2.8-A resolution.

Vitali, J.Martin, P.D.Malkowski, M.G.Robertson, W.D.Lazar, J.B.Winant, R.C.Johnson, P.H.Edwards, B.F.

(1992) J.Biol.Chem. 267: 17670-17678


  • PubMed Abstract: 
  • Crystals of the complex of bovine alpha-thrombin with recombinant hirudin variant 1 have space group C222(1) with cell constants a = 59.11, b = 102.62, and c = 143.26 A. The orientation and position of the thrombin component was determined by molecul ...

    Crystals of the complex of bovine alpha-thrombin with recombinant hirudin variant 1 have space group C222(1) with cell constants a = 59.11, b = 102.62, and c = 143.26 A. The orientation and position of the thrombin component was determined by molecular replacement and the hirudin molecule was fit in 2 magnitude of Fo - magnitude of Fc electron density maps. The structure was refined by restrained least squares and simulated annealing to R = 0.161 at 2.8-A resolution. The binding of hirudin to thrombin is generally similar to that observed in the crystals of human thrombin-hirudin. Several differences in the interactions of the COOH-terminal polypeptide of hirudin, specifically of residues Asp-55h, Phe-56h, Glu-57h, and Glu-58h, and a few differences in the interactions of the hirudin core, specifically of residues Asp-5h, Ser-19h, and Asn-20h, with thrombin from human thrombin-hirudin suggest that there is some flexibility in the binding of these 2 molecules. Most of the residues in the 9 subsites that bind fibrinopeptide A7-16 to thrombin also interact with the NH2-terminal domain of hirudin. The S1 subsite is a notable exception in that only 1 of its 6 residues, namely Ser-214, interacts with hirudin. The only difference between human and bovine thrombins that appears to influence the binding of hirudin is the replacement of Lys-149E by an acidic glutamate in the bovine enzyme.


    Organizational Affiliation

    Department of Biochemistry, Wayne State University, Detroit, Michigan 48201.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THROMBIN (SMALL SUBUNIT)
L
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 (LARGE SUBUNIT)
H
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
HIRUDIN
I
65Hirudo medicinalisMutation(s): 0 
Find proteins for P01050 (Hirudo medicinalis)
Go to UniProtKB:  P01050
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 59.110α = 90.00
b = 102.620β = 90.00
c = 143.260γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance