1HXF

HUMAN THROMBIN COMPLEX WITH HIRUDIN VARIANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The molecular environment of the Na+ binding site of thrombin.

Zhang, E.Tulinsky, A.

(1997) Biophys Chem 63: 185-200

  • DOI: 10.1016/s0301-4622(96)02227-2
  • Primary Citation of Related Structures:  
    1HXF, 1HXE

  • PubMed Abstract: 
  • When Na+ binds to thrombin, a conformational change is induced that renders the enzyme kinetically faster and more specific in the activation of fibrinogen. Two Na+ binding sites have here been identified crystallographically by exchanging Na+ with R ...

    When Na+ binds to thrombin, a conformational change is induced that renders the enzyme kinetically faster and more specific in the activation of fibrinogen. Two Na+ binding sites have here been identified crystallographically by exchanging Na+ with Rb+. One is intermolecular, found on the surface between two symmetry-related thrombin molecules. Since it is not present in thrombin crystal structures having different crystal systems, the other Na+ site is the functionally relevant one. The second site has octahedral coordination with the carbonyl oxygen atoms of Arg221A and Lys224 and four conserved water molecules. It is located near Asp189 of the S1 specificity site in an elongated solvent channel (8 x 18 A) formed by four antiparallel beta-strands between Cys182-Cys191 and Val213-Tyr228. This channel, extending from the active site to the opposite surface of the enzyme, was first noted in the hirudin-thrombin structure and contains about 20 conserved water molecules linked together by a hydrogen bonding network that connects to the main chain of thrombin. Although the antiparallel beta-strand interactions of the functional Na+ binding site are the same in prethrombin2, the loops between the strands are very different, so that Asp189 and Arg221A are not positioned properly for either substrate or Na+ binding in prethrombin2. A water molecule with octahedral coordination has also been identified in factor Xa at the topologically equivalent Na+ site position of thrombin. Since activated protein C shows enhanced activity with monovalant cation binding, the same position is probably utilized by Na+. Since thrombin crystals could not be grown in the absence of Na+, the cation was leached from Na(+)-bound thrombin crystals by diffusion/exchange. Although both Na+ and their coordinating water molecules were removed from the Na+ binding sites, the remainder of the thrombin structure was, unexpectedly, the same. The lack of an allosteric change is most likely attributable to crystal packing effects. Thus, the structure of the slow form remains to be established crystallographically.


    Related Citations: 
    • The Na+ Binding Site of Thrombin
      Di Cera, E., Guinto, E.R., Vindigni, A., Dang, Q.D., Ayala, Y.M., Wuyi, M., Tulinsky, A.
      (1995) J Biol Chem 270: 22089
    • The Isomorphous Structures of Prethrombin2, Hirugen-, and Ppack-Thrombin: Changes Accompanying Activation and Exosite Binding to Thrombin
      Vijayalakshmi, J., Padmanabhan, K.P., Mann, K.G., Tulinsky, A.
      (1994) Protein Sci 3: 2254
    • Refined Structure of the Hirudin-Thrombin Complex
      Rydel, T.J., Tulinsky, A., Bode, W., Huber, R.
      (1991) J Mol Biol 221: 583

    Organizational Affiliation

    Department of Chemistry, Michigan State University, East Lansing 48824, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THROMBINL36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
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Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
THROMBINH259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HIRUDIN VARIANTI10Hirudo medicinalisMutation(s): 0 
Find proteins for P01050 (Hirudo medicinalis)
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Go to UniProtKB:  P01050
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.151 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.66α = 90
b = 72.47β = 100.75
c = 73.09γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
PROLSQrefinement
XENGENdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance