1FPH

THE INTERACTION OF THROMBIN WITH FIBRINOGEN: A STRUCTURAL BASIS FOR ITS SPECIFICITY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The interaction of thrombin with fibrinogen. A structural basis for its specificity.

Stubbs, M.T.Oschkinat, H.Mayr, I.Huber, R.Angliker, H.Stone, S.R.Bode, W.

(1992) Eur J Biochem 206: 187-195

  • DOI: 10.1111/j.1432-1033.1992.tb16916.x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of the ternary complex of human alpha-thrombin with a covalently bound analogue of fibrinopeptide A and a C-terminal hirudin peptide has been determined by X-ray diffraction methods at 0.25 nm resolution. Fibrinopeptide A folds in a com ...

    The structure of the ternary complex of human alpha-thrombin with a covalently bound analogue of fibrinopeptide A and a C-terminal hirudin peptide has been determined by X-ray diffraction methods at 0.25 nm resolution. Fibrinopeptide A folds in a compact manner, bringing together hydrophobic residues that slot into the apolar binding site of human alpha-thrombin. Fibrinogen residue Phe8 occupies the aryl-binding site of thrombin, adjacent to fibrinogen residues Leu9 and Val15 in the S2 subsite. The species diversity of fibrinopeptide A is analysed with respect to its conformation and its interaction with thrombin. The non-covalently attached peptide fragment hirudin(54-65) exhibits an identical conformation to that observed in the hirudin-thrombin complex. The occupancy of the secondary fibrinogen-recognition exosite by this peptide imposes restrictions on the manner of fibrinogen binding. The surface topology of the thrombin molecule indicates positions P1'-P3', differ from those of the canonical serine-proteinase inhibitors, suggesting a mechanical model for the switching of thrombin activity from fibrinogen cleavage to protein-C activation on thrombomodulin complex formation. The multiple interactions between thrombin and fibrinogen provide an explanation for the narrow specificity of thrombin. Structural grounds can be put forward for certain congenital clotting disorders.


    Related Citations: 
    • A Player of Many Parts: The Spotlight Falls on Thrombin'S Structure
      Stubbs, M.T., Bode, W.
      (1993) Thromb Res 69: 1
    • The Refined 1.9 Angstroms 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
    • Refined Structure of the Hirudin-Thrombin Complex
      Rydel, T.J., Tulinsky, A., Bode, W., Huber, R.
      (1991) J Mol Biol 221: 583

    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried bei München, Federal Republic of Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-THROMBIN (SMALL SUBUNIT)
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALPHA-THROMBIN (LARGE SUBUNIT)
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HIRUDIN
I
12Hirudo medicinalisMutation(s): 0 
Find proteins for P28506 (Hirudo medicinalis)
Go to UniProtKB:  P28506
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
FIBRINOPEPTIDE A
F
12N/AMutation(s): 0 
Find proteins for P02671 (Homo sapiens)
Go to UniProtKB:  P02671
NIH Common Fund Data Resources
PHAROS  P02671
Protein Feature View
  • Reference Sequence
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000379 (0ZM)
Query on PRD_000379
FN-acetylated chloromethylated fibrinopeptide APeptide-like /  Inhibitor

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AR7
Query on AR7
FPEPTIDE-LIKEC6 H17 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.166 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.34α = 90
b = 90.34β = 90
c = 132.34γ = 90
Software Package:
Software NamePurpose
EREFrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1993-04-21 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Stubbs, M.T., Bode, W.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-06
    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
  • Version 1.3: 2012-12-12
    Changes: Other