Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.43 kDa 
• Atom Count: 2727 
• Residue Count: 319 
• Unique protein chains: 4

1FPH

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

• DOI: 10.2210/pdb1FPH/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Hirudo medicinalis
• Mutation(s): No 


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

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Experimental Data Snapshot

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

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

• PubMed: 1587268 
• DOI: 10.1111/j.1432-1033.1992.tb16916.x
• Primary Citation of Related Structures:  
  1FPH


• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-THROMBIN (SMALL SUBUNIT)	L	36	Homo sapiens	Mutation(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 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-THROMBIN (LARGE SUBUNIT)	H	259	Homo sapiens	Mutation(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 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUDIN	I	12	Hirudo medicinalis	Mutation(s): 0
Find proteins for P28506 (Hirudo medicinalis) Explore P28506  Go to UniProtKB:  P28506

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
FIBRINOPEPTIDE A	F	12	N/A	Mutation(s): 0
Find proteins for P02671 (Homo sapiens) Explore P02671  Go to UniProtKB:  P02671
NIH Common Fund Data Resources
PHAROS:  P02671 GTEx:  ENSG00000171560

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AR7	F	PEPTIDE-LIKE	C6 H17 N4 O2		ARG

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000379	F	N-acetylated chloromethylated fibrinopeptide A	Peptide-like /  Inhibitor		--

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 = 90.34	α = 90
b = 90.34	β = 90
c = 132.34	γ = 90

Software Package:

Software Name	Purpose
EREF	refinement

Structure Validation

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