Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.79 kDa 
• Atom Count: 356 
• Residue Count: 356 
• Unique protein chains: 3

3HTC

THE STRUCTURE OF A COMPLEX OF RECOMBINANT HIRUDIN AND HUMAN ALPHA-THROMBIN

• DOI: 10.2210/pdb3HTC/pdb

• Classification: HYDROLASE(SERINE PROTEASE)
• Organism(s): Homo sapiens, Poecilobdella manillensis
• Mutation(s): No 


• Deposited: 1993-06-11 Released: 1994-01-31 
• Deposition Author(s): Tulinsky, A., Rydel, T.J., Ravichandran, K.G., Huber, R., Bode, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 0.193 

Literature

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 2nd., J.W.

(1990) Science 249: 277-280

• PubMed: 2374926 
• DOI: 10.1126/science.2374926
• Primary Citation of Related Structures:  
  3HTC


• PubMed Abstract: 
  

The crystallographic structure of a recombinant hirudin-thrombin complex has been solved at 2.3 angstrom (A) resolution. Hirudin consists of an NH2-terminal globular domain and a long (39 A) COOH-terminal extended domain. Residues Ile1 to Tyr3 of hirudin form a parallel beta-strand with Ser214 to Glu217 of thrombin with the nitrogen atom of Ile1 making a hydrogen bond with Ser195 O gamma atom of the catalytic site, but the specificity pocket of thrombin is not involved in the interaction. The COOH-terminal segment makes numerous electrostatic interactions with an anion-binding exosite of thrombin, whereas the last five residues are in a helical loop that forms many hydrophobic contacts. In all, 27 of the 65 residues of hirudin have contacts less than 4.0 A with thrombin (10 ion pairs and 23 hydrogen bonds). Such abundant interactions may account for the high affinity and specificity of hirudin.

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Related Citations: 

• The Refined 1.9 Angstroms 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

• Experience with Various Techniques for the Refinement of Protein Structures
  Deisenhofer, J., Remington, S.J., Steigemann, W.
  (1985) Methods Enzymol 115: 303

• Refinement of Large Structures by Simultaneous Minimization of Energy and R Factor
  Jack, A., Levitt, M.
  (1978) Acta Crystallogr A 34: 931

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Organizational Affiliation: 

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

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 VARIANT 2	I	65	Poecilobdella manillensis	Mutation(s): 0
Find proteins for P09945 (Hirudo medicinalis) Explore P09945  Go to UniProtKB:  P09945

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 0.193 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.54	α = 90
b = 90.54	β = 90
c = 132.04	γ = 90

Software Package:

Software Name	Purpose
EREF	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1993-06-11 
• Released Date: 1994-01-31 
Deposition Author(s): Tulinsky, A., Rydel, T.J., Ravichandran, K.G., Huber, R., Bode, W.

Revision History 

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