Biological Assembly 1  

 3D View: Structure | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A3B3C3 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 120.45 kDa 
• Atom Count: 8441 
• Modelled Residue Count: 1048 
• Deposited Residue Count: 1056 
• Unique protein chains: 3

1E0F

Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding inhibitor

• DOI: 10.2210/pdb1E0F/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Haemadipsa sylvestris
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2000-03-27 Released: 2000-11-03 
• Deposition Author(s): Richardson, J.L., Kroeger, B., Hoefken, W., Pereira, P., Huber, R., Bode, W., Fuentes-Prior, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.255 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Crystal Structure of the Human Alpha-Thrombin-Haemadin Complex: An Exosite II-Binding Inhibitor

Richardson, J.L., Kroeger, B., Hoeffken, W., Sadler, J.E., Pereira, P., Huber, R., Bode, W., Fuentes-Prior, P.

(2000) EMBO J 19: 5650

• PubMed: 11060016 
• DOI: 10.1093/emboj/19.21.5650
• Primary Citation of Related Structures:  
  1E0F


• PubMed Abstract: 
  

The serine proteinase alpha-thrombin plays a pivotal role in the regulation of blood fluidity, and therefore constitutes a primary target in the treatment of various haemostatic disorders. Haemadin is a slow tight- binding thrombin inhibitor from the land-living leech Haemadipsa sylvestris. Here we present the 3.1 A crystal structure of the human alpha-thrombin- haemadin complex. The N-terminal segment of haemadin binds to the active site of thrombin, forming a parallel beta-strand with residues Ser214-Gly216 of the proteinase. This mode of binding is similar to that observed in another leech-derived inhibitor, hirudin. In contrast to hirudin, however, the markedly acidic C-terminal peptide of haemadin does not bind the fibrinogen-recognition exosite, but interacts with the heparin-binding exosite of thrombin. Thus, haemadin binds to thrombin according to a novel mechanism, despite an overall structural similarity with hirudin. Haemadin inhibits both free and thrombomodulin-bound alpha-thrombin, but not intermediate activation forms such as meizothrombin. This specific anticoagulant ability of haemadin makes it an ideal candidate for an antithrombotic agent, as well as a starting point for the design of novel antithrombotics.

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Related Citations: 

• Isolation, Sequence Analysis, and Cloning of Haemadin an Anticoagulant Peptide from the Indian Leech
  Strube, K.-H., Kroeger, B., Bialojan, S., Otte, M., Dodt, J.
  (1993) J Biol Chem 268: 8590

• The Refined 1.9 Angstrom 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 Relatioships
  Bode, W., Turk, D., Karshikov, A.
  (1992) Protein Sci 1: 426

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, D-82152 Martinsried, Department of Biotechnology, BASF Aktiengesellschaft, D-67056 Ludwigshafen, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN	A, B, C	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN	D, E, F	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HAEMADIN	G [auth I], H [auth J], I [auth K]	57	Haemadipsa sylvestris	Mutation(s): 0
UniProt
Find proteins for Q25163 (Haemadipsa sylvestris) Explore Q25163  Go to UniProtKB:  Q25163

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.255 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.67	α = 90
b = 50.57	β = 114.76
c = 129.74	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
MOSFLM	data reduction
Agrovata	data scaling
ROTAVATA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-03-27 
• Released Date: 2000-11-03 
Deposition Author(s): Richardson, J.L., Kroeger, B., Hoefken, W., Pereira, P., Huber, R., Bode, W., Fuentes-Prior, P.

Revision History  

• Version 1.0: 2000-11-03
  Type: Initial release
  
• Version 1.1: 2012-11-21
  Changes: Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.2: 2017-07-05
  Changes: Data collection
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation