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PDBsum entry 1e0f
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protein Protein-protein interface(s) links
Hydrolase PDB id
1e0f

 

 

 

 

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Contents
Protein chains
36 a.a. *
35 a.a. *
257 a.a. *
57 a.a. *
Waters ×67
* Residue conservation analysis
PDB id:
1e0f
Name: Hydrolase
Title: Crystal structure of the human alpha-thrombin-haemadin complex: an exosite ii-binding inhibitor
Structure: Thrombin. Chain: a, b, c. Thrombin. Chain: d, e, f. Fragment: no. Synonym: factor iia. Haemadin. Chain: i, j, k. Fragment: no.
Source: Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood. Other_details: human thrombin was purified from human serum according to reported protocols. Haemadipsa sylvestris. Organism_taxid: 13555. Expressed in: escherichia coli.
Biol. unit: Nonamer (from PQS)
Resolution:
3.10Å     R-factor:   0.208     R-free:   0.255
Authors: J.L.Richardson,B.Kroeger,W.Hoefken,P.Pereira,R.Huber,W.Bode, P.Fuentes-Prior
Key ref:
J.L.Richardson et al. (2000). Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding inhibitor. EMBO J, 19, 5650-5660. PubMed id: 11060016 DOI: 10.1093/emboj/19.21.5650
Date:
27-Mar-00     Release date:   03-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		622 a.a.
36 a.a.
Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		622 a.a.
35 a.a.
Protein chains
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		622 a.a.
257 a.a.*
Protein chains
Q25163  (Q25163_HAESL) -  Thrombininhibitor from Haemadipsa sylvestris
Seq:
Struc: 		77 a.a.
57 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F: E.C.3.4.21.5  - thrombin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.

 

 
DOI no: 10.1093/emboj/19.21.5650 EMBO J 19:5650-5660 (2000)
PubMed id: 11060016  
 
 
Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding inhibitor.
J.L.Richardson, B.Kröger, W.Hoeffken, J.E.Sadler, P.Pereira, R.Huber, W.Bode, P.Fuentes-Prior.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Crystal structure of the human thrombin–haemadin complex. (A) Structure of the crystallographic trimer present in the asymmetric unit. Monomers are labelled A, B and C. Thrombin molecules are shown as red, yellow and green ribbons; the C[ ]traces of the three inhibitors are presented as colour-coded van der Waals spheres (red, oxygen; blue, nitrogen; grey, carbon). (B) Stereo diagram of complex molecule A. The protease is shown in its 'standard orientation' (Bode et al., 1992), i.e. with the active-site cleft facing the viewer and substrates running from left to right. Side chains of the catalytic triad residues are shown explicitly, as well as the side chains of the interacting residues Asp189 (thrombin) and Arg2I (haemadin) (colour coded as in Figure 1A). Also shown (unlabelled) are the side chains of the basic residues of the heparin-binding site (thrombin), as well as the side chains of the acidic residues of haemadin's C-terminal tail. This figure and Figures 3, 5A, 7A and 8 were prepared with SETOR (Evans, 1993). 		Figure 4.
Figure 4 Space-filling models of human -thrombin and haemadin, showing the surface potential of the two molecules. Positive charges are displayed in blue, negative charges in red, with darkest blue and red colours corresponding to electrostatic potentials beyond -10 and +10 kT/e, respectively. The plot was prepared with GRASP (Nicholls et al., 1993). The thrombin component (B) is shown in the standard orientation, while haemadin (A) is rotated along the y-axis to present the thrombin binding surface to the viewer. Some of the residues of the interacting interfaces are labelled.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 5650-5660) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21082917 C.Y.Koh, and R.M.Kini (2008).
Anticoagulants from hematophagous animals.
  Expert Rev Hematol, 1, 135-139.  
18779330 S.Lancellotti, S.Rutella, V.De Filippis, N.Pozzi, B.Rocca, and R.De Cristofaro (2008).
Fibrinogen-elongated {gamma} Chain Inhibits Thrombin-induced Platelet Response, Hindering the Interaction with Different Receptors.
  J Biol Chem, 283, 30193-30204.  
18286181 S.Macedo-Ribeiro, C.Almeida, B.M.Calisto, T.Friedrich, R.Mentele, J.Stürzebecher, P.Fuentes-Prior, and P.J.Pereira (2008).
Isolation, cloning and structural characterisation of boophilin, a multifunctional Kunitz-type proteinase inhibitor from the cattle tick.
  PLoS ONE, 3, e1624.
PDB code: 2ody
17684009 C.Y.Koh, M.Kazimirova, A.Trimnell, P.Takac, M.Labuda, P.A.Nuttall, and R.M.Kini (2007).
Variegin, a novel fast and tight binding thrombin inhibitor from the tropical bont tick.
  J Biol Chem, 282, 29101-29113.  
17635714 P.E.Bock, P.Panizzi, and I.M.Verhamme (2007).
Exosites in the substrate specificity of blood coagulation reactions.
  J Thromb Haemost, 5, 81-94.  
  16820690 S.Roy, P.Aravind, C.Madhurantakam, A.K.Ghosh, R.Sankaranarayanan, and A.K.Das (2006).
Crystallization and preliminary X-ray diffraction analysis of a protease inhibitor from the haemolymph of the Indian tasar silkworm Antheraea mylitta.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 669-671.  
15775973 J.Otlewski, F.Jelen, M.Zakrzewska, and A.Oleksy (2005).
The many faces of protease-protein inhibitor interaction.
  EMBO J, 24, 1303-1310.  
15892855 W.Bode (2005).
The structure of thrombin, a chameleon-like proteinase.
  J Thromb Haemost, 3, 2379-2388.  
16042075 Y.S.Sa, S.J.Kim, and H.S.Choi (2005).
The anticoagulant fraction from the leaves of Diospyros kaki L. has an antithrombotic activity.
  Arch Pharm Res, 28, 667-674.  
14607082 J.A.Huntington, and T.P.Baglin (2003).
Targeting thrombin--rational drug design from natural mechanisms.
  Trends Pharmacol Sci, 24, 589-595.  
12791700 J.Mima, Y.Narita, H.Chiba, and R.Hayashi (2003).
The multiple site binding of carboxypeptidase Y inhibitor (IC) to the cognate proteinase. Implications for the biological roles of the phosphatidylethanolamine-binding protein.
  J Biol Chem, 278, 29792-29798.  
12573700 N.A.Raffler, J.Schneider-Mergener, and M.Famulok (2003).
A novel class of small functional peptides that bind and inhibit human alpha-thrombin isolated by mRNA display.
  Chem Biol, 10, 69-79.  
12791690 N.Foeger, E.M.Schmid, and T.Skern (2003).
Human rhinovirus 2 2Apro recognition of eukaryotic initiation factor 4GI. Involvement of an exosite.
  J Biol Chem, 278, 33200-33207.  
12968031 T.H.Yun, F.A.Baglia, T.Myles, D.Navaneetham, J.A.López, P.N.Walsh, and L.L.Leung (2003).
Thrombin activation of factor XI on activated platelets requires the interaction of factor XI and platelet glycoprotein Ib alpha with thrombin anion-binding exosites I and II, respectively.
  J Biol Chem, 278, 48112-48119.  
11724802 I.M.Verhamme, S.T.Olson, D.M.Tollefsen, and P.E.Bock (2002).
Binding of exosite ligands to human thrombin. Re-evaluation of allosteric linkage between thrombin exosites I and II.
  J Biol Chem, 277, 6788-6798.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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