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PDBsum entry 1e0f
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36 a.a.
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35 a.a.
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257 a.a.
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57 a.a.
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the human alpha-Thrombin-Haemadin complex: an exosite ii-Binding inhibitor.
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Authors
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J.L.Richardson,
B.Kröger,
W.Hoeffken,
J.E.Sadler,
P.Pereira,
R.Huber,
W.Bode,
P.Fuentes-Prior.
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Ref.
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EMBO J, 2000,
19,
5650-5660.
[DOI no: ]
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PubMed id
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Abstract
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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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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).
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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.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2000,
19,
5650-5660)
copyright 2000.
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Secondary reference #1
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Title
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Isolation, Sequence analysis, And cloning of haemadin. An anticoagulant peptide from the indian leech.
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Authors
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K.H.Strube,
B.Kröger,
S.Bialojan,
M.Otte,
J.Dodt.
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Ref.
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J Biol Chem, 1993,
268,
8590-8595.
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PubMed id
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Secondary reference #2
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Title
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The refined 1.9-A 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.
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Authors
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W.Bode,
D.Turk,
A.Karshikov.
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Ref.
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Protein Sci, 1992,
1,
426-471.
[DOI no: ]
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PubMed id
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Figure 3.
Fig. 3. Tosyl-m-amidinophenylalanyl-piperidine (thickconnections), NAPAP (mediumconnections),and MQPA (thincon-
nections)boundtotheactivesite of humana-thrombindisplayedtogetherwiththeConnollysurface f thrombin(Turk et al.,
1991). The naphthyl/toluene/chinolyl groups of theinhibitorsinteractwiththearyl-bindingsiteofthrombin;thesidechains
ofthe m- and thep-amidinophenylalanyl residues andofthe arginylresidueenterthespecificitypocketfrom slightly differing
sites; the S2 subsiteofthrombin is occupiedtodifferentextentsbythe(partiallysubstituted)piperidinemoieties.The viewis
similartothestandard view of Figure .
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Figure 30.
Fig. 30. Luzzatiplot f thefinalthrombinmodelafterX-PLOR
refinement.
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The above figures are
reproduced from the cited reference
with permission from the Protein Society
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