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PDBsum entry 1tb6
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Hydrolase/blood clotting
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PDB id
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1tb6
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Contents |
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43 a.a.
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259 a.a.
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412 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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Structure of the antithrombin-Thrombin-Heparin ternary complex reveals the antithrombotic mechanism of heparin.
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Authors
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W.Li,
D.J.Johnson,
C.T.Esmon,
J.A.Huntington.
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Ref.
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Nat Struct Mol Biol, 2004,
11,
857-862.
[DOI no: ]
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PubMed id
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Abstract
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The maintenance of normal blood flow depends completely on the inhibition of
thrombin by antithrombin, a member of the serpin family. Antithrombin circulates
at a high concentration, but only becomes capable of efficient thrombin
inhibition on interaction with heparin or related glycosaminoglycans. The
anticoagulant properties of therapeutic heparin are mediated by its interaction
with antithrombin, although the structural basis for this interaction is
unclear. Here we present the crystal structure at a resolution of 2.5 A of the
ternary complex between antithrombin, thrombin and a heparin mimetic (SR123781).
The structure reveals a template mechanism with antithrombin and thrombin bound
to the same heparin chain. A notably close contact interface, comprised of
extensive active site and exosite interactions, explains, in molecular detail,
the basis of the antithrombotic properties of therapeutic heparin.
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Figure 1.
Figure 1. Heparin catalysis of thrombin inhibition by
antithrombin. (a) The binding of the specific heparin
pentasaccharide to antithrombin induces a global conformational
change involving the expulsion of the hinge region (circled) of
the reactive center loop (RCL, yellow) from the central  -sheet
A (red), and extension (yellow) of the A and D helices (green
and cyan, respectively). The expulsion of the hinge region
increases the flexibility of the RCL and liberates the P1 Arg
(green ball-and-stick). The flexibility of the C-terminal
portion of the RCL (P' side) is limited, despite a three-residue
insertion (orange), owing to a tight hydrogen-bonded turn. (b)
Stereo representation of the crystal structure of the ternary
complex between antithrombin (colored as above), thrombin
(magenta) and heparin (ball-and-stick, with blue 2F[o] - F[c]
electron density contoured at 1  ).
Thrombin is docked toward the heparin-binding site of
antithrombin, and makes several exosite interactions. The
expulsion of the hinge region is not required to form this
complex, but the P' side of the RCL (orange) has been elongated.
(c) Density (calculated as in b) of the hinge region of
antithrombin in its complex with thrombin and heparin (yellow)
reveals the insertion of P15 Gly into -sheet
A, and a larger opening between strands 3 and 5A than seen for
pentasaccharide-bound antithrombin alone (gray). It has been
shown that high-affinity binding is not inconsistent with a
native-like hinge conformation, as demonstrated by the structure
in PDB entry 1NQ9 (ref. 42) (brown). (d) A comparison of the
conformations of the P' region of the RCL of pentasaccharide
activated antithrombin (gray) to that of antithrombin in the
complex with thrombin and heparin (yellow, oriented as in a and
b) reveals the requirement for P' elongation through the
breaking of hydrogen bonds.
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Figure 3.
Figure 3. Thrombin exosite interactions. (a,b) Thrombin
interacts closely with antithrombin by forming exosite
interactions in the  -loop
(a) and the Na^+-binding region (b) (colored as in Fig. 2a). (c)
The heparin mimetic (SR123781) used in crystallization is
labeled from A on the nonreducing end to P on the reducing end.
It is composed of a thrombin-binding site (ABC) and an
antithrombin-binding site (LMNOP). The interactions with
thrombin and antithrombin are indicated by lines, with solid
lines indicating a salt bridge, dashed lines hydrogen bonds,
dashed-dotted lines for water-mediated hydrogen bonds, and
dotted lines for potential interactions (only for Lys240).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2004,
11,
857-862)
copyright 2004.
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