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PDBsum entry 1xmn
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Hydrolase/hydrolase inhibitor
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PDB id
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1xmn
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Contents |
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31 a.a.
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256 a.a.
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32 a.a.
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29 a.a.
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31 a.a.
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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 thrombin bound to heparin.
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Authors
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W.J.Carter,
E.Cama,
J.A.Huntington.
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Ref.
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J Biol Chem, 2005,
280,
2745-2749.
[DOI no: ]
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PubMed id
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Abstract
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Thrombin is the final protease in the blood coagulation cascade and serves both
pro- and anticoagulant functions through the cleavage of several targets. The
ability of thrombin to specifically recognize a wide range of substrates derives
from interactions that occur outside of the active site of thrombin. Thrombin
possesses two anion binding exosites, which mediate many of its interactions
with cofactors and substrates, and although many structures of thrombin have
been solved, few such interactions have been described in molecular detail.
Glycosaminoglycan binding to exosite II of thrombin plays a major role in
switching off the procoagulant functions of thrombin by mediating its
irreversible inhibition by circulating serpins and by its binding to the
endothelial cell surface receptor thrombomodulin. Here we report the 1.85-A
structure of human alpha-thrombin bound to a heparin fragment of eight
monosaccharide units in length. The asymmetric unit is composed of two thrombin
dimers, each sharing a single heparin octasaccharide chain. The observed
interactions are fully consistent with previous mutagenesis studies and
illustrate on a molecular level the cofactor interaction that is critical for
the restriction of clotting to the site of blood vessel injury.
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Figure 1.
FIG. 1. Ribbon and surface electrostatic representations of
thrombin bound to heparin. A, the asymmetric unit consists of
four thrombin monomers organized into two nearly equivalent
dimers. Because  -thrombin is a
two-chain molecule, each monomer is denoted by two letters
according to the chain ID of the light and heavy chains, with
blue corresponding to monomer AB, red to monomer CD, orange to
monomer EF, and cyan to monomer GH. Each monomer is inhibited by
PPACK, shown in green space-filling. Two heparin chains were
independently built (ball-and-stick) between the dimer partners
in opposite orientations. B, the most intimate contact with
heparin (ball-and-stick) was found for monomer AB (surface
representation colored according to electrostatic potential,
with blue for positive and red for negative). Thrombin is
oriented so that exosite II is facing, and some of the
contacting residues are labeled (Lys236 was not fully modeled in
electron density and was rebuilt here for the purpose of
illustrating its contribution to the surface electrostatics).
The confidence in the positioning of the heparin fragment is
demonstrated by the 2F[o] - F[c] electron density map (green)
shown surrounding the modeled hexasaccharide fragment.
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Figure 2.
FIG. 2. Schematic of observed contacts between the two
heparin chains and the four thrombin monomers of the asymmetric
unit. Six heparin monosaccharide units were built into the
electron density between monomers AB and GH (A), and five were
built between monomers CD and EF (B). In both dimers, monomers
in equivalent positions (AB and CD) make them most intimate
contacts with heparin, with minimal contacts observed between
heparin and the other pair of equivalent monomers (EF and GH,
see Fig. 1A). All contacts are between heparin and atoms on the
side chains of indicated thrombin residues, with the exception
of a main chain hydrogen bond for Trp237 (dotted line). The line
style denotes the type of interaction: with a solid line
indicating a salt bridge, a dashed line indicating a hydrogen
bond, a dotted-dashed line indicating a water-mediated hydrogen
bond, and a jagged dotted line indicating potential ionic
interactions for incompletely built side chains. The packing of
the monomers against one another placed Lys236 into close
approximation with the same residue of the dimer partner,
resulting in its disorder in the crystal structure.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
2745-2749)
copyright 2005.
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