3pmb

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3pmb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PMB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PMB FirstGlance]. <br>
<table><tr><td colspan='2'>[[3pmb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PMB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PMB FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3pma|3pma]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pmb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pmb OCA], [https://pdbe.org/3pmb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pmb RCSB], [https://www.ebi.ac.uk/pdbsum/3pmb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pmb ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pmb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pmb OCA], [https://pdbe.org/3pmb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pmb RCSB], [https://www.ebi.ac.uk/pdbsum/3pmb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pmb ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/THRB_BOVIN THRB_BOVIN]] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing (By similarity).
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[https://www.uniprot.org/uniprot/THRB_BOVIN THRB_BOVIN] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing (By similarity).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The serine protease thrombin plays multiple roles in many important physiological processes, especially coagulation, where it functions as both a pro- and anticoagulant. The polyanionic glycosaminoglycan heparin modulates thrombin's activity through binding at exosite II. Sucrose octasulfate (SOS) is often used as a surrogate for heparin, but it is not known whether it is an effective heparin mimic in its interaction with thrombin. We have characterized the interaction of SOS with thrombin in solution and determined a crystal structure of their complex. SOS binds thrombin with a K(d) of approximately 1.4 muM, comparable to that of the much larger polymeric heparin measured under the same conditions. Nonionic (hydrogen bonding) interactions make a larger contribution to thrombin binding of SOS than to heparin. SOS binding to exosite II inhibits thrombin's catalytic activity with high potency but with low efficacy. Analytical ultracentrifugation shows that bovine and human thrombins are monomers in solution in the presence of SOS, in contrast to their complexes with heparin, which are dimers. In the X-ray crystal structure, two molecules of SOS are bound nonequivalently to exosite II portions of a thrombin dimer, in contrast to the 1:2 stoichiometry of the heparin-thrombin complex, which has a different monomer association mode in the dimer. SOS and heparin binding to exosite II of thrombin differ on both chemical and structural levels and, perhaps most significantly, in thrombin inhibition. These differences may offer paths to the design of more potent exosite II binding, allosteric small molecules as modulators of thrombin function.
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Interaction of Thrombin with Sucrose Octasulfate.,Desai BJ, Boothello RS, Mehta AY, Scarsdale JN, Wright HT, Desai UR Biochemistry. 2011 Jul 18. PMID:21736375<ref>PMID:21736375</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3pmb" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Thrombin 3D Structures|Thrombin 3D Structures]]
*[[Thrombin 3D Structures|Thrombin 3D Structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Thrombin]]
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[[Category: Desai BJ]]
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[[Category: Desai, B J]]
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[[Category: Scarsdale JN]]
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[[Category: Scarsdale, J N]]
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[[Category: Wright HT]]
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[[Category: Wright, H T]]
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[[Category: Fibrinolosy]]
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[[Category: Hydrolase]]
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[[Category: Protease]]
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[[Category: Thrombosis]]
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Revision as of 13:32, 1 March 2024

2.9 Angstrom crystal structure of bovine thrombin in tetragonal spacegroup

PDB ID 3pmb

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