3bv9

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(New page: 200px<br /><applet load="3bv9" size="350" color="white" frame="true" align="right" spinBox="true" caption="3bv9, resolution 1.80&Aring;" /> '''Structure of Thrombi...)
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[[Image:3bv9.jpg|left|200px]]<br /><applet load="3bv9" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:3bv9.jpg|left|200px]]
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caption="3bv9, resolution 1.80&Aring;" />
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'''Structure of Thrombin Bound to the Inhibitor FM19'''<br />
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{{Structure
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|PDB= 3bv9 |SIZE=350|CAPTION= <scene name='initialview01'>3bv9</scene>, resolution 1.80&Aring;
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|SITE= <scene name='pdbsite=AC1:Oic+Binding+Site+For+Residue+C+402'>AC1</scene>, <scene name='pdbsite=AC2:4ph+Binding+Site+For+Residue+C+405'>AC2</scene>, <scene name='pdbsite=AC3:Iod+Binding+Site+For+Residue+B+303'>AC3</scene>, <scene name='pdbsite=AC4:Na+Binding+Site+For+Residue+B+307'>AC4</scene>, <scene name='pdbsite=AC5:Nh2+Binding+Site+For+Residue+C+406'>AC5</scene> and <scene name='pdbsite=AC6:Gol+Binding+Site+For+Residue+B+305'>AC6</scene>
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|LIGAND= <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5]
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|GENE= F2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
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}}
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'''Structure of Thrombin Bound to the Inhibitor FM19'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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3BV9 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=IOD:'>IOD</scene>, <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=NH2:'>NH2</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] Known structural/functional Sites: <scene name='pdbsite=AC1:Oic+Binding+Site+For+Residue+C+402'>AC1</scene>, <scene name='pdbsite=AC2:4ph+Binding+Site+For+Residue+C+405'>AC2</scene>, <scene name='pdbsite=AC3:Iod+Binding+Site+For+Residue+B+303'>AC3</scene>, <scene name='pdbsite=AC4:Na+Binding+Site+For+Residue+B+307'>AC4</scene>, <scene name='pdbsite=AC5:Nh2+Binding+Site+For+Residue+C+406'>AC5</scene> and <scene name='pdbsite=AC6:Gol+Binding+Site+For+Residue+B+305'>AC6</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BV9 OCA].
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3BV9 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BV9 OCA].
==Reference==
==Reference==
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Molecular dissection of Na+ binding to thrombin., Pineda AO, Carrell CJ, Bush LA, Prasad S, Caccia S, Chen ZW, Mathews FS, Di Cera E, J Biol Chem. 2004 Jul 23;279(30):31842-53. Epub 2004 May 19. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15152000 15152000]
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Molecular dissection of Na+ binding to thrombin., Pineda AO, Carrell CJ, Bush LA, Prasad S, Caccia S, Chen ZW, Mathews FS, Di Cera E, J Biol Chem. 2004 Jul 23;279(30):31842-53. Epub 2004 May 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15152000 15152000]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Protein complex]]
[[Category: Protein complex]]
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[[Category: zymogen]]
[[Category: zymogen]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 5 13:24:15 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:01:28 2008''

Revision as of 17:01, 20 March 2008

Image:3bv9.jpg


PDB ID 3bv9

Drag the structure with the mouse to rotate
, resolution 1.80Å
Sites: , , , , and
Ligands: , , and
Gene: F2 (Homo sapiens)
Activity: Thrombin, with EC number 3.4.21.5
Coordinates: save as pdb, mmCIF, xml



Structure of Thrombin Bound to the Inhibitor FM19


Overview

Na(+) binding near the primary specificity pocket of thrombin promotes the procoagulant, prothrombotic, and signaling functions of the enzyme. The effect is mediated allosterically by a communication between the Na(+) site and regions involved in substrate recognition. Using a panel of 78 Ala mutants of thrombin, we have mapped the allosteric core of residues that are energetically linked to Na(+) binding. These residues are Asp-189, Glu-217, Asp-222, and Tyr-225, all in close proximity to the bound Na(+). Among these residues, Asp-189 shares with Asp-221 the important function of transducing Na(+) binding into enhanced catalytic activity. None of the residues of exosite I, exosite II, or the 60-loop plays a significant role in Na(+) binding and allosteric transduction. X-ray crystal structures of the Na(+)-free (slow) and Na(+)-bound (fast) forms of thrombin, free or bound to the active site inhibitor H-d-Phe-Pro-Arg-chloromethyl-ketone, document the conformational changes induced by Na(+) binding. The slow --> fast transition results in formation of the Arg-187:Asp-222 ion pair, optimal orientation of Asp-189 and Ser-195 for substrate binding, and a significant shift of the side chain of Glu-192 linked to a rearrangement of the network of water molecules that connect the bound Na(+) to Ser-195 in the active site. The changes in the water network and the allosteric core explain the thermodynamic signatures linked to Na(+) binding and the mechanism of thrombin activation by Na(+). The role of the water network uncovered in this study establishes a new paradigm for the allosteric regulation of thrombin and other Na(+)-activated enzymes involved in blood coagulation and the immune response.

About this Structure

3BV9 is a Protein complex structure of sequences from Homo sapiens. Full crystallographic information is available from OCA.

Reference

Molecular dissection of Na+ binding to thrombin., Pineda AO, Carrell CJ, Bush LA, Prasad S, Caccia S, Chen ZW, Mathews FS, Di Cera E, J Biol Chem. 2004 Jul 23;279(30):31842-53. Epub 2004 May 19. PMID:15152000

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