4thn

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[[Image:4thn.jpg|left|200px]]<br /><applet load="4thn" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:4thn.jpg|left|200px]]
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caption="4thn, resolution 2.5&Aring;" />
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'''THE CRYSTAL STRUCTURE OF ALPHA-THROMBIN-HIRUNORM IV COMPLEX REVEALS A NOVEL SPECIFICITY SITE RECOGNITION MODE.'''<br />
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{{Structure
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|PDB= 4thn |SIZE=350|CAPTION= <scene name='initialview01'>4thn</scene>, resolution 2.5&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=
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}}
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'''THE CRYSTAL STRUCTURE OF ALPHA-THROMBIN-HIRUNORM IV COMPLEX REVEALS A NOVEL SPECIFICITY SITE RECOGNITION MODE.'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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4THN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=NAG:'>NAG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4THN OCA].
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4THN is a [[Single protein]] structure of sequence 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=4THN OCA].
==Reference==
==Reference==
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The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode., Lombardi A, De Simone G, Nastri F, Galdiero S, Della Morte R, Staiano N, Pedone C, Bolognesi M, Pavone V, Protein Sci. 1999 Jan;8(1):91-5. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10210187 10210187]
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The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode., Lombardi A, De Simone G, Nastri F, Galdiero S, Della Morte R, Staiano N, Pedone C, Bolognesi M, Pavone V, Protein Sci. 1999 Jan;8(1):91-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10210187 10210187]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Single protein]]
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[[Category: Staiano, N.]]
[[Category: Staiano, N.]]
[[Category: NAG]]
[[Category: NAG]]
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[[Category: antithrombotics]]
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[[Category: antithrombotic]]
[[Category: complex (serine protease/inhibitor)]]
[[Category: complex (serine protease/inhibitor)]]
[[Category: hirudin-like binding mode]]
[[Category: hirudin-like binding mode]]
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[[Category: hirunorms]]
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[[Category: hirunorm]]
[[Category: thrombin]]
[[Category: thrombin]]
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[[Category: thrombin synthetic inhibitors]]
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[[Category: thrombin synthetic inhibitor]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:14:25 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:11:03 2008''

Revision as of 17:11, 20 March 2008

Image:4thn.jpg


PDB ID 4thn

Drag the structure with the mouse to rotate
, resolution 2.5Å
Ligands:
Activity: Thrombin, with EC number 3.4.21.5
Coordinates: save as pdb, mmCIF, xml



THE CRYSTAL STRUCTURE OF ALPHA-THROMBIN-HIRUNORM IV COMPLEX REVEALS A NOVEL SPECIFICITY SITE RECOGNITION MODE.


Contents

Overview

The X-ray crystal structure of the human alpha-thrombin-hirunorm IV complex has been determined at 2.5 A resolution, and refined to an R-factor of 0.173. The structure reveals an inhibitor binding mode distinctive of a true hirudin mimetic, which justifies the high inhibitory potency and the selectivity of hirunorm IV. This novel inhibitor, composed of 26 amino acids, interacts through the N-terminal end with the alpha-thrombin active site in a nonsubstrate mode, and binds specifically to the fibrinogen recognition exosite through the C-terminal end. The backbone of the N-terminal tripeptide Chg1"-Arg2"-2Na13" (Chg, cyclohexyl-glycine; 2Na1, beta-(2-naphthyl)-alanine) forms a parallel beta-strand to the thrombin main-chain segment Ser214-Gly216. The Chg1" side chain occupies the S2 site, Arg2" penetrates into the S1 specificity site, while the 2Na13" side chain occupies the aryl binding site. The Arg2" side chain enters the S1 specificity pocket from a position quite apart from the canonical P1 site. This notwithstanding, the Arg2" side chain establishes the typical ion pair with the carboxylate group of Asp189.

Disease

Known diseases associated with this structure: Dysprothrombinemia OMIM:[176930], Hyperprothrombinemia OMIM:[176930], Hypoprothrombinemia OMIM:[176930]

About this Structure

4THN is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.

Reference

The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode., Lombardi A, De Simone G, Nastri F, Galdiero S, Della Morte R, Staiano N, Pedone C, Bolognesi M, Pavone V, Protein Sci. 1999 Jan;8(1):91-5. PMID:10210187

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