1vit

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(New page: 200px<br /><applet load="1vit" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vit, resolution 3.2&Aring;" /> '''THROMBIN:HIRUDIN 51-6...)
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[[Image:1vit.gif|left|200px]]<br /><applet load="1vit" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1vit, resolution 3.2&Aring;" />
 
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'''THROMBIN:HIRUDIN 51-65 COMPLEX'''<br />
 
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==Overview==
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==THROMBIN:HIRUDIN 51-65 COMPLEX==
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Crystals of the bovine thrombin-hirudins(51-65) complex have space group, P6(1)22 with cell constants a = 116.4, and c = 200.6 A and two thrombin, molecules in the asymmetric unit. Only one thrombin molecule could be, located by generalized molecular replacement; the second was fit visually, as a rigid body to an improved electron-density difference map. The, structure was refined to R = 0.192 with two B values per residue (main, chain and side chain) at 3.2 A. The polar interactions of the peptides, with the exosite of thrombin show differences consistent with the known, flexibility in the interactions of the C-terminal peptide of hirudin with, thrombin. The hirudin peptide in complex 2 has a higher temperature factor, as compared with peptide 1 which may be correlated partly with a larger, number of short-range electrostatic interactions between peptide 1 and, thrombin and partly with the fact that thrombin 2 is epsilon-thrombin, which is cleaved at Thr149A near the peptide binding site. Later, using, this structure as a test case, it was shown that the position for the, second thrombin could also be determined by a novel modification of the, molecular-replacement method in which the contribution of the known, molecule is subtracted from the structure factors. This approach is facile, and applicable to any crystal containing two or more macromolecules in the, asymmetric unit in which some but not all of the molecules can be, determined by molecular replacement.
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<StructureSection load='1vit' size='340' side='right'caption='[[1vit]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1vit]] is a 7 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=1VIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VIT FirstGlance]. <br>
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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]] 3.2&#8491;</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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=1vit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vit OCA], [https://pdbe.org/1vit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vit RCSB], [https://www.ebi.ac.uk/pdbsum/1vit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vit ProSAT]</span></td></tr>
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</table>
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== 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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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vi/1vit_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vit ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1VIT is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with NAG 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VIT OCA].
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*[[Hirudin 3D structures|Hirudin 3D structures]]
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*[[Thrombin 3D Structures|Thrombin 3D Structures]]
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==Reference==
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__TOC__
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Structure of a bovine thrombin-hirudin51-65 complex determined by a combination of molecular replacement and graphics. Incorporation of known structural information in molecular replacement., Vitali J, Martin PD, Malkowski MG, Olsen CM, Johnson PH, Edwards BF, Acta Crystallogr D Biol Crystallogr. 1996 May 1;52(Pt 3):453-64. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15299666 15299666]
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</StructureSection>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Thrombin]]
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[[Category: Edwards BFP]]
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[[Category: Edwards, B.F.P.]]
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[[Category: Vitali J]]
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[[Category: Vitali, J.]]
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[[Category: NAG]]
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[[Category: blood coagulation]]
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[[Category: complex (serine protease/inhibitor)]]
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[[Category: hydrolase]]
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[[Category: serine protease]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:53:29 2007''
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Current revision

THROMBIN:HIRUDIN 51-65 COMPLEX

PDB ID 1vit

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