3s69: Difference between revisions
No edit summary |
No edit summary |
||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Crystal structure of saxthrombin== | ==Crystal structure of saxthrombin== | ||
<StructureSection load='3s69' size='340' side='right' caption='[[3s69]], [[Resolution|resolution]] 1.43Å' scene=''> | <StructureSection load='3s69' size='340' side='right'caption='[[3s69]], [[Resolution|resolution]] 1.43Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3s69]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3s69]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gloydius_intermedius Gloydius intermedius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S69 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S69 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.43Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=3s69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s69 OCA], [https://pdbe.org/3s69 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s69 RCSB], [https://www.ebi.ac.uk/pdbsum/3s69 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s69 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/VSPSX_GLOIT VSPSX_GLOIT] Thrombin-like snake venom serine protease that shows strong blood coagulation activity in vitro.<ref>PMID:17671373</ref> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 18: | Line 19: | ||
</div> | </div> | ||
<div class="pdbe-citations 3s69" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3s69" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Thrombin 3D Structures|Thrombin 3D Structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Gloydius | [[Category: Gloydius intermedius]] | ||
[[Category: Huang | [[Category: Large Structures]] | ||
[[Category: Niu | [[Category: Huang K]] | ||
[[Category: Teng | [[Category: Niu L]] | ||
[[Category: Zhao | [[Category: Teng M]] | ||
[[Category: Zhao W]] | |||
Latest revision as of 05:23, 21 November 2024
Crystal structure of saxthrombinCrystal structure of saxthrombin
Structural highlights
FunctionVSPSX_GLOIT Thrombin-like snake venom serine protease that shows strong blood coagulation activity in vitro.[1] Publication Abstract from PubMedSnake-venom thrombin-like enzymes (SVTLEs) are serine proteases that are widely distributed in snakes from the Crotalinae subfamily of the Viperidae. In contrast to other snake-venom serine proteases, they have a biochemical activity similar to that of thrombin and play an important role in the process of blood coagulation. However, SVTLEs cannot activate factor VIII, which is essential in blood-clot stabilization. Consequently, blood clots produced by SVTLEs are not stable and are cleared rapidly. This characteristic makes SVTLEs attractive as potential candidates for antithrombotic therapy. Saxthrombin, an SVTLE from Gloydius saxatilis, was purified and crystallized to obtain a high-quality crystal, from which data were acquired to 1.43 A resolution. Preliminary X-ray diffraction analysis showed that the crystal belonged to space group C2, with unit-cell parameters a = 94.2, b = 52.2, c = 50.1 A, beta = 96.7 degrees . The crystal structure was determined by molecular replacement and the final R factor was 18.69%; the R(free) was 20.01%. This is the first report of a crystal structure of an SVTLE. Saxthrombin belongs to the typical alpha/beta-hydrolase fold of serine proteases. Its structure was compared with those of thrombin and other snake-venom serine proteases. The observed differences in the amino-acid composition of the loops surrounding the active site appear to contribute to different surface-charge distributions and thus alter the shape of the active-site cleft, which may explain the differences in substrate affinity. Structure of saxthrombin, a thrombin-like enzyme from Gloydius saxatilis.,Huang K, Zhao W, Gao Y, Wei W, Teng M, Niu L Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Aug 1;67(Pt 8):862-5. Epub, 2011 Jul 13. PMID:21821882[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||