3url: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Endothiapepsin-DB6 complex.== | ==Endothiapepsin-DB6 complex.== | ||
<StructureSection load='3url' size='340' side='right' caption='[[3url]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='3url' size='340' side='right'caption='[[3url]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3url]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3url]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Endothia_parasitica Endothia parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3URL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3URL FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PUK:N-[(2S)-2-AMINO-3-PHENYLPROPYL]-L-PHENYLALANINE'>PUK</scene>, <scene name='pdbligand=SUI:(3-AMINO-2,5-DIOXO-1-PYRROLIDINYL)ACETIC+ACID'>SUI</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PUK:N-[(2S)-2-AMINO-3-PHENYLPROPYL]-L-PHENYLALANINE'>PUK</scene>, <scene name='pdbligand=SUI:(3-AMINO-2,5-DIOXO-1-PYRROLIDINYL)ACETIC+ACID'>SUI</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3uri|3uri]], [[3urj|3urj]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3uri|3uri]], [[3urj|3urj]]</div></td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3url FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3url OCA], [https://pdbe.org/3url PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3url RCSB], [https://www.ebi.ac.uk/pdbsum/3url PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3url ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 28: | Line 28: | ||
[[Category: Endothia parasitica]] | [[Category: Endothia parasitica]] | ||
[[Category: Endothiapepsin]] | [[Category: Endothiapepsin]] | ||
[[Category: Large Structures]] | |||
[[Category: Albert, A]] | [[Category: Albert, A]] | ||
[[Category: Bailey, D]] | [[Category: Bailey, D]] | ||
Revision as of 11:00, 20 July 2022
Endothiapepsin-DB6 complex.Endothiapepsin-DB6 complex.
Structural highlights
Publication Abstract from PubMedThe analysis reported here describes detailed structural studies of endothiapepsin (the aspartic proteinase from Endothia parasitica), with and without bound inhibitors, and human pepsin 3b. Comparison of multiple crystal structures of members of the aspartic proteinase family has revealed small but significant differences in domain orientation in different crystal forms. In this paper, it is shown that these differences in domain orientation do not necessarily correlate with the presence or absence of bound inhibitors, but appear to stem at least partly from crystal contacts mediated by sulfate ions. However, since the same inherent flexibility of the structure is observed for other enzymes in this family such as human pepsin, the native structure of which is also reported here, the observed domain movements may well have implications for the mechanism of catalysis. An analysis of subdomain orientation, conformational change and disorder in relation to crystal packing of aspartic proteinases.,Bailey D, Carpenter EP, Coker A, Coker S, Read J, Jones AT, Erskine P, Aguilar CF, Badasso M, Toldo L, Rippmann F, Sanz-Aparicio J, Albert A, Blundell TL, Roberts NB, Wood SP, Cooper JB Acta Crystallogr D Biol Crystallogr. 2012 May;68(Pt 5):541-52. Epub 2012 Apr 17. PMID:22525752[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||||||