4er1: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
 
(10 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:4er1.jpg|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_4er1", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_4er1|  PDB=4er1  |  SCENE=  }}
'''THE ACTIVE SITE OF ASPARTIC PROTEINASES'''


==THE ACTIVE SITE OF ASPARTIC PROTEINASES==
<StructureSection load='4er1' size='340' side='right'caption='[[4er1]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4er1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ER1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ER1 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0ZP:N-[(1R,2R,4R)-1-(CYCLOHEXYLMETHYL)-2-HYDROXY-6-METHYL-4-{[(2R)-2-METHYLBUTYL]CARBAMOYL}HEPTYL]-3-(1H-IMIDAZOL-3-IUM-4-YL)-N~2~-[3-NAPHTHALEN-1-YL-2-(NAPHTHALEN-1-YLMETHYL)PROPANOYL]-L-ALANINAMIDE'>0ZP</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=4er1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4er1 OCA], [https://pdbe.org/4er1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4er1 RCSB], [https://www.ebi.ac.uk/pdbsum/4er1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4er1 ProSAT]</span></td></tr>
</table>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/er/4er1_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=4er1 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The active site of the aspartic proteinase, endothiapepsin, has been defined by X-ray analysis and restrained least-squares refinement at 2.1 A resolution with a crystallographic agreement value of 0.16. The environments of the two catalytically important aspartyl groups are remarkably similar and the contributions of the NH2- and COOH-terminal domains to the catalytic centre are related by a local 2-fold axis. The carboxylates of the aspartyls share a hydrogen bond and have equivalent contacts to a bound water molecule or hydroxonium ion lying on the local diad. The main chains around 32 and 215 are connected by a novel interaction involving diad-related threonines. It is suggested that the two pKa values of the active site aspartyls arise from a structure not unlike that in maleic acid with a hydrogen-bonded intermediate species and a dicarboxylate characterised by electrostatic repulsions between the two negatively charged groups.


==Overview==
The active site of aspartic proteinases.,Pearl L, Blundell T FEBS Lett. 1984 Aug 20;174(1):96-101. PMID:6381096<ref>PMID:6381096</ref>
The active site of the aspartic proteinase, endothiapepsin, has been defined by X-ray analysis and restrained least-squares refinement at 2.1 A resolution with a crystallographic agreement value of 0.16. The environments of the two catalytically important aspartyl groups are remarkably similar and the contributions of the NH2- and COOH-terminal domains to the catalytic centre are related by a local 2-fold axis. The carboxylates of the aspartyls share a hydrogen bond and have equivalent contacts to a bound water molecule or hydroxonium ion lying on the local diad. The main chains around 32 and 215 are connected by a novel interaction involving diad-related threonines. It is suggested that the two pKa values of the active site aspartyls arise from a structure not unlike that in maleic acid with a hydrogen-bonded intermediate species and a dicarboxylate characterised by electrostatic repulsions between the two negatively charged groups.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
4ER1 is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ER1 OCA].
</div>
<div class="pdbe-citations 4er1" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
The active site of aspartic proteinases., Pearl L, Blundell T, FEBS Lett. 1984 Aug 20;174(1):96-101. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/6381096 6381096]
*[[Pepsin|Pepsin]]
[[Category: Hydrolase]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Blundell, T L.]]
__TOC__
[[Category: Cooper, J B.]]
</StructureSection>
[[Category: Quail, J W.]]
[[Category: Cryphonectria parasitica]]
[[Category: Szelke, M.]]
[[Category: Large Structures]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 22:23:30 2008''
[[Category: Blundell TL]]
[[Category: Cooper JB]]
[[Category: Quail JW]]
[[Category: Szelke M]]
Retrieved from "https://proteopedia.org/4er1"