3dpe

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:13, 1 November 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3dpe.png|left|200px]]
 
-
<!--
+
==Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor==
-
The line below this paragraph, containing "STRUCTURE_3dpe", creates the "Structure Box" on the page.
+
<StructureSection load='3dpe' size='340' side='right'caption='[[3dpe]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3dpe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPE FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AXB:N-{[2-(2-AMINO-3,4-DIOXOCYCLOBUT-1-EN-1-YL)-1,2,3,4-TETRAHYDROISOQUINOLIN-7-YL]METHYL}-4-OXO-3,5,6,8-TETRAHYDRO-4H-THIOPYRANO[4,3 4,5]THIENO[2,3-D]PYRIMIDINE-2-CARBOXAMIDE+7,7-DIOXIDE'>AXB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
{{STRUCTURE_3dpe| PDB=3dpe | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpe OCA], [https://pdbe.org/3dpe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dpe RCSB], [https://www.ebi.ac.uk/pdbsum/3dpe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpe ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/MMP8_HUMAN MMP8_HUMAN] Can degrade fibrillar type I, II, and III collagens.
 +
== 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/dp/3dpe_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3dpe ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The mode of binding and the activity of the first two non-zinc chelating, potent, and selective inhibitors of human neutrophil collagenase are reported. The crystal structures of the catalytic domain of MMP-8, respectively complexed with each inhibitor, reveals that both ligands are deeply inserted into the primary specificity subsite S(1)', where they induce a similar conformational change of the surrounding loop that is endowed with the main specificity determinants of MMPs. Accord to this rearrangement, both inhibitors remove the floor of the pocket formed by the Y227 side-chain, rendering available an extra binding region never explored before. The present data show that potent and more selective inhibitors can be obtained by developing ligands able to interact with the selectivity regions of the enzyme rather than with the catalytic zinc ion, which is the common feature of all MMP members.
-
===Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor===
+
Extra Binding Region Induced by Non-Zinc Chelating Inhibitors into the S(1)' Subsite of Matrix Metalloproteinase 8 (MMP-8) (dagger).,Pochetti G, Montanari R, Gege C, Chevrier C, Taveras AG, Mazza F J Med Chem. 2009 Jan 27. PMID:19173605<ref>PMID:19173605</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3dpe" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_19173605}}, adds the Publication Abstract to the page
+
*[[Matrix metalloproteinase 3D structures|Matrix metalloproteinase 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 19173605 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_19173605}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
[[3dpe]] is a 1 chain structure with 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=3DPE OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:19173605</ref><ref group="xtra">PMID:15734640</ref><ref group="xtra">PMID:17623656</ref><ref group="xtra">PMID:15289103</ref><references group="xtra"/>
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Neutrophil collagenase]]
+
[[Category: Large Structures]]
-
[[Category: Mazza, F.]]
+
[[Category: Mazza F]]
-
[[Category: Montanari, R.]]
+
[[Category: Montanari R]]
-
[[Category: Pochetti, G.]]
+
[[Category: Pochetti G]]
-
[[Category: Calcium]]
+
-
[[Category: Collagen degradation]]
+
-
[[Category: Extracellular matrix]]
+
-
[[Category: Glycoprotein]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Metalloprotease]]
+
-
[[Category: Non-zinc chelating inhibitor]]
+
-
[[Category: Polymorphism]]
+
-
[[Category: Protease]]
+
-
[[Category: Secreted]]
+
-
[[Category: Selective inhibition]]
+
-
[[Category: Zinc]]
+
-
[[Category: Zymogen]]
+

Current revision

Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor

PDB ID 3dpe

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3dpe"
Personal tools