This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3lka

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:38, 6 September 2023) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3lka.jpg|left|200px]]
 
-
<!--
+
==Catalytic domain of human MMP-12 complexed with hydroxamic acid and paramethoxy-sulfonyl amide==
-
The line below this paragraph, containing "STRUCTURE_3lka", creates the "Structure Box" on the page.
+
<StructureSection load='3lka' size='340' side='right'caption='[[3lka]], [[Resolution|resolution]] 1.80&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'>[[3lka]] 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=3LKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LKA 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]] 1.8&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HAE:ACETOHYDROXAMIC+ACID'>HAE</scene>, <scene name='pdbligand=M4S:4-METHOXYBENZENESULFONAMIDE'>M4S</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
{{STRUCTURE_3lka| PDB=3lka | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3lka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lka OCA], [https://pdbe.org/3lka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lka RCSB], [https://www.ebi.ac.uk/pdbsum/3lka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lka ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/MMP12_HUMAN MMP12_HUMAN] May be involved in tissue injury and remodeling. Has significant elastolytic activity. Can accept large and small amino acids at the P1' site, but has a preference for leucine. Aromatic or hydrophobic residues are preferred at the P1 site, with small hydrophobic residues (preferably alanine) occupying P3.
 +
== 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/lk/3lka_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=3lka ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
For several drug leads obtained by tethering weak binding ligands, the dissociation constant is smaller than the product of those of the individual fragments by a factor named the linking coefficient, E. This favorable contribution is attributed to the entropic gain that is realized when two weak binding ligands are tethered. Here we show a case study where the linking coefficient is strikingly small (E = 2.1 x 10(-3) M(-1)) and its totally entropic nature is demonstrated.
-
===Catalytic domain of human MMP-12 complexed with hydroxamic acid and paramethoxy-sulfonyl amide===
+
Entropic Contribution to the Linking Coefficient in Fragment Based Drug Design: A Case Study.,Borsi V, Calderone V, Fragai M, Luchinat C, Sarti N J Med Chem. 2010 Apr 23. PMID:20415416<ref>PMID:20415416</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3lka" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_20415416}}, adds the Publication Abstract to the page
+
*[[MHC 3D structures|MHC 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 20415416 is the PubMed ID number.
+
*[[MHC I 3D structures|MHC I 3D structures]]
-
-->
+
*[[Matrix metalloproteinase 3D structures|Matrix metalloproteinase 3D structures]]
-
{{ABSTRACT_PUBMED_20415416}}
+
== References ==
-
 
+
<references/>
-
==About this Structure==
+
__TOC__
-
3LKA 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=3LKA OCA].
+
</StructureSection>
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:20415416</ref><references group="xtra"/>
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Macrophage elastase]]
+
[[Category: Large Structures]]
-
[[Category: Calderone, V.]]
+
[[Category: Calderone V]]
-
[[Category: Calcium]]
+
-
[[Category: Elastase]]
+
-
[[Category: Extracellular matrix]]
+
-
[[Category: Glycoprotein]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Matrix metalloproteinase]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Metallo elastase]]
+
-
[[Category: Metalloprotease]]
+
-
[[Category: Mmp12]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 12 11:11:10 2010''
+

Current revision

Catalytic domain of human MMP-12 complexed with hydroxamic acid and paramethoxy-sulfonyl amide

PDB ID 3lka

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/3lka"
Personal tools