3dkt: Difference between revisions

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-[[Image:3dkt.png|left|200px]]
-<!--
+==Crystal structure of Thermotoga maritima encapsulin==
-The line below this paragraph, containing "STRUCTURE_3dkt", creates the "Structure Box" on the page.
+<StructureSection load='3dkt' size='340' side='right'caption='[[3dkt]], [[Resolution|resolution]] 3.10&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'>[[3dkt]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. The June 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vaults''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_6 10.2210/rcsb_pdb/mom_2009_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DKT 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]] 3.104&#8491;</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=3dkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dkt OCA], [https://pdbe.org/3dkt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dkt RCSB], [https://www.ebi.ac.uk/pdbsum/3dkt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dkt ProSAT]</span></td></tr>
-{{STRUCTURE_3dkt|  PDB=3dkt  |  SCENE=  }}
+</table>
+== Function ==
-===Crystal structure of Thermotoga maritima encapsulin===
+[https://www.uniprot.org/uniprot/ENCAP_THEMA ENCAP_THEMA] Shell component of a type 1 encapsulin nanocompartment. Assembles into proteinaceous shells 23-24 nm in diameter with 2-2.5 nm thick walls. Cargo protein Flp (ferritin-like protein, may store iron) is targeted to the interior via its C-terminal extension; empty intact shells can be isolated in the absence of cargo protein (PubMed:19172747, PubMed:27224728, PubMed:32961724, PubMed:30376298, PubMed:33769792, PubMed:33953921, PubMed:34815415). Fe(2+) may be able to pass though the 5-fold and dimer channels in the protein shell (Probable).<ref>PMID:19172747</ref> <ref>PMID:27224728</ref> <ref>PMID:30376298</ref> <ref>PMID:32961724</ref> <ref>PMID:33769792</ref> <ref>PMID:33953921</ref> <ref>PMID:34815415</ref> <ref>PMID:33953921</ref>   Protease that exhibits activity toward chymotrypsin and trypsin substrates (PubMed:9872409, PubMed:11210524). Probably does not have antibacterial activity (Probable).<ref>PMID:11210524</ref> <ref>PMID:9872409</ref> <ref>PMID:19172747</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
-<!--
+Check<jmol>
-The line below this paragraph, {{ABSTRACT_PUBMED_18758469}}, adds the Publication Abstract to the page
+  <jmolCheckbox>
-(as it appears on PubMed at http://www.pubmed.gov), where 18758469 is the PubMed ID number.
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/3dkt_consurf.spt"</scriptWhenChecked>
--->
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-{{ABSTRACT_PUBMED_18758469}}
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
-==About this Structure==
+</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=3dkt ConSurf].
-[[3dkt]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_sp. Thermotoga sp.]. The June 2009 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vaults''  by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_6 10.2210/rcsb_pdb/mom_2009_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DKT OCA].
+<div style="clear:both"></div>
+== References ==
-==See Also==
+<references/>
-*[[Teaching Scenes%2C Tutorials%2C and Educators' Pages]]
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-<ref group="xtra">PMID:18758469</ref><references group="xtra"/>
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Thermotoga sp.]]
+[[Category: Thermotoga maritima]]
 [[Category: Vaults]]
-[[Category: Ban, N.]]
+[[Category: Ban N]]
-[[Category: Boehringer, D.]]
+[[Category: Boehringer D]]
-[[Category: Gutmann, S.]]
+[[Category: Gutmann S]]
-[[Category: Sutter, M.]]
+[[Category: Sutter M]]
-[[Category: Weber-Ban, E.]]
+[[Category: Weber-Ban E]]
-[[Category: Antibiotic]]
-[[Category: Antimicrobial]]
-[[Category: Bacteriocin]]
-[[Category: Calcium]]
-[[Category: Cobalt]]
-[[Category: Enzyme encapsulation]]
-[[Category: Ferritin-like protein]]
-[[Category: Hk97-fold]]
-[[Category: Hydrolase]]
-[[Category: Nanocompartment]]
-[[Category: Oxidative stress]]
-[[Category: Protease]]
-[[Category: Secreted]]
-[[Category: Structural protein/virus like particle complex]]