3gt4: Difference between revisions

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==Structure of proteinase K with the magic triangle I3C==
==Structure of proteinase K with the magic triangle I3C==
<StructureSection load='3gt4' size='340' side='right' caption='[[3gt4]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
<StructureSection load='3gt4' size='340' side='right'caption='[[3gt4]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3gt4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Engyodontium_album Engyodontium album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GT4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GT4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3gt4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Engyodontium_album Engyodontium album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GT4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GT4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <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=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gt3|3gt3]], [[3e3d|3e3d]], [[3e3s|3e3s]], [[3e3t|3e3t]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gt3|3gt3]], [[3e3d|3e3d]], [[3e3s|3e3s]], [[3e3t|3e3t]]</div></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidase_K Peptidase K], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.64 3.4.21.64] </span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptidase_K Peptidase K], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.64 3.4.21.64] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gt4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gt4 RCSB], [http://www.ebi.ac.uk/pdbsum/3gt4 PDBsum]</span></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=3gt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gt4 OCA], [https://pdbe.org/3gt4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gt4 RCSB], [https://www.ebi.ac.uk/pdbsum/3gt4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gt4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/PRTK_TRIAL PRTK_TRIAL]] Hydrolyzes keratin at aromatic and hydrophobic residues.  
[[https://www.uniprot.org/uniprot/PRTK_TRIAL PRTK_TRIAL]] Hydrolyzes keratin at aromatic and hydrophobic residues.  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gt/3gt4_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gt/3gt4_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata ConSurf].
</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=3gt4 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 3gt4" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Proteinase|Proteinase]]
*[[Proteinase 3D structures|Proteinase 3D structures]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Engyodontium album]]
[[Category: Engyodontium album]]
[[Category: Large Structures]]
[[Category: Peptidase K]]
[[Category: Peptidase K]]
[[Category: Beck, T]]
[[Category: Beck, T]]

Latest revision as of 10:54, 16 March 2022

Structure of proteinase K with the magic triangle I3CStructure of proteinase K with the magic triangle I3C

Structural highlights

3gt4 is a 1 chain structure with sequence from Engyodontium album. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
Activity:Peptidase K, with EC number 3.4.21.64
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PRTK_TRIAL] Hydrolyzes keratin at aromatic and hydrophobic residues.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteins via hydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br K edge was successfully carried out. Radiation damage to the bromine-carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out.

The magic triangle goes MAD: experimental phasing with a bromine derivative.,Beck T, Gruene T, Sheldrick GM Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):374-80. Epub 2010, Mar 24. PMID:20382990[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. Beck T, Gruene T, Sheldrick GM. The magic triangle goes MAD: experimental phasing with a bromine derivative. Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):374-80. Epub 2010, Mar 24. PMID:20382990 doi:http://dx.doi.org/10.1107/S0907444909051609

3gt4, resolution 1.76Å

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OCA