7zxw: Difference between revisions

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'''Unreleased structure'''


The entry 7zxw is ON HOLD  until Paper Publication
==Catalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum in complex with the 5-[(morpholin-4-yl)methyl]quinolin-8-ol inhibitor==
<StructureSection load='7zxw' size='340' side='right'caption='[[7zxw]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7zxw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chaetomium_thermophilum_var._thermophilum_DSM_1495 Chaetomium thermophilum var. thermophilum DSM 1495]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZXW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZXW 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]] 2.246&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=JM3:5-(morpholin-4-ylmethyl)quinolin-8-ol'>JM3</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</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=7zxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zxw OCA], [https://pdbe.org/7zxw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zxw RCSB], [https://www.ebi.ac.uk/pdbsum/7zxw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zxw ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/G0SB58_CHATD G0SB58_CHATD]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
None of the current data processing pipelines for X-ray crystallography fragment-based lead discovery (FBLD) consults all the information available when deciding on the lattice and symmetry (i.e., the polymorph) of each soaked crystal. Often, X-ray crystallography FBLD pipelines either choose the polymorph based on cell volume and point-group symmetry of the X-ray diffraction data or leave polymorph attribution to manual intervention on the part of the user. Thus, when the FBLD crystals belong to more than one crystal polymorph, the discovery pipeline can be plagued by space group ambiguity, especially if the polymorphs at hand are variations of the same lattice and, therefore, difficult to tell apart from their morphology and/or their apparent crystal lattices and point groups. In the course of a fragment-based lead discovery effort aimed at finding ligands of the catalytic domain of UDP-glucose glycoprotein glucosyltransferase (UGGT), we encountered a mixture of trigonal crystals and pseudotrigonal triclinic crystals-with the two lattices closely related. In order to resolve that polymorphism ambiguity, we have written and described here a series of Unix shell scripts called CoALLA (crystal polymorph and ligand likelihood-based assignment). The CoALLA scripts are written in Unix shell and use autoPROC for data processing, CCP4-Dimple/REFMAC5 and BUSTER for refinement, and RHOFIT for ligand docking. The choice of the polymorph is effected by carrying out (in each of the known polymorphs) the tasks of diffraction data indexing, integration, scaling, and structural refinement. The most likely polymorph is then chosen as the one with the best structure refinement R(free) statistic. The CoALLA scripts further implement a likelihood-based ligand assignment strategy, starting with macromolecular refinement and automated water addition, followed by removal of the water molecules that appear to be fitting ligand density, and a final round of refinement after random perturbation of the refined macromolecular model, in order to obtain unbiased difference density maps for automated ligand placement. We illustrate the use of CoALLA to discriminate between H3 and P1 crystals used for an FBLD effort to find fragments binding to the catalytic domain of Chaetomium thermophilum UGGT.


Authors: Le Cornu, J.D., Ibba, R., Roversi, P., Zitzmann, N.
Crystal polymorphism in fragment-based lead discovery of ligands of the catalytic domain of UGGT, the glycoprotein folding quality control checkpoint.,Caputo AT, Ibba R, Le Cornu JD, Darlot B, Hensen M, Lipp CB, Marciano G, Vasiljevic S, Zitzmann N, Roversi P Front Mol Biosci. 2022 Dec 14;9:960248. doi: 10.3389/fmolb.2022.960248. , eCollection 2022. PMID:36589243<ref>PMID:36589243</ref>


Description: Catalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum in complex with the 5-[(morpholin-4-yl)methyl]quinolin-8-ol inhibitor
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Zitzmann, N]]
<div class="pdbe-citations 7zxw" style="background-color:#fffaf0;"></div>
[[Category: Ibba, R]]
== References ==
[[Category: Le Cornu, J.D]]
<references/>
[[Category: Roversi, P]]
__TOC__
</StructureSection>
[[Category: Chaetomium thermophilum var. thermophilum DSM 1495]]
[[Category: Large Structures]]
[[Category: Ibba R]]
[[Category: Le Cornu JD]]
[[Category: Roversi P]]
[[Category: Zitzmann N]]
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