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.


5r09

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:31, 21 February 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='5r09' size='340' side='right'caption='[[5r09]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
<StructureSection load='5r09' size='340' side='right'caption='[[5r09]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5r09]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5R09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5R09 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5r09]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5R09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5R09 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SYG:2-[(1~{S})-1-azanylpropyl]phenol'>SYG</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.56&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), AAR2, YBL074C, YBL06.06, YBL0611 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SYG:2-[(1~{S})-1-azanylpropyl]phenol'>SYG</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=5r09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r09 OCA], [https://pdbe.org/5r09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5r09 RCSB], [https://www.ebi.ac.uk/pdbsum/5r09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5r09 ProSAT]</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=5r09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r09 OCA], [https://pdbe.org/5r09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5r09 RCSB], [https://www.ebi.ac.uk/pdbsum/5r09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5r09 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/PRP8_YEAST PRP8_YEAST]] Required for pre-spliceosome formation, which is the first step of pre-mRNA splicing. This protein is associated with snRNP U5. Has a role in branch site-3' splice site selection. Associates with the branch site-3' splice 3'-exon region. Also has a role in cell cycle.<ref>PMID:2835658</ref> <ref>PMID:9150140</ref> <ref>PMID:12773561</ref> <ref>PMID:18779563</ref> [[https://www.uniprot.org/uniprot/AAR2_YEAST AAR2_YEAST]] Involved in splicing pre-mRNA of the A1 cistron and other genes that are important for cell growth.
+
[https://www.uniprot.org/uniprot/PRP8_YEAST PRP8_YEAST] Required for pre-spliceosome formation, which is the first step of pre-mRNA splicing. This protein is associated with snRNP U5. Has a role in branch site-3' splice site selection. Associates with the branch site-3' splice 3'-exon region. Also has a role in cell cycle.<ref>PMID:2835658</ref> <ref>PMID:9150140</ref> <ref>PMID:12773561</ref> <ref>PMID:18779563</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Crystallographic fragment screening (CFS) provides excellent starting points for projects concerned with drug discovery or biochemical tool compound development. One of the fundamental prerequisites for effective CFS is the availability of a versatile fragment library. Here, we report on the assembly of the 1,103-compound F2X-Universal Library and its 96-compound sub-selection, the F2X-Entry Screen. Both represent the available fragment chemistry and are highly diverse in terms of their 3D-pharmacophore variations. Validation of the F2X-Entry Screen in CFS campaigns using endothiapepsin and the Aar2/RNaseH complex yielded hit rates of 30% and 21%, respectively, and revealed versatile binding sites. Dry presentation of the libraries allows CFS campaigns to be carried out with or without the co-solvent DMSO present. Most of the hits in our validation campaigns could be reproduced also in the absence of DMSO. Consequently, CFS can be carried out more efficiently and for a wider range of conditions and targets.
+
-
F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening.,Wollenhaupt J, Metz A, Barthel T, Lima GMA, Heine A, Mueller U, Klebe G, Weiss MS Structure. 2020 Jun 2;28(6):694-706.e5. doi: 10.1016/j.str.2020.04.019. Epub 2020, May 14. PMID:32413289<ref>PMID:32413289</ref>
+
==See Also==
-
 
+
*[[Pre-mRNA splicing factors 3D structures|Pre-mRNA splicing factors 3D structures]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 5r09" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Baker's yeast]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Barthel, T]]
+
[[Category: Saccharomyces cerevisiae S288C]]
-
[[Category: Heine, A]]
+
[[Category: Barthel T]]
-
[[Category: Klebe, G]]
+
[[Category: Heine A]]
-
[[Category: Lima, G M.A]]
+
[[Category: Klebe G]]
-
[[Category: Metz, A]]
+
[[Category: Lima GMA]]
-
[[Category: Mueller, U]]
+
[[Category: Metz A]]
-
[[Category: Weiss, M S]]
+
[[Category: Mueller U]]
-
[[Category: Wollenhaupt, J]]
+
[[Category: Weiss MS]]
-
[[Category: Fragmax]]
+
[[Category: Wollenhaupt J]]
-
[[Category: Fragmaxapp]]
+
-
[[Category: Fragment screening]]
+
-
[[Category: Rnaseh like domain]]
+
-
[[Category: Splicing]]
+
-
[[Category: U5 snrnp assembly]]
+
-
[[Category: Vhs like domain]]
+

Current revision

PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment F2X-Entry B03, DMSO-free

PDB ID 5r09

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/5r09"
Personal tools