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.


5pqa

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:11, 6 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 47)==
==PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 47)==
-
<StructureSection load='5pqa' size='340' side='right' caption='[[5pqa]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
+
<StructureSection load='5pqa' size='340' side='right'caption='[[5pqa]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5pqa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PQA FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5pqa]] is a 2 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=5PQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PQA FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.78&#8491;</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=5pqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pqa OCA], [http://pdbe.org/5pqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pqa RCSB], [http://www.ebi.ac.uk/pdbsum/5pqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pqa ProSAT]</span></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5pqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pqa OCA], [https://pdbe.org/5pqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pqa RCSB], [https://www.ebi.ac.uk/pdbsum/5pqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pqa ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/BRD1_HUMAN BRD1_HUMAN]] Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity.<ref>PMID:16387653</ref> <ref>PMID:21880731</ref>
+
[https://www.uniprot.org/uniprot/BRD1_HUMAN BRD1_HUMAN] Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity.<ref>PMID:16387653</ref> <ref>PMID:21880731</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous ('weak' or 'noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state-even from inaccurate maps-by subtracting a proportion of the confounding 'ground state'; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches.
+
-
A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.,Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F Nat Commun. 2017 Apr 24;8:15123. doi: 10.1038/ncomms15123. PMID:28436492<ref>PMID:28436492</ref>
+
==See Also==
-
 
+
*[[Bromodomain-containing protein 3D structures|Bromodomain-containing protein 3D structures]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 5pqa" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Arrowsmith, C H]]
+
[[Category: Homo sapiens]]
-
[[Category: Bountra, C]]
+
[[Category: Large Structures]]
-
[[Category: Bradley, A R]]
+
[[Category: Arrowsmith CH]]
-
[[Category: Brandao-Neto, J]]
+
[[Category: Bountra C]]
-
[[Category: Brennan, P E]]
+
[[Category: Bradley AR]]
-
[[Category: Collins, P]]
+
[[Category: Brandao-Neto J]]
-
[[Category: Cox, O]]
+
[[Category: Brennan PE]]
-
[[Category: Delft, F von]]
+
[[Category: Collins P]]
-
[[Category: Dias, A]]
+
[[Category: Cox O]]
-
[[Category: Douangamath, A]]
+
[[Category: Dias A]]
-
[[Category: Edwards, A]]
+
[[Category: Douangamath A]]
-
[[Category: Fairhead, M]]
+
[[Category: Edwards A]]
-
[[Category: Krojer, T]]
+
[[Category: Fairhead M]]
-
[[Category: MacLean, E]]
+
[[Category: Krojer T]]
-
[[Category: Ng, J]]
+
[[Category: MacLean E]]
-
[[Category: Pearce, N M]]
+
[[Category: Ng J]]
-
[[Category: Renjie, Z]]
+
[[Category: Pearce NM]]
-
[[Category: Sethi, R]]
+
[[Category: Renjie Z]]
-
[[Category: Talon, R]]
+
[[Category: Sethi R]]
-
[[Category: Wright, N]]
+
[[Category: Talon R]]
-
[[Category: Bromodomain]]
+
[[Category: Wright N]]
-
[[Category: Epigenetic]]
+
[[Category: Von Delft F]]
-
[[Category: Gene regulation]]
+
-
[[Category: Pandda]]
+
-
[[Category: Sgc - diamond i04-1 fragment screening]]
+
-
[[Category: Xchemexplorer]]
+

Current revision

PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 47)

PDB ID 5pqa

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/5pqa"
Personal tools