4mmm: Difference between revisions

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==Human Pdrx5 complex with a ligand BP7==
==Human Pdrx5 complex with a ligand BP7==
<StructureSection load='4mmm' size='340' side='right' caption='[[4mmm]], [[Resolution|resolution]] 1.47&Aring;' scene=''>
<StructureSection load='4mmm' size='340' side='right'caption='[[4mmm]], [[Resolution|resolution]] 1.47&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4mmm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MMM FirstGlance]. <br>
<table><tr><td colspan='2'>[[4mmm]] is a 4 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=4MMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MMM FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BP7:1,1-BIPHENYL-3,4-DIOL'>BP7</scene><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]] 1.47&#8491;</td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4k7i|4k7i]], [[4k7n|4k7n]], [[4k7o|4k7o]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BP7:1,1-BIPHENYL-3,4-DIOL'>BP7</scene></td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </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=4mmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mmm OCA], [https://pdbe.org/4mmm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mmm RCSB], [https://www.ebi.ac.uk/pdbsum/4mmm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mmm ProSAT]</span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4mmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mmm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mmm RCSB], [http://www.ebi.ac.uk/pdbsum/4mmm PDBsum]</span></td></tr>
</table>
<table>
== Function ==
<div style="background-color:#fffaf0;">
[https://www.uniprot.org/uniprot/PRDX5_HUMAN PRDX5_HUMAN] Reduces hydrogen peroxide and alkyl hydroperoxides with reducing equivalents provided through the thioredoxin system. Involved in intracellular redox signaling.
== Publication Abstract from PubMed ==
Fragment-based drug design is one of the most promising approaches for discovering novel and potent inhibitors against therapeutic targets. The first step of the process consists of identifying fragments that bind the protein target. The determination of the fragment binding mode plays a major role in the selection of the fragment hits that will be processed into drug-like compounds. Comparing the binding modes of analogous fragments is a critical task, not only to identify specific interactions between the protein target and the fragment, but also to verify whether the binding mode is conserved or differs according to the fragment modification. While X-ray crystallography is the technique of choice, NMR methods are helpful when this fails. We show here how the ligand-observed saturation transfer difference (STD) experiment and the protein-observed 15N-HSQC experiment, two popular NMR screening experiments, can be used to compare the binding modes of analogous fragments. We discuss the application and limitations of these approaches based on STD-epitope mapping, chemical shift perturbation (CSP) calculation and comparative CSP sign analysis, using the human peroxiredoxin 5 as a protein model.
 
Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5.,Aguirre C, Brink TT, Guichou JF, Cala O, Krimm I PLoS One. 2014 Jul 15;9(7):e102300. doi: 10.1371/journal.pone.0102300., eCollection 2014. PMID:25025339<ref>PMID:25025339</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==See Also==
</div>
*[[Peroxiredoxin 3D structures|Peroxiredoxin 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Peroxiredoxin]]
[[Category: Homo sapiens]]
[[Category: Guichou, J F.]]
[[Category: Large Structures]]
[[Category: Enzyme]]
[[Category: Guichou JF]]
[[Category: Oxidoreductase]]

Latest revision as of 11:56, 20 March 2024

Human Pdrx5 complex with a ligand BP7Human Pdrx5 complex with a ligand BP7

Structural highlights

4mmm is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.47Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PRDX5_HUMAN Reduces hydrogen peroxide and alkyl hydroperoxides with reducing equivalents provided through the thioredoxin system. Involved in intracellular redox signaling.

See Also

4mmm, resolution 1.47Å

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