5dnl: Difference between revisions

Latest revision as of 21:51, 28 June 2023

Crystal structure of IGPD from Pyrococcus furiosus in complex with (S)-C348

Structural highlights

5dnl is a 3 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.53Å
Ligands:	5DL, MN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HIS7_PYRFU

Publication Abstract from PubMed

Programs of drug discovery generally exploit one enantiomer of a chiral compound for lead development following the principle that enantiomer recognition is central to biological specificity. However, chiral promiscuity has been identified for a number of enzyme families, which have shown that mirror-image packing can enable opposite enantiomers to be accommodated in an enzyme's active site. Reported here is a series of crystallographic studies of complexes between an enzyme and a potent experimental herbicide whose chiral center forms an essential part of the inhibitor pharmacophore. Initial studies with a racemate at 1.85 A resolution failed to identify the chirality of the bound inhibitor, however, by extending the resolution to 1.1 A and by analyzing high-resolution complexes with the enantiopure compounds, we determined that both enantiomers make equivalent pseudosymmetric interactions in the active site, thus mimicking an achiral reaction intermediate.

Mirror-Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide.,Bisson C, Britton KL, Sedelnikova SE, Rodgers HF, Eadsforth TC, Viner RC, Hawkes TR, Baker PJ, Rice DW Angew Chem Int Ed Engl. 2016 Oct 17;55(43):13485-13489. doi:, 10.1002/anie.201607185. Epub 2016 Sep 26. PMID:27717128^[1]

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

References

↑ Bisson C, Britton KL, Sedelnikova SE, Rodgers HF, Eadsforth TC, Viner RC, Hawkes TR, Baker PJ, Rice DW. Mirror-Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide. Angew Chem Int Ed Engl. 2016 Oct 17;55(43):13485-13489. doi:, 10.1002/anie.201607185. Epub 2016 Sep 26. PMID:27717128 doi:https://dx.doi.org/10.1002/anie.201607185

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OCA

[1] Bisson C, Britton KL, Sedelnikova SE, Rodgers HF, Eadsforth TC, Viner RC, Hawkes TR, Baker PJ, Rice DW. Mirror-Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide. Angew Chem Int Ed Engl. 2016 Oct 17;55(43):13485-13489. doi:, 10.1002/anie.201607185. Epub 2016 Sep 26. PMID:27717128 doi:https://dx.doi.org/10.1002/anie.201607185

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='5dnl' size='340' side='right'caption='[[5dnl]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5dnl]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DNL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DNL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5dnl]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DNL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DNL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5DL:[(2S)-2-HYDROXY-3-(1H-1,2,4-TRIAZOL-1-YL)PROPYL]PHOSPHONIC+ACID'>5DL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.53&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hisB, PF1660 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5DL:[(2S)-2-HYDROXY-3-(1H-1,2,4-TRIAZOL-1-YL)PROPYL]PHOSPHONIC+ACID'>5DL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Imidazoleglycerol-phosphate_dehydratase Imidazoleglycerol-phosphate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.19 4.2.1.19] </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=5dnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dnl OCA], [https://pdbe.org/5dnl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dnl RCSB], [https://www.ebi.ac.uk/pdbsum/5dnl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dnl ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5dnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dnl OCA], [http://pdbe.org/5dnl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dnl RCSB], [http://www.ebi.ac.uk/pdbsum/5dnl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dnl ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/HIS7_PYRFU HIS7_PYRFU]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 43587]]
-[[Category: Imidazoleglycerol-phosphate dehydratase]]
 [[Category: Large Structures]]
-[[Category: Baker, P J]]
+[[Category: Pyrococcus furiosus]]
-[[Category: Bisson, C]]
+[[Category: Baker PJ]]
-[[Category: Britton, K L]]
+[[Category: Bisson C]]
-[[Category: Eadsforth, T C]]
+[[Category: Britton KL]]
-[[Category: Hawkes, T R]]
+[[Category: Eadsforth TC]]
-[[Category: Rice, D W]]
+[[Category: Hawkes TR]]
-[[Category: Rodgers, H F]]
+[[Category: Rice DW]]
-[[Category: Sedelnikova, S E]]
+[[Category: Rodgers HF]]
-[[Category: Viner, R C]]
+[[Category: Sedelnikova SE]]
-[[Category: Complex]]
+[[Category: Viner RC]]
-[[Category: Cytoplasmic]]
-[[Category: Dehydratase]]
-[[Category: Inhibitor]]
-[[Category: Lyase]]

5dnl: Difference between revisions

Latest revision as of 21:51, 28 June 2023

Crystal structure of IGPD from Pyrococcus furiosus in complex with (S)-C348

Structural highlights

Function

Publication Abstract from PubMed

References

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