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7f3z
From Proteopedia
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==Double mutant Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS-K1, C59R+S108N) complexed with Trimethoprim (TOP), NADPH and dUMP== | ==Double mutant Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS-K1, C59R+S108N) complexed with Trimethoprim (TOP), NADPH and dUMP== | ||
| - | <StructureSection load='7f3z' size='340' side='right'caption='[[7f3z]]' scene=''> | + | <StructureSection load='7f3z' size='340' side='right'caption='[[7f3z]], [[Resolution|resolution]] 2.60Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F3Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F3Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7f3z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F3Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F3Z FirstGlance]. <br> |
| - | </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=7f3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f3z OCA], [https://pdbe.org/7f3z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f3z RCSB], [https://www.ebi.ac.uk/pdbsum/7f3z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f3z ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=TOP:TRIMETHOPRIM'>TOP</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</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=7f3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f3z OCA], [https://pdbe.org/7f3z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f3z RCSB], [https://www.ebi.ac.uk/pdbsum/7f3z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f3z ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [[https://www.uniprot.org/uniprot/C3S7P8_PLAFA C3S7P8_PLAFA]] Bifunctional enzyme. Involved in de novo dTMP biosynthesis. Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, DNA precursor synthesis, and for the conversion of dUMP to dTMP.[ARBA:ARBA00025154] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The MANORAA platform uses structure-based approaches to provide information on drug design originally derived from mapping tens of thousands of amino acids on a grid. In-depth analyses of the pockets, frequently occurring atoms, influential distances, and active-site boundaries are used for the analysis of active sites. The algorithms derived provide model equations that can predict whether changes in distances, such as contraction or expansion, will result in improved binding affinity. The algorithm is confirmed using kinetic studies of dihydrofolate reductase (DHFR), together with two DHFR-TS crystal structures. Empirical analyses of 881 crystal structures involving 180 ligands are used to interpret protein-ligand binding affinities. MANORAA links to major biological databases for web-based analysis of drug design. The frequency of atoms inside the main protease structures, including those from SARS-CoV-2, shows how the rigid part of the ligand can be used as a probe for molecular design (http://manoraa.org). | ||
| + | |||
| + | MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances.,Tanramluk D, Pakotiprapha D, Phoochaijaroen S, Chantravisut P, Thampradid S, Vanichtanankul J, Narupiyakul L, Akavipat R, Yuvaniyama J Structure. 2022 Jan 6;30(1):181-189.e5. doi: 10.1016/j.str.2021.09.004. Epub 2021, Oct 5. PMID:34614393<ref>PMID:34614393</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7f3z" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Chitnumsub P]] | + | [[Category: Chitnumsub, P]] |
| - | [[Category: Tanramluk D]] | + | [[Category: Tanramluk, D]] |
| - | [[Category: Vanichtanankul J]] | + | [[Category: Vanichtanankul, J]] |
| - | [[Category: Yuthavong Y]] | + | [[Category: Yuthavong, Y]] |
| - | [[Category: Yuvaniyama J]] | + | [[Category: Yuvaniyama, J]] |
| + | [[Category: Dihydrofolate reductase]] | ||
| + | [[Category: Pfdhfr]] | ||
| + | [[Category: Plasmodium falciparum]] | ||
| + | [[Category: Structural protein]] | ||
| + | [[Category: Trimethoprim]] | ||
Revision as of 07:15, 16 March 2022
Double mutant Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS-K1, C59R+S108N) complexed with Trimethoprim (TOP), NADPH and dUMP
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