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| | <StructureSection load='6szh' size='340' side='right'caption='[[6szh]], [[Resolution|resolution]] 1.65Å' scene=''> | | <StructureSection load='6szh' size='340' side='right'caption='[[6szh]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6szh]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SZH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SZH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6szh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SZH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SZH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=M2H:3,5-dimethyl-1~{H}-pyrrole-2-carbonitrile'>M2H</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]] 1.65Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ditrans,polycis-undecaprenyl-diphosphate_synthase_((2E,6E)-farnesyl-_diphosphate_specific) Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl- diphosphate specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.31 2.5.1.31] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=M2H:3,5-dimethyl-1~{H}-pyrrole-2-carbonitrile'>M2H</scene></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=6szh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6szh OCA], [http://pdbe.org/6szh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6szh RCSB], [http://www.ebi.ac.uk/pdbsum/6szh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6szh 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=6szh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6szh OCA], [https://pdbe.org/6szh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6szh RCSB], [https://www.ebi.ac.uk/pdbsum/6szh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6szh ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/V5VCK8_ACIBA V5VCK8_ACIBA]] Catalyzes the sequential condensation of isopentenyl diphosphate (IPP) with (2E,6E)-farnesyl diphosphate (E,E-FPP) to yield (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E,38E)-undecaprenyl diphosphate (di-trans,octa-cis-UPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide.[HAMAP-Rule:MF_01139] | + | [https://www.uniprot.org/uniprot/V5VCK8_ACIBA V5VCK8_ACIBA] Catalyzes the sequential condensation of isopentenyl diphosphate (IPP) with (2E,6E)-farnesyl diphosphate (E,E-FPP) to yield (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E,38E)-undecaprenyl diphosphate (di-trans,octa-cis-UPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide.[HAMAP-Rule:MF_01139] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6szh" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6szh" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Undecaprenyl pyrophosphate synthase|Undecaprenyl pyrophosphate synthase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Acinetobacter baumannii]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Thorpe, J H]] | + | [[Category: Thorpe JH]] |
| - | [[Category: Inhibitor complex]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
V5VCK8_ACIBA Catalyzes the sequential condensation of isopentenyl diphosphate (IPP) with (2E,6E)-farnesyl diphosphate (E,E-FPP) to yield (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E,38E)-undecaprenyl diphosphate (di-trans,octa-cis-UPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide.[HAMAP-Rule:MF_01139]
Publication Abstract from PubMed
Direct soaking of protein crystals with small-molecule fragments grouped into complementary clusters is a useful technique when assessing the potential of a new crystal system to support structure-guided drug discovery. It provides a robustness check prior to any extensive crystal screening, a double check for assay binding cutoffs and structural data for binding pockets that may or may not be picked out in assay measurements. The structural output from this technique for three novel fragment molecules identified to bind to the antibacterial target Acinetobacter baumannii undecaprenyl pyrophosphate synthase are reported, and the different physicochemical requirements of a successful antibiotic are compared with traditional medicines.
Cocktailed fragment screening by X-ray crystallography of the antibacterial target undecaprenyl pyrophosphate synthase from Acinetobacter baumannii.,Thorpe JH, Wall ID, Sinnamon RH, Taylor AN, Stavenger RA Acta Crystallogr F Struct Biol Commun. 2020 Jan 1;76(Pt 1):40-46. doi:, 10.1107/S2053230X19017199. Epub 2020 Jan 1. PMID:31929185[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Thorpe JH, Wall ID, Sinnamon RH, Taylor AN, Stavenger RA. Cocktailed fragment screening by X-ray crystallography of the antibacterial target undecaprenyl pyrophosphate synthase from Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun. 2020 Jan 1;76(Pt 1):40-46. doi:, 10.1107/S2053230X19017199. Epub 2020 Jan 1. PMID:31929185 doi:http://dx.doi.org/10.1107/S2053230X19017199
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