4yeo
From Proteopedia
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(New page: ==Triclinic HEWL co-crystallised with cisplatin, studied at a data collection temperature of 150K - new refinement== <StructureSection load='4yeo' size='340' side='right' caption='4yeo...) |
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==Triclinic HEWL co-crystallised with cisplatin, studied at a data collection temperature of 150K - new refinement== | ==Triclinic HEWL co-crystallised with cisplatin, studied at a data collection temperature of 150K - new refinement== | ||
| - | <StructureSection load='4yeo' size='340' side='right' caption='[[4yeo]], [[Resolution|resolution]] 0.98Å' scene=''> | + | <StructureSection load='4yeo' size='340' side='right'caption='[[4yeo]], [[Resolution|resolution]] 0.98Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[4yeo]] is a 1 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[4yeo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YEO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YEO FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CPT:CISPLATIN'>CPT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.98Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CPT:CISPLATIN'>CPT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</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=4yeo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yeo OCA], [https://pdbe.org/4yeo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yeo RCSB], [https://www.ebi.ac.uk/pdbsum/4yeo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yeo ProSAT]</span></td></tr> | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | |
</table> | </table> | ||
== Function == | == Function == | ||
| - | [ | + | [https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref> |
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The anticancer activity of platinum-containing drugs such as cisplatin and carboplatin is considered to primarily arise from their interactions with nucleic acids; nevertheless, these drugs, or the products of their hydrolysis, also bind to proteins, potentially leading to the known side effects of the treatments. Here, over 40 crystal structures deposited in the Protein Data Bank (PDB) of cisplatin and carboplatin complexes of several proteins were analysed. Significant problems of either a crystallographic or a chemical nature were found in most of the presented atomic models and they could be traced to less or more serious deficiencies in the data-collection and refinement procedures. The re-evaluation of these data and models was possible thanks to their mandatory or voluntary deposition in publicly available databases, emphasizing the point that the availability of such data is critical for making structural science reproducible. Based on this analysis of a selected group of macromolecular structures, the importance of deposition of raw diffraction data is stressed and a procedure for depositing, tracking and using re-refined crystallographic models is suggested. | ||
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| + | Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.,Shabalin I, Dauter Z, Jaskolski M, Minor W, Wlodawer A Acta Crystallogr D Biol Crystallogr. 2015 Sep 1;71(Pt 9):1965-79. doi:, 10.1107/S139900471500629X. Epub 2015 Aug 28. PMID:26327386<ref>PMID:26327386</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 4yeo" style="background-color:#fffaf0;"></div> | ||
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| + | ==See Also== | ||
| + | *[[Lysozyme 3D structures|Lysozyme 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Gallus gallus]] | [[Category: Gallus gallus]] | ||
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: Dauter | + | [[Category: Dauter Z]] |
| - | [[Category: Jaskolski | + | [[Category: Jaskolski M]] |
| - | [[Category: Minor | + | [[Category: Minor W]] |
| - | [[Category: Shabalin | + | [[Category: Shabalin IG]] |
| - | [[Category: Wlodawer | + | [[Category: Wlodawer A]] |
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Current revision
Triclinic HEWL co-crystallised with cisplatin, studied at a data collection temperature of 150K - new refinement
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