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| | <StructureSection load='4yem' size='340' side='right'caption='[[4yem]], [[Resolution|resolution]] 1.47Å' scene=''> | | <StructureSection load='4yem' size='340' side='right'caption='[[4yem]], [[Resolution|resolution]] 1.47Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4yem]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YEM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4yem]] 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=4YEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YEM 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=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</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]] 1.47Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xan|4xan]]</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=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=4yem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yem OCA], [https://pdbe.org/4yem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yem RCSB], [https://www.ebi.ac.uk/pdbsum/4yem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yem ProSAT]</span></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=4yem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yem OCA], [http://pdbe.org/4yem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yem RCSB], [http://www.ebi.ac.uk/pdbsum/4yem PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yem ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | [[Category: Gallus gallus]] | | [[Category: Gallus gallus]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lysozyme]]
| + | [[Category: Dauter Z]] |
| - | [[Category: Dauter, Z]] | + | [[Category: Jaskolski M]] |
| - | [[Category: Jaskolski, M]] | + | [[Category: Minor W]] |
| - | [[Category: Minor, W]] | + | [[Category: Shabalin IG]] |
| - | [[Category: Shabalin, I G]] | + | [[Category: Wlodawer A]] |
| - | [[Category: Wlodawer, A]] | + | |
| - | [[Category: Carboplatin]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metal binding]]
| + | |
| - | [[Category: Re-refinement of 4xan]]
| + | |
| Structural highlights
4yem is a 1 chain structure with sequence from Gallus gallus. 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
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.[1]
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.
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Maehashi K, Matano M, Irisawa T, Uchino M, Kashiwagi Y, Watanabe T. Molecular characterization of goose- and chicken-type lysozymes in emu (Dromaius novaehollandiae): evidence for extremely low lysozyme levels in emu egg white. Gene. 2012 Jan 15;492(1):244-9. doi: 10.1016/j.gene.2011.10.021. Epub 2011 Oct, 25. PMID:22044478 doi:10.1016/j.gene.2011.10.021
- ↑ Shabalin I, Dauter Z, Jaskolski M, Minor W, Wlodawer A. Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin. Acta Crystallogr D Biol Crystallogr. 2015 Sep 1;71(Pt 9):1965-79. doi:, 10.1107/S139900471500629X. Epub 2015 Aug 28. PMID:26327386 doi:http://dx.doi.org/10.1107/S139900471500629X
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