5dpf: Difference between revisions
New page: '''Unreleased structure''' The entry 5dpf is ON HOLD Authors: Krimmer, S.G., Heine, A., Klebe, G. Description: Thermolysin in complex with inhibitor. [[Category: Unreleased Structures]... |
No edit summary |
||
| (4 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
The | ==Thermolysin in complex with inhibitor.== | ||
<StructureSection load='5dpf' size='340' side='right'caption='[[5dpf]], [[Resolution|resolution]] 1.47Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5dpf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DPF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DPF FirstGlance]. <br> | |||
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5H9:N-[(S)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-L-LEUCYL-4-METHYL-L-LEUCINE'>5H9</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5dpf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dpf OCA], [https://pdbe.org/5dpf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dpf RCSB], [https://www.ebi.ac.uk/pdbsum/5dpf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dpf ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
For a conscientious interpretation of thermodynamic parameters (Gibbs free energy, enthalpy and entropy) obtained by isothermal titration calorimetry (ITC), it is necessary to first evaluate the experimental setup and conditions at which the data were measured. The data quality must be assessed and the precision and accuracy of the measured parameters must be estimated. This information provides the basis at which level discussion of the data is appropriate, and allows insight into the significance of comparisons with other data. The aim of this article is to provide the reader with basic understanding of the ITC technique and the experimental practices commonly applied, in order to foster an appreciation for how much measured thermodynamic parameters can deviate from ideal, error-free values. Particular attention is paid to the shape of the recorded isotherm (c-value), the influence of the applied buffer used for the reaction (protonation reactions, pH), the chosen experimental settings (temperature), impurities of protein and ligand, sources of systematic errors (solution concentration, solution activity, and device calibration) and to the applied analysis software. Furthermore, we comment on enthalpy-entropy compensation, heat capacities and van't Hoff enthalpies. | |||
Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data.,Krimmer SG, Klebe G J Comput Aided Mol Des. 2015 Sep;29(9):867-83. doi: 10.1007/s10822-015-9867-y., Epub 2015 Sep 16. PMID:26376645<ref>PMID:26376645</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5dpf" style="background-color:#fffaf0;"></div> | ||
[[Category: Klebe | |||
[[Category: | ==See Also== | ||
*[[Thermolysin 3D structures|Thermolysin 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus thermoproteolyticus]] | |||
[[Category: Large Structures]] | |||
[[Category: Heine A]] | |||
[[Category: Klebe G]] | |||
[[Category: Krimmer SG]] | |||