4ab8: Difference between revisions
New page: '''Unreleased structure''' The entry 4ab8 is ON HOLD until sometime in the future Authors: Newman, J., Peat, T.S. Description: Fragments bound to bovine trypsin |
No edit summary |
||
| (11 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Fragments bound to bovine trypsin for the SAMPL challenge== | |||
<StructureSection load='4ab8' size='340' side='right'caption='[[4ab8]], [[Resolution|resolution]] 1.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4ab8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AB8 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]] 1.6Å</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=VXU:3,4-DIHYDRO-2H-1,5-BENZODIOXEPIN-6-YLMETHANAMINE'>VXU</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=4ab8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ab8 OCA], [https://pdbe.org/4ab8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ab8 RCSB], [https://www.ebi.ac.uk/pdbsum/4ab8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ab8 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Part of the latest SAMPL challenge was to predict how a small fragment library of 500 commercially available compounds would bind to a protein target. In order to assess the modellers' work, a reasonably comprehensive set of data was collected using a number of techniques. These included surface plasmon resonance, isothermal titration calorimetry, protein crystallization and protein crystallography. Using these techniques we could determine the kinetics of fragment binding, the energy of binding, how this affects the ability of the target to crystallize, and when the fragment did bind, the pose or orientation of binding. Both the final data set and all of the raw images have been made available to the community for scrutiny and further work. This overview sets out to give the parameters of the experiments done and what might be done differently for future studies. | |||
The DINGO dataset: a comprehensive set of data for the SAMPL challenge.,Newman J, Dolezal O, Fazio V, Caradoc-Davies T, Peat TS J Comput Aided Mol Des. 2012 May;26(5):497-503. doi: 10.1007/s10822-011-9521-2., Epub 2011 Dec 21. PMID:22187139<ref>PMID:22187139</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4ab8" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Trypsin 3D structures|Trypsin 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bos taurus]] | |||
[[Category: Large Structures]] | |||
[[Category: Newman J]] | |||
[[Category: Peat TS]] | |||
Latest revision as of 14:23, 20 December 2023
Fragments bound to bovine trypsin for the SAMPL challengeFragments bound to bovine trypsin for the SAMPL challenge
Structural highlights
FunctionPublication Abstract from PubMedPart of the latest SAMPL challenge was to predict how a small fragment library of 500 commercially available compounds would bind to a protein target. In order to assess the modellers' work, a reasonably comprehensive set of data was collected using a number of techniques. These included surface plasmon resonance, isothermal titration calorimetry, protein crystallization and protein crystallography. Using these techniques we could determine the kinetics of fragment binding, the energy of binding, how this affects the ability of the target to crystallize, and when the fragment did bind, the pose or orientation of binding. Both the final data set and all of the raw images have been made available to the community for scrutiny and further work. This overview sets out to give the parameters of the experiments done and what might be done differently for future studies. The DINGO dataset: a comprehensive set of data for the SAMPL challenge.,Newman J, Dolezal O, Fazio V, Caradoc-Davies T, Peat TS J Comput Aided Mol Des. 2012 May;26(5):497-503. doi: 10.1007/s10822-011-9521-2., Epub 2011 Dec 21. PMID:22187139[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||