View source for 4ab8

==Fragments bound to bovine trypsin for the SAMPL challenge==
<StructureSection load='4ab8' size='340' side='right' caption='[[4ab8]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4ab8]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AB8 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=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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ptp|5ptp]], [[1o2s|1o2s]], [[1o2t|1o2t]], [[1bjv|1bjv]], [[1c2d|1c2d]], [[1c2e|1c2e]], [[1mts|1mts]], [[1tps|1tps]], [[1tng|1tng]], [[1o2m|1o2m]], [[1c1p|1c1p]], [[1jrt|1jrt]], [[2btc|2btc]], [[1c1t|1c1t]], [[1tnk|1tnk]], [[1o2x|1o2x]], [[1d6r|1d6r]], [[1c2h|1c2h]], [[1o38|1o38]], [[1utp|1utp]], [[1f2s|1f2s]], [[1gi1|1gi1]], [[1tio|1tio]], [[1v2k|1v2k]], [[1tpo|1tpo]], [[2blw|2blw]], [[1v2o|1v2o]], [[2fx6|2fx6]], [[1c1n|1c1n]], [[1y3u|1y3u]], [[1y3x|1y3x]], [[1c5p|1c5p]], [[1o2i|1o2i]], [[1c2j|1c2j]], [[1n6x|1n6x]], [[1c5u|1c5u]], [[1o3m|1o3m]], [[1k1o|1k1o]], [[1v2v|1v2v]], [[1ghz|1ghz]], [[1y5u|1y5u]], [[2fi3|2fi3]], [[1qb1|1qb1]], [[2ptc|2ptc]], [[1k1l|1k1l]], [[2tgd|2tgd]], [[1y5b|1y5b]], [[1c5t|1c5t]], [[1p2j|1p2j]], [[1smf|1smf]], [[1btp|1btp]], [[1ppe|1ppe]], [[2ayw|2ayw]], [[1btx|1btx]], [[2by8|2by8]], [[1gi6|1gi6]], [[1cu8|1cu8]], [[1ntp|1ntp]], [[1c5q|1c5q]], [[1qb9|1qb9]], [[1g3e|1g3e]], [[1o35|1o35]], [[3btk|3btk]], [[1ejm|1ejm]], [[3ptn|3ptn]], [[1uto|1uto]], [[1o3h|1o3h]], [[2fi4|2fi4]], [[1o2k|1o2k]], [[1y3y|1y3y]], [[1o3i|1o3i]], [[1ppc|1ppc]], [[1o3d|1o3d]], [[1o2y|1o2y]], [[1j8a|1j8a]], [[1c1q|1c1q]], [[1o2l|1o2l]], [[1y59|1y59]], [[2tgt|2tgt]], [[3btm|3btm]], [[1v2s|1v2s]], [[1xui|1xui]], [[1o2o|1o2o]], [[1ql8|1ql8]], [[3btf|3btf]], [[1s0q|1s0q]], [[1o2w|1o2w]], [[1bju|1bju]], [[1qb6|1qb6]], [[1gi5|1gi5]], [[1o39|1o39]], [[1tab|1tab]], [[1gi2|1gi2]], [[1g3d|1g3d]], [[1cu7|1cu7]], [[1tpa|1tpa]], [[1o2h|1o2h]], [[2ftl|2ftl]], [[1v2r|1v2r]], [[1mtv|1mtv]], [[1o3l|1o3l]], [[1o2r|1o2r]], [[1tx8|1tx8]], [[3bth|3bth]], [[1v2j|1v2j]], [[1c2i|1c2i]], [[1o3c|1o3c]], [[1o3k|1o3k]], [[1ezx|1ezx]], [[1k1m|1k1m]], [[1utn|1utn]], [[1ce5|1ce5]], [[2by7|2by7]], [[1o32|1o32]], [[1k1i|1k1i]], [[1yp9|1yp9]], [[1max|1max]], [[1tgc|1tgc]], [[1oph|1oph]], [[3bte|3bte]], [[1v2n|1v2n]], [[1eb2|1eb2]], [[2tio|2tio]], [[3tpi|3tpi]], [[2tld|2tld]], [[1bty|1bty]], [[2ptn|2ptn]], [[2fi5|2fi5]], [[1c2l|1c2l]], [[1v2t|1v2t]], [[2tga|2tga]], [[1o2v|1o2v]], [[1o36|1o36]], [[2cmy|2cmy]], [[1f0u|1f0u]], [[2by6|2by6]], [[1o33|1o33]], [[1tgt|1tgt]], [[1c2f|1c2f]], [[3btq|3btq]], [[1az8|1az8]], [[1tgb|1tgb]], [[1qcp|1qcp]], [[1o3e|1o3e]], [[3btt|3btt]], [[1o3o|1o3o]], [[1p2i|1p2i]], [[1tx7|1tx7]], [[1c2m|1c2m]], [[1o30|1o30]], [[1aq7|1aq7]], [[1o2z|1o2z]], [[1s0r|1s0r]], [[1sbw|1sbw]], [[1y5a|1y5a]], [[1oyq|1oyq]], [[1qbo|1qbo]], [[1btw|1btw]], [[1xuj|1xuj]], [[1v2q|1v2q]], [[1utq|1utq]], [[1mtu|1mtu]], [[1tgn|1tgn]], [[1k1p|1k1p]], [[1k1j|1k1j]], [[1tpp|1tpp]], [[1gi3|1gi3]], [[1o2q|1o2q]], [[1o3a|1o3a]], [[1hj9|1hj9]], [[1g9i|1g9i]], [[1c9t|1c9t]], [[1gi4|1gi4]], [[1ox1|1ox1]], [[2ftm|2ftm]], [[2xtt|2xtt]], [[2blv|2blv]], [[1v2w|1v2w]], [[1ql7|1ql7]], [[1g3b|1g3b]], [[1tld|1tld]], [[1mtw|1mtw]], [[1qa0|1qa0]], [[1lqe|1lqe]], [[1o3f|1o3f]], [[1tnh|1tnh]], [[1xug|1xug]], [[1o3b|1o3b]], [[1o3j|1o3j]], [[1rxp|1rxp]], [[1tni|1tni]], [[1c1r|1c1r]], [[1btz|1btz]], [[1y3v|1y3v]], [[3btw|3btw]], [[1v2m|1v2m]], [[1nc6|1nc6]], [[1o2u|1o2u]], [[1yyy|1yyy]], [[1c2g|1c2g]], [[1c1s|1c1s]], [[3btd|3btd]], [[1taw|1taw]], [[1zzz|1zzz]], [[2tgp|2tgp]], [[1jrs|1jrs]], [[1tnl|1tnl]], [[2fx4|2fx4]], [[1c1o|1c1o]], [[1f0t|1f0t]], [[1n6y|1n6y]], [[1k1n|1k1n]], [[1zr0|1zr0]], [[1jir|1jir]], [[1v2u|1v2u]], [[1may|1may]], [[2by5|2by5]], [[2ah4|2ah4]], [[1xuk|1xuk]], [[1gi0|1gi0]], [[2uuy|2uuy]], [[1tgs|1tgs]], [[1tyn|1tyn]], [[1o31|1o31]], [[1v2p|1v2p]], [[2a7h|2a7h]], [[1o37|1o37]], [[2tpi|2tpi]], [[1qbn|1qbn]], [[2bya|2bya]], [[1v2l|1v2l]], [[1o2j|1o2j]], [[4tpi|4tpi]], [[1sfi|1sfi]], [[1p2k|1p2k]], [[1o34|1o34]], [[2bza|2bza]], [[1xuh|1xuh]], [[1g36|1g36]], [[1g3c|1g3c]], [[1gbt|1gbt]], [[1c5v|1c5v]], [[3btg|3btg]], [[1pph|1pph]], [[1cu9|1cu9]], [[3ptb|3ptb]], [[1o3n|1o3n]], [[1o3g|1o3g]], [[1xuf|1xuf]], [[1c5s|1c5s]], [[1c5r|1c5r]], [[2by9|2by9]], [[1tnj|1tnj]], [[1o2n|1o2n]], [[1gj6|1gj6]], [[1c2k|1c2k]], [[1y3w|1y3w]], [[1auj|1auj]], [[1o2p|1o2p]], [[2j9n|2j9n]], [[4abd|4abd]], [[4abg|4abg]], [[4ab9|4ab9]], [[4abf|4abf]], [[4aba|4aba]], [[4abb|4abb]], [[4abh|4abh]], [[4abe|4abe]]</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </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=4ab8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ab8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ab8 RCSB], [http://www.ebi.ac.uk/pdbsum/4ab8 PDBsum]</span></td></tr>
</table>
<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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>

==See Also==
*[[Trypsin|Trypsin]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bos taurus]]
[[Category: Trypsin]]
[[Category: Newman, J]]
[[Category: Peat, T S]]
[[Category: Fragment screening]]
[[Category: Hydrolase]]
[[Category: Modelling]]