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5moq

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==Joint X-ray/neutron structure of cationic trypsin in complex with benzamidine==
==Joint X-ray/neutron structure of cationic trypsin in complex with benzamidine==
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<StructureSection load='5moq' size='340' side='right' caption='[[5moq]], [[Resolution|resolution]] 0.93&Aring;' scene=''>
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<StructureSection load='5moq' size='340' side='right'caption='[[5moq]], [[Resolution|resolution]] 0.93&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5moq]] 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=5MOQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MOQ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5moq]] 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=5MOQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MOQ FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAM:BENZAMIDINE'>BAM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution|Resolution]] 0.93&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5mnh|5mnh]], [[5mo0|5mo0]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5moq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5moq OCA], [https://pdbe.org/5moq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5moq RCSB], [https://www.ebi.ac.uk/pdbsum/5moq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5moq ProSAT]</span></td></tr>
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<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=5moq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5moq OCA], [http://pdbe.org/5moq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5moq RCSB], [http://www.ebi.ac.uk/pdbsum/5moq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5moq ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
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Hydrogen bonds are key interactions determining protein-ligand binding affinity and therefore fundamental to any biological process. Unfortunately, explicit structural information about hydrogen positions and thus H-bonds in protein-ligand complexes is extremely rare and similarly the important role of water during binding remains poorly understood. Here, we report on neutron structures of trypsin determined at very high resolutions &lt;/=1.5 A in uncomplexed and inhibited state complemented by X-ray and thermodynamic data and computer simulations. Our structures show the precise geometry of H-bonds between protein and the inhibitors N-amidinopiperidine and benzamidine along with the dynamics of the residual solvation pattern. Prior to binding, the ligand-free binding pocket is occupied by water molecules characterized by a paucity of H-bonds and high mobility resulting in an imperfect hydration of the critical residue Asp189. This phenomenon likely constitutes a key factor fueling ligand binding via water displacement and helps improving our current view on water influencing protein-ligand recognition.
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Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.,Schiebel J, Gaspari R, Wulsdorf T, Ngo K, Sohn C, Schrader TE, Cavalli A, Ostermann A, Heine A, Klebe G Nat Commun. 2018 Sep 3;9(1):3559. doi: 10.1038/s41467-018-05769-2. PMID:30177695<ref>PMID:30177695</ref>
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==See Also==
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*[[Trypsin 3D structures|Trypsin 3D structures]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5moq" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
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[[Category: Trypsin]]
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[[Category: Large Structures]]
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[[Category: Heine, A]]
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[[Category: Heine A]]
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[[Category: Klebe, G]]
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[[Category: Klebe G]]
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[[Category: Ostermann, A]]
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[[Category: Ostermann A]]
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[[Category: Schiebel, J]]
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[[Category: Schiebel J]]
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[[Category: Schrader, T E]]
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[[Category: Schrader TE]]
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[[Category: Hydrogen bonding]]
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[[Category: Hydrolase]]
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[[Category: Protein-ligand interaction]]
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[[Category: Protonation]]
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Current revision

Joint X-ray/neutron structure of cationic trypsin in complex with benzamidine

PDB ID 5moq

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